NGI Stockholm (Genomics Production)

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Publications

2021 (24)

2020 (599)

2019 (747)

2018 (664)

2017 (705)

2016 (673)

2015 (434)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

1989 (1)

All (5088)


Facilities

Journals

SciLifeLab National facility since 2013.

865 publications

Year 2021

PubMed DOI Crossref
Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1.
Silva Cascales H, Burdova K, Middleton A, ..., Macurek L, Lindqvist A
pii: 4/3/e202000980
Life Sci. Alliance 4 (3) - [2021-03-00; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.
Lagou V, Mägi R, Hottenga JJ, ..., Prokopenko I, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)
pii: 10.1038/s41467-020-19366-9
Nat Commun 12 (1) 24 [2021-01-05; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Year 2020

PubMed DOI Crossref
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A
pii: 10.1007/s00439-020-02242-3
Hum. Genet. - (-) - [2020-12-14; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing
Morarach K, Mikhailova A, Knoflach V, ..., Ernfors P, Marklund U
Nat Neurosci 24 (1) 34-46 [2020-12-07; online 2020-12-07]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Moose genomes reveal past glacial demography and the origin of modern lineages.
Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D
pii: 10.1186/s12864-020-07208-3
BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.
Nilsson H, Lindgren D, Axelson H, ..., Lundgren J, Johansson ME
J. Pathol. 252 (4) 384-397 [2020-12-00; online 2020-09-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species.
Vetukuri RR, Kalyandurg PB, Saripella GV, ..., Grenville-Briggs LJ, Savenkov EI
pii: 10.1007/s00705-020-04832-y pmc: PMC7588395
Arch Virol 165 (12) 2953-2959 [2020-12-00; online 2020-10-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine
Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX
BMC Genomics 21 (1) 796 [2020-12-00; online 2020-11-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice
Purhonen J, Grigorjev V, Ekiert R, ..., Fellman V, Kallijärvi J
Nat Commun 11 (1) - [2020-12-00; online 2020-01-16]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-12-00; online 2020-07-16]
BioImage Informatics Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
Feuerborn TR, Palkopoulou E, van der Valk T, ..., Dalén L, Díez-Del-Molino D
pii: 10.1186/s12864-020-07229-y
BMC Genomics 21 (1) 844 [2020-11-30; online 2020-11-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.
Sousa JAB, Bolgár A, Christel S, ..., Stams AJM, Plugge CM
pii: S0048-9697(20)34546-0
Sci. Total Environ. 745 (-) 141017 [2020-11-25; online 2020-07-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.
Liao Z, Hodén KP, Singh RK, Dixelius C
pii: 10.1038/s41598-020-77593-y pmc: PMC7689493
Sci Rep 10 (1) 20577 [2020-11-25; online 2020-11-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.
Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N
Mol. Ecol. 30 (2) 499-516 [2020-11-20; online 2020-11-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B
Br. J. Haematol. - (-) - [2020-11-18; online 2020-11-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
pii: 10.1038/s41467-020-19453-x pmc: PMC7673029
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Development of a highly efficient 50K SNP genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome re-sequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
Mol Ecol Resour - (-) - [2020-11-11; online 2020-11-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M
mSystems 5 (6) - [2020-11-10; online 2020-11-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.
Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K
pii: 10.1038/s41398-020-01056-1 pmc: PMC7652854
Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.
Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R
pii: 5922798 pmc: PMC7641766
Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evolution from adherent to suspension: systems biology of HEK293 cell line development.
Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J
pii: 10.1038/s41598-020-76137-8 pmc: PMC7642379
Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the "PI-POC" Trial.
Gaudenzi G, Kumbakumba E, Rasti R, ..., Mwanga-Amumpaire J, Alfvén T
pii: v9i11e21430 pmc: PMC7690656 ClinicalTrials.gov: NCT03900091
JMIR Res Protoc 9 (11) e21430 [2020-11-04; online 2020-11-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.
Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F
pii: 5912529 pmc: PMC7674688
Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.
Pértille F, Ibelli AMG, Sharif ME, ..., Guerrero-Bosagna C, Coutinho LL
pmc: PMC7667380
Front Genet 11 (-) 508809 [2020-11-02; online 2020-11-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dense sampling of bird diversity increases power of comparative genomics.
Feng S, Stiller J, Deng Y, ..., Paten B, Zhang G
pii: 10.1038/s41586-020-2873-9
Nature 587 (7833) 252-257 [2020-11-00; online 2020-11-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Leaf shape in Populus tremula is a complex, omnigenic trait.
Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR
pii: ECE36691 pmc: PMC7663049 Dryad: 10.5061/dryad.3n5tb2rdt
Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cytogenetically visible inversions are formed by multiple molecular mechanisms.
Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A
Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Origins and genetic legacy of prehistoric dogs.
Bergström A, Frantz L, Schmidt R, ..., Larson G, Skoglund P
pii: 370/6516/557 pmc: PMC7116352 mid: EMS103415
Science 370 (6516) 557-564 [2020-10-30; online 2020-10-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.
Liang D, Andersen CB, Vetukuri RR, Dou D, Grenville-Briggs LJ
pmc: PMC7720654
Front Microbiol 11 (-) 581698 [2020-10-29; online 2020-10-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.
Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L
pii: 10.1038/s41598-020-75315-y pmc: PMC7591532
Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome.
Zhang C, Mazzeu JF, Eisfeldt J, ..., Sutton VR, Carvalho CMB
Am. J. Med. Genet. A - (-) - [2020-10-13; online 2020-10-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A
Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.
Barnett R, Westbury MV, Sandoval-Velasco M, ..., Yamaguchi N, Gilbert MTP
pii: S0960-9822(20)31421-4
Curr. Biol. - (-) - [2020-10-09; online 2020-10-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D
pii: 10.1186/s12859-020-03784-z pmc: PMC7542881
BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.
Arroyo Mühr LS, Lagheden C, Lei J, ..., Sundström K, Dillner J
pii: 10.1038/s41416-020-01111-0
Br. J. Cancer - (-) - [2020-10-06; online 2020-10-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.
Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M
pii: 10.1186/s12870-020-02656-1 pmc: PMC7541206
BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.
Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U
pii: S0014-4827(20)30403-1
Exp. Cell Res. 395 (1) 112156 [2020-10-01; online 2020-07-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.
Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C
pii: 10.1038/s41598-020-73166-1 pmc: PMC7527340
Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U
Mol. Microbiol. - (-) - [2020-09-28; online 2020-09-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.
Pontiller B, Martínez-García S, Lundin D, Pinhassi J
pmc: PMC7546218
Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.
Ignatov D, Vaitkevicius K, Johansson J
pii: S2666-1667(20)30033-2 pmc: PMC7580233
STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.
Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S
pii: 10.1038/s41598-020-71939-2 pmc: PMC7486370
Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.
Svedberg A, Björn N, Sigurgeirsson B, ..., Lundeberg J, Gréen H
pii: S0169-5002(20)30516-X
Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.
Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J
pii: 6/38/eaba8196 pmc: PMC7494341
Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.
Guerrero-Bosagna C, Pértille F, Gomez Y, ..., Voelkl B, Toscano MJ
pii: S1744-117X(20)30047-2
Comp Biochem Physiol Part D Genomics Proteomics 35 (-) 100700 [2020-09-00; online 2020-06-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reconstructing marine plankton food web interactions using DNA metabarcoding.
Zamora-Terol S, Novotny A, Winder M
Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The impact of damage-associated molecular patterns on the neurotransmitter release and gene expression in the ex vivo rat carotid body.
Mkrtchian S, Kåhlin J, Gómez-Galán M, ..., Erlandsson Harris H, Eriksson LI
Exp. Physiol. 105 (9) 1634-1647 [2020-09-00; online 2020-07-24]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.
Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B
pii: 9/35/e00934-20 pmc: PMC7453295
Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.
Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H
pii: 10.1038/s41540-020-00146-6 pmc: PMC7445166
npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".
Woods R, Turvey ST, Brace S, ..., Brown MJF, Barnes I
pii: 10.1186/s12862-020-01668-7 pmc: PMC7437022
BMC Evol. Biol. 20 (1) 106 [2020-08-18; online 2020-08-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.
Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F
pii: 10.1038/s41467-020-17871-5 pmc: PMC7426940
Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.
Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K
pii: 10.1038/s41598-020-70412-4 pmc: PMC7419513
Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A 3D Cell Culture Model Identifies Wnt/ β-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.
Oliva-Vilarnau N, Vorrink SU, Ingelman-Sundberg M, Lauschke VM
pii: ADVS1906 pmc: PMC7404138
Adv Sci (Weinh) 7 (15) 2000248 [2020-08-00; online 2020-06-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.
Xu F, Jiménez-González A, Einarsson E, ..., Svärd SG, Jerlström-Hultqvist J
pmc: PMC7641422
Microb Genom 6 (8) - [2020-08-00; online 2020-07-03]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L
Current Biology 30 (19) 3871-3879.e7 [2020-08-00; online 2020-08-00]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.
Stanton DWG, Alberti F, Plotnikov V, ..., Skoglund P, Dalén L
pii: 10.1038/s41598-020-69474-1 pmc: PMC7387438
Sci Rep 10 (1) 12621 [2020-07-28; online 2020-07-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.
Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA
Mol. Ecol. - (-) - [2020-07-24; online 2020-07-24]
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Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
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Systems biology of acidophile biofilms for efficient metal extraction.
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Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.
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Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.
Zhong X, Lundberg M, Råberg L
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Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.
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Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.
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Interspecific gene flow and the evolution of specialisation in black and white rhinoceros.
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RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.
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Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.
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Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.
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Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
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CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.
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Size-Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe-by-Design.
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Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.
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Stem Cells 38 (6) 741-755 [2020-06-00; online 2020-03-10]
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Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.
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Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
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Linked-read sequencing enables haplotype-resolved resequencing at population scale.
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Mol Ecol Resour 20 (5) 1311-1322 [2020-05-18; online 2020-05-18]
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.
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Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.
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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.
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Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.
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Srebf1 Controls Midbrain Dopaminergic Neurogenesis.
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Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]
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Single-cell RNA counting at allele and isoform resolution using Smart-seq3
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Nat Biotechnol - (-) - [2020-05-04; online 2020-05-04]
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Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.
Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA
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Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]
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Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.
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Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.
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Mol Oncol 14 (5) 1101-1117 [2020-05-00; online 2020-03-13]
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Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.
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Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.
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Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.
Atherton S, Jondelius U
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Biodivers Data J 8 (-) e51813 [2020-04-27; online 2020-04-27]
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Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.
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Stem Cells Transl Med - (-) - [2020-04-22; online 2020-04-22]
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Molecular profiling of driver events in metastatic uveal melanoma.
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Nat Commun 11 (1) 1894 [2020-04-20; online 2020-04-20]
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Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.
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Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.
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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
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Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.
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Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.
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Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.
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Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.
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Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome.
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Transcriptome Profiling and Toxicity Following Long-Term, Low Dose Exposure of Human Lung Cells to Ni and NiO Nanoparticles-Comparison with NiCl 2.
Gliga AR, Di Bucchianico S, Åkerlund E, Karlsson HL
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Nanomaterials (Basel) 10 (4) - [2020-03-31; online 2020-03-31]
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Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.
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An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.
Ignatov D, Vaitkevicius K, Durand S, ..., Condon C, Johansson J
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Cell Rep 30 (12) 4027-4040.e7 [2020-03-24; online 2020-03-27]
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Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.
Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F
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Genes 11 (3) 314 [2020-03-14; online 2020-03-14]
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Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike ( Esox lucius) and a Synthesis of Previous Studies.
Sunde J, Yıldırım Y, Tibblin P, Forsman A
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Front Genet 11 (-) 218 [2020-03-13; online 2020-03-13]
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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.
Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF
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Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]
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Uncovering diversity and metabolic spectrum of animals in dead zone sediments.
Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA
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An atlas of the protein-coding genes in the human, pig, and mouse brain.
Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J
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The nf-core framework for community-curated bioinformatics pipelines
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Nat Biotechnol 38 (3) 276-278 [2020-03-00; online 2020-02-13]
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Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.
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Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.
Westbury MV, Hartmann S, Barlow A, ..., Heller R, Hofreiter M
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Sci Adv 6 (11) eaay0456 [2020-03-00; online 2020-03-13]
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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK
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Mol. Ecol. 29 (6) 1120-1136 [2020-03-00; online 2020-03-09]
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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.
Dussex N, Stanton DWG, Sigeman H, ..., Hansson B, Dalén L
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Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.
Tzelepis G, Hodén KP, Fogelqvist J, ..., Vetukuri RR, Dixelius C
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Front Microbiol 11 (-) 252 [2020-02-21; online 2020-02-21]
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Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry.
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Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.
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PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]
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Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).
Wang X, Bernhardsson C, Ingvarsson PK
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Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]
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The Molecular Anatomy of Mouse Skin during Hair Growth and Rest
Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M
Cell Stem Cell 26 (3) 441-457.e7 [2020-02-00; online 2020-02-00]
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.
Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K
pii: v12020158 pmc: PMC7077304
Viruses 12 (2) 158 [2020-01-30; online 2020-01-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.
Ekhteraei-Tousi S, Lewerentz J, Larsson J
pii: cells9020323 pmc: PMC7072490
Cells 9 (2) 323 [2020-01-30; online 2020-01-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.
Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M
pii: 10.1186/s12859-019-3337-9 pmc: PMC6975020
BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.
Rugiu L, Panova M, Pereyra RT, Jormalainen V
pii: 10.1186/s12864-020-6470-y pmc: PMC6958763
BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.
Lethin J, Shakil SSM, Hassan S, ..., Olsson O, Aronsson H
pii: 10.1186/s12870-019-2137-8 pmc: PMC6958588
BMC Plant Biol. 20 (1) 18 [2020-01-13; online 2020-01-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A regulatory role for CHD2 in myelopoiesis.
Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A
Epigenetics 15 (6-7) 1-13 [2020-01-10; online 2020-01-10]
Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.
Gelabert P, Sandoval-Velasco M, Serres A, ..., Gilbert MTP, Lalueza-Fox C
pii: S0960-9822(19)31438-1
Curr. Biol. 30 (1) 108-114.e5 [2020-01-06; online 2019-12-12]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions.
Ingvarsson PK, Bernhardsson C
pii: EVA12792 pmc: PMC6935590
Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2019

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A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver
Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C
Thromb. Haemost. 120 (02) 229-242 [2019-12-30; online 2019-12-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
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Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox
Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L
Phil. Trans. R. Soc. B 374 (1788) 20190212 [2019-12-23; online 2019-11-04]
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A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.
Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P
pii: 366/6472/eaax9198
Science 366 (6472) - [2019-12-20; online 2019-12-21]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers.
Arroyo Mühr LS, Lagheden C, Eklund C, ..., Sundström K, Dillner J
J. Gen. Virol. - (-) - [2019-12-20; online 2019-12-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A transposable element insertion is associated with an alternative life history strategy.
Woronik A, Tunström K, Perry MW, ..., Käkelä R, Wheat CW
pii: 10.1038/s41467-019-13596-2 pmc: PMC6917731
Nat Commun 10 (1) 5757 [2019-12-17; online 2019-12-17]
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NGS targeted screening of 100 Scandinavian patients with coronal synostosis.
Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L
Am. J. Med. Genet. A - (-) - [2019-12-14; online 2019-12-14]
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BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.
Ueberschär M, Wang H, Zhang C, ..., Wen J, Dai Q
pii: 10.1038/s41467-019-13558-8 pmc: PMC6911014
Nat Commun 10 (1) 5700 [2019-12-13; online 2019-12-13]
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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
pii: S0092-8674(19)31282-6
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.
Pineau C, Hikmet F, Zhang C, ..., Uhlén M, Lindskog C
J. Proteome Res. 18 (12) 4215-4230 [2019-12-06; online 2019-08-29]
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Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.
Ameen C, Feuerborn TR, Brown SK, ..., Darwent CM, Evin A
Proc. Biol. Sci. 286 (1916) 20191929 [2019-12-04; online 2019-11-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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High throughput barcoding method for genome-scale phasing.
Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A
pii: 10.1038/s41598-019-54446-x pmc: PMC6889410
Sci Rep 9 (1) 18116 [2019-12-02; online 2019-12-02]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
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A cell fitness selection model for neuronal survival during development
Wang Y, Wu H, Fontanet P, ..., Hadjab S, Lallemend F
Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]
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A Spatiomolecular Map of the Striatum
Märtin A, Calvigioni D, Tzortzi O, ..., Wärnberg E, Meletis K
Cell Rep 29 (13) 4320-4333.e5 [2019-12-00; online 2019-12-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
Marathe NP, Berglund F, Razavi M, ..., Kristiansson E, Larsson DGJ
Microbiome 7 (1) - [2019-12-00; online 2019-06-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C
GEO: GSE129383
Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]
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Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å
Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]
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Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type
Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M
Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]
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An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition.
Wessels B, Seyfferth C, Escamez S, ..., Felten J, Tuominen H
New Phytol. 224 (4) 1585-1599 [2019-12-00; online 2019-07-02]
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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J
Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.
Morales HE, Faria R, Johannesson K, ..., Westram AM, Butlin RK
pii: aav9963 pmc: PMC6892616
Sci Adv 5 (12) eaav9963 [2019-12-00; online 2019-12-04]
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PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding
Kloth KJ, Abreu IN, Delhomme N, ..., Moritz T, Albrectsen BR
Plant Physiol. 181 (4) 1704-1720 [2019-12-00; online 2019-09-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
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From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability
Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D
Genome Med 11 (1) 68 [2019-12-00; online 2019-11-07]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Programmed DNA elimination of germline development genes in songbirds.
Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, ..., Forstmeier W, Suh A
pii: 10.1038/s41467-019-13427-4 pmc: PMC6884545
Nat Commun 10 (1) 5468 [2019-11-29; online 2019-11-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The human secretome
Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å
Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Translational Plasma Profiling [Collaborative]
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Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.
Stiller C, Aghelpasand H, Frick T, ..., Ahmadian A, Karlström AE
Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.
Panula S, Kurek M, Kumar P, ..., Lanner F, Stukenborg JB
pii: 5621184
Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).
Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK
pii: g3.119.400504
G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K
pii: 10.1038/s41380-019-0584-0
Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions.
Al-Farsi HM, Al-Adwani S, Ahmed S, ..., Giske CG, Bergman P
pmc: PMC6870453
Front Microbiol 10 (-) 2632 [2019-11-14; online 2019-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Carnivores, competition and genetic connectivity in the Anthropocene.
Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C
pii: 10.1038/s41598-019-52904-0 pmc: PMC6841969
Sci Rep 9 (1) 16339 [2019-11-08; online 2019-11-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.
Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M
pmc: PMC6854034
Front Microbiol 10 (-) 2579 [2019-11-07; online 2019-11-07]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.
Marquina D, Esparza-Salas R, Roslin T, Ronquist F
pmc: PMC6899807
Mol Ecol Resour 19 (6) 1516-1530 [2019-11-00; online 2019-09-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.
Saremi NF, Supple MA, Byrne A, ..., Wilmers CC, Shapiro B
pii: 10.1038/s41467-019-12741-1 pmc: PMC6800433
Nat Commun 10 (1) 4769 [2019-10-18; online 2019-10-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation
Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC
J. Pathol - (-) - [2019-10-17; online 2019-10-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, ..., Engblom S, Dopson M
pii: 10.1038/s41597-019-0222-3 pmc: PMC6795848
Sci Data 6 (1) 207 [2019-10-16; online 2019-10-16]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbe-host interplay in atopic dermatitis and psoriasis.
Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H
pii: 10.1038/s41467-019-12253-y pmc: PMC6795799
Nat Commun 10 (1) 4703 [2019-10-16; online 2019-10-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.
Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H
pii: 10.1038/s41397-019-0099-8
Pharmacogenomics J. - (-) - [2019-10-15; online 2019-10-15]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.
Nascimento FJA, Dahl M, Deyanova D, ..., Creer S, Gullström M
pii: 610 pmc: PMC6778119
Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.
Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N
pii: 5580498 pmc: PMC6795238
Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee.
Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT
pii: 5505446
Mol. Biol. Evol. 36 (10) 2277-2291 [2019-10-01; online 2019-05-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.
Schweizer M, Warmuth VM, Alaei Kakhki N, ..., Suh A, Burri R
pii: S1055-7903(19)30221-0
Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
pii: 10.1038/s41592-019-0548-y pmc: PMC6765407 mid: NIHMS1536533
Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.
Cappellini E, Welker F, Pandolfi L, ..., Lordkipanidze D, Willerslev E
pii: 10.1038/s41586-019-1555-y
Nature 574 (7776) 103-107 [2019-10-00; online 2019-09-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.
Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C
Cancer Med - (-) - [2019-09-30; online 2019-09-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.
Dussex N, von Seth J, Knapp M, ..., Robertson BC, Dalén L
pmc: PMC6769136
Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]
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Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.
Seyfferth C, Wessels BA, Gorzsás A, ..., Sundberg B, Felten J
pmc: PMC6775489
Front Plant Sci 10 (-) 1101 [2019-09-26; online 2019-09-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.
Lorent J, Kusnadi EP, van Hoef V, ..., Larsson O, Furic L
GEO: GSE120917 GEO: GSE107590 GEO: GSE117569 GEO: GSE35428 GEO: GSE104399 GEO: GSE72249
EMBO J. - (-) e101323 [2019-09-26; online 2019-09-26]
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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
pii: 47791 pmc: PMC6779467 GEO: GSE78136
Elife 8 (-) - [2019-09-25; online 2019-09-25]
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PubMed DOI Crossref
Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.
Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A
pmc: PMC6769111
Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]
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Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A
pii: bloodadvances.2018028795
Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Discovery of Novel Sequences in 1,000 Swedish Genomes.
Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A
pii: 5555682
Mol. Biol. Evol. - (-) - [2019-09-24; online 2019-09-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.
Nilsson E, Li K, Fridlund J, ..., Pinhassi J, Holmfeldt K
pii: AEM.01003-19 pmc: PMC6715854
Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.
Poux C, Dondalska A, Bergenstråhle J, ..., Tregoning JS, Spetz AL
pmc: PMC6751283
Front Immunol 10 (-) 2161 [2019-09-12; online 2019-09-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.
Das I, Wilhelm M, Höiom V, ..., Tuominen R, Egyhàzi Brage S
pii: 10.1038/s41419-019-1875-8 pmc: PMC6737096
Cell Death Dis 10 (9) 663 [2019-09-10; online 2019-09-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.
Pederson ERA, Warshan D, Rasmussen U
pii: g3.119.400279 pmc: PMC6723128 figshare: 10.6084/m9.figshare.7775951
G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]
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Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.
Höök L, Leal L, Talla V, Backström N
pii: 5545957 pmc: PMC6761951
Genome Biol Evol 11 (9) 2633-2652 [2019-09-01; online 2019-08-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.
Happel EM, Markussen T, Teikari JE, ..., Kisand V, Riemann L
pii: 5545591
FEMS Microbiol. Ecol. 95 (9) - [2019-09-01; online 2019-08-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.
Morais EB, Schönenberger J, Conti E, Antonelli A, Szövényi P
pii: APS311290 pmc: PMC6764435
Appl Plant Sci 7 (9) e11290 [2019-09-00; online 2019-09-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.
Karlsson CMG, Cerro-Gálvez E, Lundin D, ..., Vila-Costa M, Pinhassi J
pmc: PMC6680617 GENBANK: KM586890
Microb Biotechnol 12 (5) 892-906 [2019-09-00; online 2019-07-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors.
Aralaguppe SG, Ambikan AT, Ashokkumar M, ..., Sönnerborg A, Neogi U
pii: v11090806 pmc: PMC6784143
Viruses 11 (9) - [2019-08-30; online 2019-08-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology.
Lázaro-Ibáñez E, Lässer C, Shelke GV, ..., García-Rodríguez A, Lötvall J
pii: 1656993 pmc: PMC6719264
J Extracell Vesicles 8 (1) 1656993 [2019-08-27; online 2019-08-27]
Centre for Cellular Imaging [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.
Marquardt N, Kekäläinen E, Chen P, ..., Ljunggren HG, Michaëlsson J
pii: 10.1038/s41467-019-11632-9 pmc: PMC6710242
Nat Commun 10 (1) 3841 [2019-08-26; online 2019-08-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.
Fernandes SJ, Morikawa H, Ewing E, ..., Tegnér J, Gomez-Cabrero D
pii: 10.1038/s41598-019-48493-7 pmc: PMC6700160
Sci Rep 9 (1) 11996 [2019-08-19; online 2019-08-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.
Lopez-Fernandez M, Broman E, Simone D, Bertilsson S, Dopson M
pii: mBio.01470-19 pmc: PMC6692508
MBio 10 (4) - [2019-08-13; online 2019-08-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.
Costa TDF, Zhuang T, Lorent J, ..., Defilippi P, Strömblad S
pii: 10.1038/s41467-019-11510-4 pmc: PMC6689091
Nat Commun 10 (1) 3589 [2019-08-09; online 2019-08-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species
Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N
ENA: PRJEB21838
Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]
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Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.
Herlemann DPR, Markert S, Meeske C, ..., Jürgens K, Schweder T
pii: AEM.00825-19 pmc: PMC6643244
Appl. Environ. Microbiol. 85 (15) - [2019-08-01; online 2019-07-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells.
Amaral PP, Engström PG, Robson SC, ..., Kouzarides T, Castelo-Branco G
pii: S0014-4827(19)30239-3
Exp. Cell Res. 381 (1) 129-138 [2019-08-01; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).
Garg KM, Sam K, Chattopadhyay B, ..., Ericson PGP, Rheindt FE
pii: 5550337 pmc: PMC6735254
Genome Biol Evol 11 (8) 2332-2343 [2019-08-01; online 2019-08-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
31° South: The physiology of adaptation to arid conditions in a passerine bird.
Ribeiro ÂM, Puetz L, Pattinson NB, ..., Smit B, Gilbert MTP
GENBANK: PRJNA492976
Mol. Ecol. 28 (16) 3709-3721 [2019-08-00; online 2019-08-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.
Frisk S, Taylan F, Blaszczyk I, ..., Laurell T, Nordgren A
pmc: PMC6851821
Clin. Genet. 96 (2) 118-125 [2019-08-00; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades
Hiltunen M, Grudzinska-Sterno M, Wallerman O, Ryberg M, Johannesson H
Current Biology 29 (16) 2758-2765.e6 [2019-08-00; online 2019-08-00]
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Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M
pii: S1055-7903(18)30644-4
Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]
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Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.
Kawakami T, Wallberg A, Olsson A, ..., Rundlöf M, Webster MT
pii: genetics.119.302008 pmc: PMC6707477
Genetics 212 (4) 1101-1119 [2019-08-00; online 2019-05-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.
Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA
pmc: PMC6852176 GENBANK: PRJNA497177
Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]
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PubMed DOI Crossref
Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.
von Holst S, Jiao X, Liu W, ..., Bryant P, Lindblom A
pii: 10.1038/s41431-019-0388-3
Eur. J. Hum. Genet. 27 (8) 1286-1295 [2019-08-00; online 2019-04-05]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.
Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Ekström TJ
pii: S2352-3964(19)30441-4 pmc: PMC6710853
EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.
Saini A, Björkhem-Bergman L, Boström J, ..., Rullman E, Gustafsson T
pii: EC-19-0194.R1 pmc: PMC6652245
Endocr Connect 8 (7) 1070-1081 [2019-07-29; online 2019-07-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.
Ericson PGP, Qu Y, Rasmussen PC, ..., Rheindt FE, Irestedt M
pii: 10.1186/s12862-019-1481-5 pmc: PMC6657069
BMC Evol. Biol. 19 (1) 151 [2019-07-24; online 2019-07-24]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.
Wallander K, Liu W, von Holst S, ..., Lindblom A, Lagerstedt-Robinson K
Genes Chromosomes Cancer - (-) - [2019-07-23; online 2019-07-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity
Espinoza JA, Zisi A, Kanellis DC, ..., Lindström MS, Bartek J
Cell Death Differ - (-) - [2019-07-08; online 2019-07-08]
Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.
Ranade SS, Delhomme N, García-Gil MR
pii: PONE-D-19-06007 pmc: PMC6611632
PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]
Biochemical Imaging Centre Umeå [Service] Bioinformatics Compute and Storage [Service] Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.
Christel S, Yu C, Wu X, ..., Åström ME, Dopson M
pii: S0923-2508(19)30059-2
Res. Microbiol. 170 (6-7) 288-295 [2019-07-03; online 2019-07-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection.
Kalyandurg PB, Tahmasebi A, Vetukuri RR, ..., Grenville-Briggs LJ, Savenkov EI
pii: S0042-6822(19)30172-2
Virology 535 (-) 111-121 [2019-07-01; online 2019-07-01]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome analysis of shade avoidance and shade tolerance in conifers.
Ranade SS, Delhomme N, García-Gil MR
pii: 10.1007/s00425-019-03160-z
Planta 250 (1) 299-318 [2019-07-00; online 2019-04-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality
Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A
Experimental Cell Research 383 (1) 111469 [2019-07-00; online 2019-07-00]
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PubMed DOI Crossref
Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS G13D mutation.
Charitou T, Srihari S, Lynn MA, ..., Kolch W, Lynn DJ
pii: 10.1038/s41416-019-0477-7 pmc: PMC6738113
Br. J. Cancer 121 (1) 37-50 [2019-07-00; online 2019-05-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.
Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM
Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.
Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A
pii: genes10070494 pmc: PMC6678668
Genes 10 (7) - [2019-06-28; online 2019-06-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.
Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B
pii: mBio.01286-19 pmc: PMC6593409
MBio 10 (3) - [2019-06-25; online 2019-06-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.
Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T
pmc: PMC6598052
Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.
Smythe AB, Holovachov O, Kocot KM
pii: 10.1186/s12862-019-1444-x pmc: PMC6567515
BMC Evol. Biol. 19 (1) 121 [2019-06-13; online 2019-06-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Modeling Motor Neuron Resilience in ALS Using Stem Cells.
Allodi I, Nijssen J, Benitez JA, ..., Kiehn O, Hedlund E
pii: S2213-6711(19)30131-6 pmc: PMC6565614
Stem Cell Reports 12 (6) 1329-1341 [2019-06-11; online 2019-05-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I
Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-06]
Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.
Maffezzini C, Laine I, Dallabona C, ..., Wredenberg A, Wedell A
pmc: PMC6565557
Mol Genet Genomic Med 7 (6) e654 [2019-06-00; online 2019-03-28]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.
Hill J, Rastas P, Hornett EA, ..., Nylin S, Wheat CW
pii: aau3648 pmc: PMC6561736
Sci Adv 5 (6) eaau3648 [2019-06-00; online 2019-06-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.
Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A
pmc: PMC6565582
Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells
Tibbitt CA, Stark JM, Martens L, ..., Saeys Y, Coquet JM
Immunity 51 (1) 169-184.e5 [2019-06-00; online 2019-06-00]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.
Kashuba N, Kırdök E, Damlien H, ..., Persson P, Götherström A
pii: 399 pmc: PMC6520363 Dryad: 10.5061/dryad.j3k19p9
Commun Biol 2 (-) 185 [2019-05-15; online 2019-05-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.
Sankavaram SR, Hakim R, Covacu R, ..., Svensson M, Brundin L
pii: S2213-6711(19)30098-0 pmc: PMC6524946
Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.
Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T
pii: jcm8050630 pmc: PMC6572048
J Clin Med 8 (5) - [2019-05-08; online 2019-05-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.
Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA
pii: PONE-D-18-32972 pmc: PMC6497305
PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.
Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V
pii: PONE-D-18-32895 pmc: PMC6493715
PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M
pii: 5300102 pmc: PMC6497032
Gigascience 8 (5) - [2019-05-01; online 2019-01-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.
Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q
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Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]
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Gene expression profile of extraocular muscles following resection strabismus surgery
Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F
Experimental Eye Research 182 (-) 182-193 [2019-05-00; online 2019-05-00]
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An Atlas of Vagal Sensory Neurons and Their Molecular Specialization
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Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M
Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]
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PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.
Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G
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Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]
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The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement
Abramova A, Lind U, Blomberg A, Rosenblad MA
Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]
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The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.
Boman J, Frankl-Vilches C, da Silva Dos Santos M, ..., Gahr M, Suh A
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Genes 10 (4) - [2019-04-13; online 2019-04-13]
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SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A
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Stem Cell Reports 12 (4) 696-711 [2019-04-09; online 2019-02-28]
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SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.
Hu FJ, Lundqvist M, Uhlén M, Rockberg J
pii: 5304719 pmc: PMC6451119
Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H
pii: 364/6435/89
Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.
Wang K, Sybers D, Maklad HR, ..., Lindås AC, Peeters E
pii: 10.1038/s41467-019-09479-1 pmc: PMC6449355
Nat Commun 10 (1) 1542 [2019-04-04; online 2019-04-04]
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Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.
Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O
pii: 126180 pmc: PMC6483641
JCI Insight 4 (7) - [2019-04-04; online 2019-04-04]
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PubMed DOI Crossref
Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.
Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M
pii: 10.1186/s13287-019-1218-9 pmc: PMC6448247
Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gain-of-function mutation of microRNA-140 in human skeletal dysplasia.
Grigelioniene G, Suzuki HI, Taylan F, ..., Sharp PA, Kobayashi T
pii: 10.1038/s41591-019-0353-2 pmc: PMC6622181 mid: NIHMS1518562
Nat. Med. 25 (4) 583-590 [2019-04-00; online 2019-02-25]
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PubMed DOI Crossref
A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis
Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E
PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]
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PubMed DOI Crossref
The repertoire of maternal anti-viral antibodies in human newborns.
Pou C, Nkulikiyimfura D, Henckel E, ..., Bohlin K, Brodin P
pii: 10.1038/s41591-019-0392-8
Nat. Med. - (-) - [2019-03-18; online 2019-03-18]
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Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.
Chyleński M, Ehler E, Somel M, ..., Juras A, Marciniak A
pii: genes10030207 pmc: PMC6471721
Genes 10 (3) - [2019-03-11; online 2019-03-11]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.
van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K
Mol Ecol Resour - (-) - [2019-03-08; online 2019-03-08]
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PubMed DOI Crossref
Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.
Cheng S, Pei Y, He L, ..., Jing N, Deng Q
pii: S2211-1247(19)30202-5
Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]
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PubMed DOI Crossref
A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.
Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS
pii: 10.1038/s41586-019-0989-6
Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]
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Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.
Kuruvilla J, Bayat N, Cristobal S
Proteomics 19 (5) e1800228 [2019-03-00; online 2019-02-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.
Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B
pii: 10.1038/s41598-019-39445-2 pmc: PMC6395693
Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]
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PubMed DOI Crossref
Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract.
Sahara M, Santoro F, Sohlmér J, ..., Gruber P, Chien KR
pii: S1534-5807(19)30005-X
Dev. Cell 48 (4) 475-490.e7 [2019-02-25; online 2019-01-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.
Wang D, Eraslan B, Wieland T, ..., Hahne H, Kuster B
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Mol. Syst. Biol. 15 (2) e8503 [2019-02-18; online 2019-02-18]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).
Kryvokhyzha D, Salcedo A, Eriksson MC, ..., Wright SI, Lascoux M
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PLoS Genet. 15 (2) e1007949 [2019-02-00; online 2019-02-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.
Eisfeldt J, Pettersson M, Vezzi F, ..., Carvalho CMB, Lindstrand A
pii: PGENETICS-D-18-00854 pmc: PMC6368290
PLoS Genet. 15 (2) e1007858 [2019-02-00; online 2019-02-08]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.
Lindefeldt M, Eng A, Darban H, ..., Dahlin M, Prast-Nielsen S
pii: 73 pmc: PMC6344533
NPJ Biofilms Microbiomes 5 (-) 5 [2019-01-23; online 2019-01-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Altered human oligodendrocyte heterogeneity in multiple sclerosis
Jäkel S, Agirre E, Falcão AM, ..., Williams A, Castelo-Branco G
Nature - (-) - [2019-01-23; online 2019-01-23]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.
Karkman A, Pärnänen K, Larsson DGJ
pii: 10.1038/s41467-018-07992-3 pmc: PMC6325112
Nat Commun 10 (1) 80 [2019-01-08; online 2019-01-08]
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Year 2018

PubMed DOI Crossref
PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.
Chase A, Pellagatti A, Singh S, ..., Boultwood J, Cross NCP
pii: 10.1038/s41375-018-0340-5
Leukemia - (-) - [2018-12-20; online 2018-12-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.
van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L
pii: S0960-9822(18)31554-9
Curr. Biol. - (-) - [2018-12-18; online 2018-12-18]
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PubMed DOI Crossref
Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.
Taylan F, Bang B, Öfverholm II, ..., Zachariadis V, Nordgren A
pii: clinchem.2018.293548
Clin. Chem. - (-) - [2018-12-05; online 2018-12-05]
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PubMed DOI Crossref
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.
Ni G, Simone D, Palma D, ..., Turner S, Dopson M
pmc: PMC6289977
Front Microbiol 9 (-) 2945 [2018-12-05; online 2018-12-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A major locus controls local adaptation and adaptive life history variation in a perennial plant
Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK
SRA: PRJNA297202
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
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PubMed DOI Crossref
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M
Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]
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The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.
Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ
pii: S1936-5233(18)30358-9 pmc: PMC6132178
Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL
ArrayExpress: E-MTAB-6321 ArrayExpress: E-MTAB-6331
Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]
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Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing
Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K
Nat Commun 9 (1) - [2018-12-00; online 2018-12-04]
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PubMed DOI Crossref
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S
BioProject: PRJNA408072 SRA: SRP118970
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
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PubMed DOI Crossref
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons
Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J
GEO: GSE107656
Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]
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PubMed DOI Crossref
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J
BioProject: PRJNA273799 SRA: SRP058493
Microbiome 6 (1) - [2018-12-00; online 2018-09-28]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.
Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M
pmc: PMC6277548
Front Microbiol 9 (-) 2880 [2018-11-27; online 2018-11-27]
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PubMed DOI Crossref
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M
MBio 9 (6) - [2018-11-20; online 2018-11-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.
Pedersen JN, Bombar D, Paerl RW, Riemann L
pmc: PMC6250843
Front Microbiol 9 (-) 2759 [2018-11-16; online 2018-11-16]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.
De Wit P, Yamada K, Panova M, André C, Johannesson K
pii: 10.1038/s41598-018-34937-z pmc: PMC6235865
Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).
Salgado MG, van Velzen R, Nguyen TV, ..., Lundin D, Pawlowski K
pmc: PMC6246699
Front Plant Sci 9 (-) 1629 [2018-11-14; online 2018-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Parallel plumage colour evolution and introgressive hybridization in wheatears.
Schweizer M, Warmuth V, Alaei Kakhki N, ..., Suh A, Burri R
J. Evol. Biol. - (-) - [2018-11-12; online 2018-11-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G
GEO: GSE113973
Nat Med - (-) - [2018-11-12; online 2018-11-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.
Nazaryan-Petersen L, Eisfeldt J, Pettersson M, ..., Tümer Z, Lindstrand A
pii: PGENETICS-D-18-01290 pmc: PMC6258378
PLoS Genet. 14 (11) e1007780 [2018-11-00; online 2018-11-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J
pii: 10.1038/s41596-018-0045-2
Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.
Xu J, Gruber PJ, Chien KR
Stem Cells - (-) - [2018-10-30; online 2018-10-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR
European Nucleotide Archive: PRJEB23585 PlantGenie.org: pnas201801437
Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]
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PubMed DOI Crossref
Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.
Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL
pii: 10.1038/s41598-018-33960-4 pmc: PMC6203749
Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.
Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P
Cancer Med - (-) - [2018-10-26; online 2018-10-26]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.
Joost S, Jacob T, Sun X, ..., Sur I, Kasper M
pii: S2211-1247(18)31504-3 ArrayExpress: E-MTAB-6583 ArrayExpress: E-MTAB-6686
Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J
pii: 0008-5472.CAN-18-0747
Cancer Res. 78 (20) 5970-5979 [2018-10-15; online 2018-08-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.
Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K
pii: 26225 pmc: PMC6205557
Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]
Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Service]
PubMed DOI Crossref
Enhanced validation of antibodies for research applications.
Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M
pii: 10.1038/s41467-018-06642-y pmc: PMC6175901 ProteomeXchange: PXD005914 ProteomeXchange: PXD010178 Panorama Public Datasets: https://panoramaweb.org/western_blot.url BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA183192 BioProject: PRJNA183192
Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]
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Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.
Pettersson M, Vaz R, Hammarsjö A, ..., Grigelioniene G, Lindstrand A
Hum. Mutat. 39 (10) 1456-1467 [2018-10-00; online 2018-08-22]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Partial genomic survival of cave bears in living brown bears.
Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M
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Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads
Krzewińska M, Kılınç GM, Juras A, ..., Storå J, Götherström A
Sci Adv 4 (10) eaat4457 [2018-10-00; online 2018-10-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.
Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M
pmc: PMC6172326 BioProject: PRJNA473625
Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.
Ritter CD, Zizka A, Roger F, ..., Nilsson RH, Antonelli A
pii: 5661 pmc: PMC6161700
PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.
Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N
pii: 5025902 pmc: PMC6144808 GEO: GSE95236
Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.
Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Lundberg ES
Clin. Genet. - (-) - [2018-09-16; online 2018-09-16]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.
Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F
pii: 10.1038/s41467-018-06033-3 pmc: PMC6135759 GEO: GSE117055
Nat Commun 9 (1) 3691 [2018-09-12; online 2018-09-12]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Contribution of allelic imbalance to colorectal cancer.
Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA
pii: 10.1038/s41467-018-06132-1 pmc: PMC6131244 European Nucleotide Archive: PRJEB25645 European Genome-phenome Archive: EGAS00001002966 European Genome-phenome Archive: EGAS00001003010 Zenodo: https://doi.org/10.5281/zenodo.1222172
Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]
Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.
Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A
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Curr. Biol. 28 (17) 2730-2738.e10 [2018-09-10; online 2018-08-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.
Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC
pii: 5061551 pmc: PMC6152947
Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation
Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O
Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.
Johansson US, Irestedt M, Qu Y, Ericson PGP
pii: S1055-7903(17)30880-1
Mol. Phylogenet. Evol. 126 (-) 17-22 [2018-09-00; online 2018-04-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The molecular genetic basis of herbivory between butterflies and their host plants.
Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR
pii: 10.1038/s41559-018-0629-9 pmc: PMC6149523 mid: NIHMS979338 SRA: SRP134094 Transcriptome Shotgun Assembly Sequence Database: GGJX00000000 Transcriptome Shotgun Assembly Sequence Database: GGKA00000000 Transcriptome Shotgun Assembly Sequence Database: GGJQ00000000 Transcriptome Shotgun Assembly Sequence Database: GGJO00000000 Transcriptome Shotgun Assembly Sequence Database: GGJY00000000 Transcriptome Shotgun Assembly Sequence Database: GGJZ00000000 Transcriptome Shotgun Assembly Sequence Database: GGKB00000000 Transcriptome Shotgun Assembly Sequence Database: GGKC00000000
Nat Ecol Evol 2 (9) 1418-1427 [2018-09-00; online 2018-08-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.
Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ
GENBANK: NSDL00000000
Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.
Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M
pii: IAI.00244-18 pmc: PMC6105892
Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.
Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE
pii: 10.1038/s41598-018-31074-5 pmc: PMC6109123 BioProject: PRJNA392017
Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Stereotypic Immune System Development in Newborn Children.
Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P
pii: S0092-8674(18)30848-1 FlowRepository: FR-FCM-ZYKQ Mendeley: 10.17632/ynhdrcxtcc.1
Cell 174 (5) 1277-1292.e14 [2018-08-23; online 2018-08-25]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Translational Plasma Profiling [Service]
PubMed DOI Crossref
Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype
Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D
Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.
He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C
pii: sdata2018160 pmc: PMC6103262 GEO: GSE98816 GEO: GSE99235 GEO: GSE99058 figshare: https://doi.org/10.6084/m9.figshare.c.4077260).
Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G
pii: S1534-5807(18)30558-6 pmc: PMC6104814 GEO: GSE95194 GEO: GSE95093
Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]
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PubMed DOI Crossref
BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence
Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B
PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Molecular Architecture of the Mouse Nervous System.
Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S
pii: S0092-8674(18)30789-X pmc: PMC6086934 SRA: SRP135960
Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
pii: 10.1038/s41598-018-29920-7 pmc: PMC6085348 European Nucleotide Archive: PRJEB20562
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
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PubMed DOI Crossref
Clonal relatedness in tumour pairs of breast cancer patients.
Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K
pii: 10.1186/s13058-018-1022-y GEO: GSE97293 GEO: GSE97177
Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.
Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J
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Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.
Nascimento FJA, Lallias D, Bik HM, Creer S
pii: 10.1038/s41598-018-30179-1 pmc: PMC6078945 figshare: doi:10.6084/m9.figshare.4993667
Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
RNA velocity of single cells.
La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV
pii: 10.1038/s41586-018-0414-6 pmc: PMC6130801 mid: EMS78511
Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy
Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC
SRA: SRP102619
Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.
Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O
pii: EJE-18-0176
Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.
Thörnqvist L, Ohlin M
pii: S2352-3409(18)30478-5 pmc: PMC5992955 European Nucleotide Archive: PRJEB18926
Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.
Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V
Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.
Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF
pii: sdata2018146 pmc: PMC6067050 European Nucleotide Archive: PRJEB22997 SRA: SRP058493 figshare: https://doi.org/10.6084/m9.figshare.c.3831631 SRA: SRP077551
Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]
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PubMed DOI Crossref
Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.
Berner C, Bertos-Fortis M, Pinhassi J, Legrand C
pmc: PMC6068395 SRA: SRP120581
Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.
Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA
pii: 10.1038/s41419-018-0865-6 pmc: PMC6057880
Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.
Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M
pii: 10.1007/s00248-018-1229-6 BioProject: PRJNA323408
Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A
SRA: SRP131660 Zenodo: 10.5281/zenodo.1162653
PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.
Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U
pii: 10.1038/s41388-018-0400-3
Oncogene - (-) - [2018-07-11; online 2018-07-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.
Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A
pii: 5035166 pmc: PMC6030852 GEO: GSE112698
Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.
Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A
pmc: PMC6011928 GENBANK: KJ701175 GENBANK: MG356789 GENBANK: MG356790 GENBANK: MG012806 GENBANK: MG012840 GENBANK: MG385064 GENBANK: MG385074
Microb Biotechnol 11 (4) 680-693 [2018-07-00; online 2017-12-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J
pii: 10.1038/s41467-018-04724-5 pmc: PMC6010471 European Genome-phenome Archive: EGAS0000100300
Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.
Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T
pii: 10.1038/s41598-018-27627-3 pmc: PMC6008462
Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Investigating Holocene human population history in North Asia using ancient mitogenomes.
Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A
pii: 10.1038/s41598-018-27325-0 pmc: PMC5997703 Popset: 1405681532
Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response
Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J
Nat Med - (-) - [2018-06-11; online 2018-06-11]
High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.
Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P
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Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).
Blåhed IM, Königsson H, Ericsson G, Spong G
pii: PONE-D-17-39125 pmc: PMC5976195 Zenodo: https://doi.org/10.5281/zenodo.1237474
PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.
Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N
pii: 10.1186/s12864-018-4746-2 pmc: PMC5960078 GEO: GSE95236
BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]
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PubMed DOI Crossref
Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.
Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S
pii: 10.1007/s00234-018-2033-1 pmc: PMC5995995
Neuroradiology - (-) - [2018-05-14; online 2018-05-14]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.
Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K
pii: 25329 pmc: PMC5963621 GEO: GSE97293
Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.
Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M
pii: 4924857 pmc: PMC5913678
Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function
Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K
pii: 1721764115
Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling.
Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA
pii: 10.1038/s41590-018-0091-5
Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.
Dussex N, von Seth J, Robertson BC, Dalén L
pii: genes9040220 pmc: PMC5924562 European Nucleotide Archive: PRJEB25924
Genes 9 (4) - [2018-04-19; online 2018-04-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.
La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J
Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.
Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E
pii: 24808 pmc: PMC5929421 GEO: GSE109367
Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.
Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P
pii: S2352-3964(18)30094-X pmc: PMC5952343
EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.
Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H
pii: pp.17.01590 pmc: PMC5884607
Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.
Thörnqvist L, Ohlin M
pii: S0161-5890(18)30043-9 European Nucleotide Archive: PRJEB18926
Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.
Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A
pmc: PMC5874392 ArrayExpress: E-MTAB-5143
Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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AMYCNE: Confident copy number assessment using whole genome sequencing data.
Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A
pii: PONE-D-17-18300 pmc: PMC5868770
PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb
Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM
SRA: SRP132598 SRA: SRP132591
New Phytol - (-) - [2018-03-24; online 2018-03-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J
pii: S0092-8674(18)30148-X pmc: PMC5871719 GEO: GSE93976
Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Ethylene-Related Gene Expression Networks in Wood Formation.
Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H
pmc: PMC5861219 European Nucleotide Archive: ERP012528
Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.
Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G
pii: PONE-D-17-38103 pmc: PMC5846771 SRA: SRP121435
PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Global analysis of A-to-I RNA editing reveals association with common disease variants
Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM
PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.
Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV
pii: PONE-D-17-39048 pmc: PMC5834160 ENA: PRJEB22154
PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.
James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I
pii: 4792999
Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.
Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M
pii: S1055-7903(17)30354-8
Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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A molecular atlas of cell types and zonation in the brain vasculature.
Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C
pii: nature25739 GEO: GSE98816 GEO: GSE99058 GEO: GSE99235
Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.
Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S
pii: 10.1038/s41593-017-0056-2
Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.
Leal L, Talla V, Källman T, ..., Vila R, Backström N
BioProject: PRJEB24745 ArrayExpress: E‐MTAB‐6454
Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus
Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L
Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M
BioProject: PRJEB21940
PLoS Biol. 16 (1) e2003703 [2018-01-09; online 2018-01-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Discovering viral genomes in human metagenomic data by predicting unknown protein families.
Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL
pii: 10.1038/s41598-017-18341-7 pmc: PMC5758519 European Nucleotide Archive: PRJEB17838
Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.
Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C
pii: 10.1186/s12864-017-4407-x pmc: PMC5753508
BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.
Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE
pii: 10.1038/s41437-017-0026-1 pmc: PMC5837122
Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2017

PubMed DOI Crossref
Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.
Hofmeister W, Pettersson M, Kurtoglu D, ..., Gustavsson P, Lindstrand A
Hum. Mutat. - (-) - [2017-12-28; online 2017-12-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.
Högfors-Rönnholm E, Christel S, Dalhem K, ..., Österholm P, Dopson M
pii: S0048-9697(17)33720-8 BioProject: PRJNA407753
Sci. Total Environ. 625 (-) 39-49 [2017-12-26; online 2017-12-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Discovery of the fourth mobile sulfonamide resistance gene.
Razavi M, Marathe NP, Gillings MR, ..., Kristiansson E, Joakim Larsson DG
pii: 10.1186/s40168-017-0379-y pmc: PMC5732528 BioProject: PRJNA400874 GENBANK: MG649394 GENBANK: MG649395 GENBANK: MG649396 GENBANK: MG649397 GENBANK: MG649398 GENBANK: MG649399 GENBANK: MG649400 GENBANK: MG649401 GENBANK: MG649402 GENBANK: MG649403
Microbiome 5 (1) 160 [2017-12-15; online 2017-12-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.
Zhang W, Ambikan AT, Sperk M, ..., Sönnerborg A, Neogi U
pii: S2352-3964(17)30473-5 BioProject: PRJNA420459 SRA: SRP125882
EBioMedicine - (-) - [2017-12-12; online 2017-12-12]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Unique ISR Program Determines Cellular Responses to Chronic Stress.
Guan BJ, van Hoef V, Jobava R, ..., Larsson O, Hatzoglou M
pii: S1097-2765(17)30842-0 pmc: PMC5730339 mid: NIHMS919694 GEO: GSE90070
Mol. Cell 68 (5) 885-900.e6 [2017-12-07; online 2017-12-09]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration
Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A
SRA: SRP116714 BioProject: PRJNA353981
Nat Commun 8 (1) - [2017-12-00; online 2017-12-22]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Inflammatory infiltrates in parathyroid tumors.
Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C
pii: EJE-17-0277 pmc: PMC5642267
Eur. J. Endocrinol. 177 (6) 445-453 [2017-12-00; online 2017-08-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)
Talla V, Kalsoom F, Shipilina D, Marova I, Backström N
BioProject: PRJEB21643 SRA: ERP023915
G3 (Bethesda) 7 (12) 3983-3998 [2017-12-00; online 2017-10-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.
Karthik GM, Rantalainen M, Stålhammar G, ..., Bergh J, Hartman J
pii: 10.1186/s12885-017-3815-2 pmc: PMC5708109
BMC Cancer 17 (1) 802 [2017-11-29; online 2017-11-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.
Hochgerner H, Lönnerberg P, Hodge R, ..., Zeisel A, Linnarsson S
pii: 10.1038/s41598-017-16546-4 pmc: PMC5703850 GEO: GSE101601
Sci Rep 7 (1) 16327 [2017-11-27; online 2017-11-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Activating FGFR1 Mutations in Sporadic Pheochromocytomas.
Welander J, Łysiak M, Brauckhoff M, ..., Söderkvist P, Gimm O
pii: 10.1007/s00268-017-4320-0
World J Surg - (-) - [2017-11-20; online 2017-11-20]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.
Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L
pii: S0960-9822(17)31264-2 BioProject: PRJEB22575
Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT
Christel S, Herold M, Bellenberg S, ..., Poetsch A, Dopson M
BioProject: PRJEB21703 BioProject: PRJEB21842
Appl Environ Microbiol 84 (3) e02091-17 [2017-11-17; online 2018-01-17]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.
Hammarsjö A, Wang Z, Vaz R, ..., Grigelioniene G, Ikegawa S
pii: 10.1038/s41598-017-15442-1 pmc: PMC5686170
Sci Rep 7 (1) 15585 [2017-11-14; online 2017-11-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.
Rodríguez-Varela R, Günther T, Krzewińska M, ..., Götherström A, Girdland-Flink L
pii: S0960-9822(17)31257-5 BioProject: PRJEB86458
Curr. Biol. 27 (21) 3396-3402.e5 [2017-11-06; online 2017-10-26]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.
Jiao H, Olin M, Hansson M, ..., Angelin B, Björkhem I
J. Intern. Med. - (-) - [2017-11-02; online 2017-11-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.
Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ
pii: S0043-1354(17)30633-4 MG-RAST: 19878
Water Res. 124 (-) 388-397 [2017-11-01; online 2017-07-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High abundance and expression of transposases in bacteria from the Baltic Sea.
Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M
pii: ismej2017114 pmc: PMC5649170
ISME J 11 (11) 2611-2623 [2017-11-00; online 2017-07-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.
Svartström O, Alneberg J, Terrapon N, ..., Aspeborg H, Andersson AF
pii: ismej2017108 pmc: PMC5648042 mid: EMS73237 BioProject: PRJEB12797
ISME J 11 (11) 2538-2551 [2017-11-00; online 2017-07-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.
Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U
pii: ejhg2017130 swefreq: swegen
Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Efficient protein production by yeast requires global tuning of metabolism.
Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J
pii: 10.1038/s41467-017-00999-2 pmc: PMC5656615 ENA: ERP019558
Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Polysome-profiling in small tissue samples.
Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O
pii: 4561642 BioProject: PRJNA390060
Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.
Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J
pii: 10.1038/s41598-017-13462-5 pmc: PMC5636908
Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.
Broman E, Sachpazidou V, Dopson M, Hylander S
pii: rspb.2017.1617 pmc: PMC5647304 BioProject: PRJNA347538 BioProject: PRJNA322450
Proc. Biol. Sci. 284 (1864) - [2017-10-11; online 2017-10-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.
Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L
Am. J. Med. Genet. B Neuropsychiatr. Genet. - (-) - [2017-10-09; online 2017-10-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Demographic inference from whole genome and RAD sequencing data suggests alternating human impacts on goose populations since the Last Ice Age.
Pujolar JM, Dalén L, Hansen MM, Madsen J
BioProject: PRJNA400851 Dryad: https://doi.org/10.5061/dryad.c4r81
Mol. Ecol. - (-) - [2017-10-05; online 2017-10-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.
Talla V, Suh A, Kalsoom F, ..., Wiklund C, Backström N
pii: 4091610 BioProject: PRJEB21838 GENBANK: FZQP00000000
Genome Biol Evol 9 (10) 2491-2505 [2017-10-01; online 2017-10-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
NorWood: a gene expression resource for evo-devo studies of conifer wood development.
Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H
ENA: ERP017340
New Phytol. 216 (2) 482-494 [2017-10-00; online 2017-02-10]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny
Rydin C, Wikström N, Bremer B
Am. J. Bot. 104 (10) 1522-1532 [2017-10-00; online 2017-10-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.
Zieba A, Ponten F, Uhlén M, Landegren U
pii: modpathol2017102
Mod. Pathol. - (-) - [2017-09-22; online 2017-09-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Technology development] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.
Quin JE, Bujila I, Chérif M, ..., Nebie I, Östlund Farrants AK
pmc: PMC5629023 GEO: GSE100563
Elife 6 (-) - [2017-09-19; online 2017-09-19]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.
Yu NY, Bieder A, Raman A, ..., Daub CO, Kere J
pii: 10.1038/s41598-017-11574-6 pmc: PMC5597620 BioProject: PRJEB20092
Sci Rep 7 (1) 11458 [2017-09-13; online 2017-09-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A female Viking warrior confirmed by genomics.
Hedenstierna-Jonson C, Kjellström A, Zachrisson T, ..., Götherström A, Storå J
Am. J. Phys. Anthropol. - (-) - [2017-09-08; online 2017-09-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.
Hugerth LW, Andersson AF
pmc: PMC5591341
Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.
Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV
pii: 4097580 pmc: PMC5622374 BioProject: PRJNA281995
Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.
Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S
pii: cddis2017406 pmc: PMC5596587 ProteomXchange: PXD001682
Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]
Clinical Proteomics Mass spectrometry [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Proteogenomics [Service]
PubMed DOI Crossref
First de novo whole genome sequencing and assembly of the pink-footed goose.
Pujolar JM, Dalén L, Olsen RA, Hansen MM, Madsen J
pii: S0888-7543(17)30075-7 BioProject: PRJNA404647
Genomics - (-) - [2017-08-30; online 2017-08-30]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cerium oxide nanoparticles inhibit differentiation of neural stem cells.
Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B
pii: 10.1038/s41598-017-09430-8 pmc: PMC5570910 ArrayExpress: E-MTAB-4398
Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]
Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of NCAN as a candidate gene for developmental dyslexia.
Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J
pii: 10.1038/s41598-017-10175-7 pmc: PMC5570950 BioProject: PRJEB12695
Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A pathology atlas of the human cancer transcriptome.
Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F
pii: 357/6352/eaan2507
Science 357 (6352) - [2017-08-18; online 2017-08-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Technology development]
PubMed DOI Crossref
Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.
Broman E, Sjöstedt J, Pinhassi J, Dopson M
pii: 10.1186/s40168-017-0311-5 pmc: PMC5549381
Microbiome 5 (1) 96 [2017-08-09; online 2017-08-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rho-associated kinase is a therapeutic target in neuroblastoma.
Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M
pii: 1706011114 pmc: PMC5559038
Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.
Kämpe AJ, Costantini A, Levy-Shraga Y, ..., Grasemann C, Mäkitie O
J. Bone Miner. Res. - (-) - [2017-08-04; online 2017-08-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.
Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E
pii: ERC-17-0196 pmc: PMC5527373
Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Data on haplotype-supported immunoglobulin germline gene inference.
Kirik U, Greiff L, Levander F, Ohlin M
pii: S2352-3409(17)30275-5 pmc: PMC5502703
Data Brief 13 (-) 620-640 [2017-08-00; online 2017-06-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.
Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M
pii: 10.1007/s10532-017-9796-7 pmc: PMC5500686
Biodegradation 28 (4) 287-301 [2017-08-00; online 2017-06-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks
Lundberg M, Liedvogel M, Larson K, ..., Åkesson S, Bensch S
Evolution Letters 1 (3) 155-168 [2017-08-00; online 2017-06-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.
Redin D, Borgström E, He M, ..., Käller M, Ahmadian A
pii: 3835310 pmc: PMC5569991
Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.
Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O
pii: 10.1007/s00198-017-4150-9 pmc: PMC5624974
Osteoporos Int - (-) - [2017-07-26; online 2017-07-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.
Neogi U, Siddik AB, Kalaghatgi P, ..., Marrone G, Sönnerborg A
pii: 10.1038/s41598-017-06860-2 pmc: PMC5527090
Sci Rep 7 (1) 6371 [2017-07-25; online 2017-07-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression.
Westerlund I, Shi Y, Toskas K, ..., Schlisio S, Holmberg J
pii: 1700655114 pmc: PMC5544284
Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6137-E6146 [2017-07-25; online 2017-07-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.
Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B
pii: PONE-D-17-11371 pmc: PMC5513432 GEO: GSE73627
PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.
Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A
pii: PONE-D-17-05123 pmc: PMC5513457 GENBANK: KY508284 GENBANK: KY508285 GENBANK: KY508286 GENBANK: KY508287 GENBANK: KY508289 GENBANK: KY508290 GENBANK: KY508291 GENBANK: KY508292 GENBANK: KY508288 GENBANK: KY508293 GENBANK: KY508294 GENBANK: KY508295 GENBANK: KY508296 GENBANK: KY508297 GENBANK: KY508298
PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Does antifouling paint select for antibiotic resistance?
Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG
pii: S0048-9697(17)30230-9
Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.
van der Valk T, Lona Durazo F, Dalén L, Guschanski K
Mol Ecol Resour - (-) - [2017-07-04; online 2017-07-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Mineral Type Structures Soil Microbial Communities
Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM
Geomicrobiology Journal - (-) 1-8 [2017-07-03; online 2016-08-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.
Mead AJ, Neo WH, Barkas N, ..., Nerlov C, Jacobsen SEW
pii: jem.20161418 pmc: PMC5502426
J. Exp. Med. 214 (7) 2005-2021 [2017-07-03; online 2017-06-21]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).
Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR
pii: 3104592 pmc: PMC5455968
Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.
Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P
Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
Hernandez-Castro LE, Paterno M, Villacís AG, ..., Grijalva MJ, Llewellyn MS
pii: PNTD-D-16-01890 pmc: PMC5536387
PLoS Negl Trop Dis 11 (7) e0005710 [2017-07-00; online 2017-07-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.
Kirik U, Greiff L, Levander F, Ohlin M
pii: S0161-5890(17)30081-0
Mol. Immunol. 87 (-) 12-22 [2017-07-00; online 2017-04-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomewide analysis of admixture and adaptation in the Africanized honeybee.
Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT
BioProject: PRJNA236426 BioProject: PRJNA350769
Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.
Pasanen P, Mäkinen J, Myllykangas L, ..., Pöyhönen M, Baumann P
Acta Neurol. Scand. 136 (1) 59-63 [2017-07-00; online 2016-10-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.
Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, ..., Dalén L, Gilbert MTP
pii: 10.1186/s12864-017-3883-3 pmc: PMC5492679
BMC Genomics 18 (1) 495 [2017-06-29; online 2017-06-29]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.
Kerkhoven EJ, Kim YM, Wei S, ..., Metz TO, Nielsen J
pii: mBio.00857-17 pmc: PMC5478895
MBio 8 (3) - [2017-06-20; online 2017-06-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.
Neubeck A, Sun L, Müller B, ..., Broman C, Schnürer A
pii: AEM.03430-16 pmc: PMC5452829
Appl. Environ. Microbiol. 83 (12) - [2017-06-15; online 2017-05-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.
Töpel M, Pinder MIM, Johansson ON, ..., Godhe A, Clarke AK
pii: 5/22/e00394-17 pmc: PMC5454192
Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability
Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P
Grass Forage Sci - (-) - [2017-06-00; online 2016-06-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E
pii: science.aal3321
Science 356 (6340) - [2017-05-26; online 2017-05-11]
Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.
Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ
pii: 5/21/e00346-17 pmc: PMC5477391
Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.
Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J
pii: 10.1186/s13073-017-0432-2 pmc: PMC5444103
Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
pmc: PMC5521161
F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
pii: nplants201761
NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.
Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M
pii: nmicrobiol201768
Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
Cluster Flow: A user-friendly bioinformatics workflow tool
Ewels P, Krueger F, Käller M, Andrews S
F1000Res 5 (-) 2824 [2017-05-02; online 2017-05-02]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.
Wallberg A, Schöning C, Webster MT, Hasselmann M
pii: PGENETICS-D-17-00165 pmc: PMC5444601 BioProject: PRJNA357367 Dryad: https://doi.org/10.5061/dryad.jn630
PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K
pii: 10.1007/s00204-016-1879-4 pmc: PMC5399044
Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.
Pettersson M, Bergendal B, Norderyd J, ..., Nordgren A, Lindstrand A
Am. J. Med. Genet. A 173 (5) 1396-1399 [2017-05-00; online 2017-03-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.
Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW
pii: gr.215095.116 pmc: PMC5411765
Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.
Rivetti di Val Cervo P, Romanov RA, Spigolon G, ..., Fisone G, Arenas E
pii: nbt.3835
Nat. Biotechnol. 35 (5) 444-452 [2017-05-00; online 2017-04-10]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.
Hou C, Wikström N, Rydin C
Mitochondrial DNA A DNA Mapp Seq Anal 28 (3) 330-331 [2017-05-00; online 2015-12-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.
Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ER
pii: 5/14/e00125-17 pmc: PMC5383892
Genome Announc 5 (14) - [2017-04-06; online 2017-04-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).
Grigelioniene G, Nevalainen PI, Reyes M, ..., Mäkitie O, Jüppner H
pmc: PMC5395346 mid: NIHMS843464
J. Bone Miner. Res. 32 (4) 776-783 [2017-04-00; online 2017-02-24]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout
Huyben D, Nyman A, Vidaković A, ..., Dicksved J, Lundh T
Aquaculture 473 (-) 528-537 [2017-04-00; online 2017-04-00]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.
Zangenah S, Andersson AF, Özenci V, Bergman P
pii: 10.1007/s10096-016-2842-2 pmc: PMC5366173
Eur. J. Clin. Microbiol. Infect. Dis. 36 (4) 657-662 [2017-04-00; online 2016-12-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gene co-expression network connectivity is an important determinant of selective constraint.
Mähler N, Wang J, Terebieniec BK, ..., Street NR, Hvidsten TR
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PLoS Genet. 13 (4) e1006402 [2017-04-00; online 2017-04-13]
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Lamei S, Hu YO, Olofsson TC, ..., Forsgren E, Vásquez A
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PLoS ONE 12 (3) e0174614 [2017-03-27; online 2017-03-27]
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Wu X, Pedersen K, Edlund J, ..., Bertilsson S, Dopson M
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Microbiome 5 (1) 37 [2017-03-23; online 2017-03-23]
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Chang D, Knapp M, Enk J, ..., Hofreiter M, Shapiro B
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Sci Rep 7 (-) 44585 [2017-03-22; online 2017-03-22]
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Juras A, Krzewińska M, Nikitin AG, ..., Dabert M, Götherström A
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Sci Rep 7 (-) 43950 [2017-03-07; online 2017-03-07]
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Levin M, Levander F, Palmason R, Greiff L, Ohlin M
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J. Allergy Clin. Immunol. 139 (3) 1026-1030 [2017-03-00; online 2016-08-09]
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Lindh MV, Sjöstedt J, Ekstam B, ..., Legrand C, Pinhassi J
Environ. Microbiol. 19 (3) 1222-1236 [2017-03-00; online 2017-02-06]
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Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.
Sandmann S, de Graaf AO, Karimi M, ..., Jansen JH, Dugas M
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Sci Rep 7 (-) 43169 [2017-02-24; online 2017-02-24]
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Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.
Danielsson R, Dicksved J, Sun L, ..., Schnürer A, Bertilsson J
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Front Microbiol 8 (-) 226 [2017-02-17; online 2017-02-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J
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PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]
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Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P
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BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.
Zeigler Allen L, McCrow JP, Ininbergs K, ..., Bergman B, Venter JC
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Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C
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PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]
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Zhou Y, Frings O, Branca RM, ..., Agami R, Orre LM
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Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-01]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy.
Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO
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Int. J. Cardiol. 228 (-) 742-748 [2017-02-01; online 2016-11-26]
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The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.
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Nilsson D, Pettersson M, Gustavsson P, ..., Carvalho CMB, Lindstrand A
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Hum. Mutat. 38 (2) 180-192 [2017-02-00; online 2016-12-05]
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Hum. Genet. 136 (2) 179-192 [2017-02-00; online 2016-11-15]
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Celepli N, Sundh J, Ekman M, ..., Bergman B, Ininbergs K
Environ. Microbiol. 19 (2) 673-686 [2017-02-00; online 2017-01-27]
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Cimdins A, Lüthje P, Li F, ..., Brauner A, Römling U
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Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]
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Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae)
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Mitochondrial DNA Part B 2 (2) 548-549 [2017-01-02; online 2017-08-22]
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Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.
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pii: 2725477 GEO: GSE86491
Biol. Reprod. 96 (1) 24-33 [2017-01-01; online 2017-04-11]
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Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.
Fletcher E, Feizi A, Bisschops MM, ..., Siewers V, Nielsen J
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Metab. Eng. 39 (-) 19-28 [2017-01-00; online 2016-11-02]
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Journal of Thoracic Oncology 12 (1) S526-S527 [2017-01-00; online 2017-01-00]
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NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2016

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Disentangling genetic and epigenetic determinants of ultrafast adaptation.
Gjuvsland AB, Zörgö E, Samy JK, ..., Omholt SW, Warringer J
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Mol. Syst. Biol. 12 (12) 892 [2016-12-15; online 2016-12-15]
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Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.
Acevedo N, Bornacelly A, Mercado D, ..., Scheynius A, Caraballo L
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PLoS ONE 11 (12) e0167453 [2016-12-15; online 2016-12-15]
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The In Vitro Stability of Circulating Tumour DNA.
Henao Diaz E, Yachnin J, Grönberg H, Lindberg J
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PLoS ONE 11 (12) e0168153 [2016-12-13; online 2016-12-13]
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Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.
Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DG
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Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-21]
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Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.
Brindefalk B, Ekman M, Ininbergs K, ..., Pinhassi J, Bergman B
Environ. Microbiol. 18 (12) 4442-4455 [2016-12-00; online 2016-06-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.
Brace S, Thomas JA, Dalén L, ..., Barnes I, Turvey ST
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Mol. Biol. Evol. 33 (12) 3095-3103 [2016-12-00; online 2016-09-15]
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Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea.
Herlemann DP, Lundin D, Andersson AF, Labrenz M, Jürgens K
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Front Microbiol 7 (-) 1883 [2016-11-24; online 2016-11-24]
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A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.
Hefzi H, Ang KS, Hanscho M, ..., Lee DY, Lewis NE
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Cell Syst 3 (5) 434-443.e8 [2016-11-23; online 2016-11-25]
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An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.
Jemt A, Salmén F, Lundmark A, ..., Yucel-Lindberg T, Lundeberg J
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Sci Rep 6 (-) 37137 [2016-11-16; online 2016-11-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile.
Christel S, Fridlund J, Watkin EL, Dopson M
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Extremophiles 20 (6) 903-913 [2016-11-00; online 2016-10-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.
Ma Y, Miao Y, Peng Z, ..., Nilsson S, Li C
pii: 3543 pmc: PMC5078122
Springerplus 5 (1) 1861 [2016-10-24; online 2016-10-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.
Baltar F, Lundin D, Palovaara J, ..., Herndl GJ, Pinhassi J
pmc: PMC5073097
Front Microbiol 7 (-) 1670 [2016-10-21; online 2016-10-21]
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Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.
Panula S, Reda A, Stukenborg JB, ..., Reijo Pera RA, Hovatta O
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PLoS ONE 11 (10) e0165268 [2016-10-21; online 2016-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Gene-specific correlation of RNA and protein levels in human cells and tissues.
Edfors F, Danielsson F, Hallström BM, ..., Forsström B, Uhlén M
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Mol. Syst. Biol. 12 (10) 883 [2016-10-20; online 2016-10-20]
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The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.
Sävneby A, Luthman J, Nordenskjöld F, Andersson B, Lindberg AM
pii: PONE-D-16-25162 pmc: PMC5070843
PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Massive and parallel expression profiling using microarrayed single-cell sequencing.
Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J
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Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]
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Grijseels S, Nielsen JC, Randelovic M, ..., Workman M, Frisvad JC
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Sci Rep 6 (-) 35112 [2016-10-14; online 2016-10-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia.
Bogdanovic G, Pou C, Barrientos-Somarribas M, ..., Andersson B, Gustafsson B
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Br. J. Cancer 115 (8) 1008-1014 [2016-10-11; online 2016-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG
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Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]
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Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.
La Manno G, Gyllborg D, Codeluppi S, ..., Arenas E, Linnarsson S
pii: S0092-8674(16)31309-5 pmc: PMC5055122
Cell 167 (2) 566-580.e19 [2016-10-06; online 2016-10-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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MultiQC: summarize analysis results for multiple tools and samples in a single report.
Ewels P, Magnusson M, Lundin S, Käller M
pii: btw354 pmc: PMC5039924
Bioinformatics 32 (19) 3047-3048 [2016-10-01; online 2016-06-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]
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Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity.
Jiao H, Kulyté A, Näslund E, ..., Arner P, Dahlman I
pii: db16-0522
Diabetes 65 (10) 2980-2989 [2016-10-00; online 2016-07-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Towards integration of population and comparative genomics in forest trees.
Ingvarsson PK, Hvidsten TR, Street NR
New Phytol. 212 (2) 338-344 [2016-10-00; online 2016-08-31]
NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples.
Wang J, Skoog T, Einarsdottir E, ..., Kere J, Jiao H
pii: srep33256 pmc: PMC5025741
Sci Rep 6 (-) 33256 [2016-09-16; online 2016-09-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Absence of the Autophagy Adaptor SQSTM1/p62 Causes Childhood-Onset Neurodegeneration with Ataxia, Dystonia, and Gaze Palsy.
Haack TB, Ignatius E, Calvo-Garrido J, ..., Carroll CJ, Klopstock T
pii: S0002-9297(16)30230-0 pmc: PMC5010644
Am. J. Hum. Genet. 99 (3) 735-743 [2016-09-01; online 2016-08-23]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ
pmc: PMC5033478 pii: PGENETICS-D-16-01025
PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.
Ni G, Christel S, Roman P, ..., Bijmans MF, Dopson M
pii: S0923-2508(16)30012-2 pmc: PMC5015573
Res. Microbiol. 167 (7) 568-575 [2016-09-00; online 2016-05-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.
Rydén M, Hrydziuszko O, Mileti E, ..., Daub CO, Arner P
pii: S2211-1247(16)31014-2
Cell Rep 16 (9) 2317-2326 [2016-08-30; online 2016-08-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.
Luo D, Callari R, Hamberger B, ..., Staerk D, Hamberger B
pii: 1607504113 pmc: PMC5003294 GENBANK: KR350665 GENBANK: KR350666 GENBANK: KR350667 GENBANK: KR350668 GENBANK: KR350669 GENBANK: KR350671 GENBANK: KX428471
Proc. Natl. Acad. Sci. U.S.A. 113 (34) E5082-E5089 [2016-08-23; online 2016-08-11]
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Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea
Vaquer-Sunyer R, Reader HE, Muthusamy S, ..., Conley DJ, Kritzberg ES
Biogeosciences 13 (16) 4751-4765 [2016-08-23; online 2016-08-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.
Franzén O, Ermel R, Cohain A, ..., Schadt EE, Björkegren JL
pii: 353/6301/827
Science 353 (6301) 827-830 [2016-08-19; online 2016-08-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.
Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M
pii: gkw316 pmc: PMC5001587
Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]
Bioinformatics Compute and Storage [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.
Liu H, Wang K, Lindås AC, Peeters E
pii: 10.1186/s12864-016-2890-0 pmc: PMC4977709
BMC Genomics 17 (-) 569 [2016-08-08; online 2016-08-08]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Adaptation to different types of stress converge on mitochondrial metabolism.
Lahtvee PJ, Kumar R, Hallström BM, Nielsen J
pii: mbc.E16-03-0187 pmc: PMC4966989
Mol. Biol. Cell 27 (15) 2505-2514 [2016-08-01; online 2016-06-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.
Taylan F, Costantini A, Coles N, ..., Tüysüz B, Mäkitie O
J. Bone Miner. Res. 31 (8) 1577-1585 [2016-08-00; online 2016-03-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Profiling cancer testis antigens in non-small-cell lung cancer.
Djureinovic D, Hallström BM, Horie M, ..., Uhlén M, Micke P
pii: 86837 pmc: PMC5033889
JCI Insight 1 (10) e86837 [2016-07-07; online 2016-07-07]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.
Kaartokallio T, Wang J, Heinonen S, ..., Kere J, Laivuori H
pii: srep29085 pmc: PMC4935848
Sci Rep 6 (-) 29085 [2016-07-07; online 2016-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.
Asplund-Samuelsson J, Sundh J, Dupont CL, ..., Ininbergs K, Ekman M
pmc: PMC4933709
Front Microbiol 7 (-) 1043 [2016-07-06; online 2016-07-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J
pii: 353/6294/78
Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.
Wang J, Street NR, Scofield DG, Ingvarsson PK
pii: msw051 pmc: PMC4915356
Mol. Biol. Evol. 33 (7) 1754-1767 [2016-07-00; online 2016-03-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes.
Olsson L, Zettermark S, Biloglav A, ..., Paulsson K, Johansson B
Br. J. Haematol. 174 (2) 292-301 [2016-07-00; online 2016-03-31]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.
Scott AD, Stenz NW, Ingvarsson PK, Baum DA
New Phytol. 211 (1) 186-193 [2016-07-00; online 2016-03-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.
Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V
Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Draft Genome Sequence ofMoraxella catarrhalisType Strain CCUG 353T
Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ERB
Genome Announc 4 (3) e00552-16 [2016-06-30; online 2016-06-16]
Clinical Genomics Gothenburg [Service] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.
Yau AC, Tuncel J, Haag S, ..., Padyukov L, Holmdahl R
pii: 1600567113 pmc: PMC4932949
Proc. Natl. Acad. Sci. U.S.A. 113 (26) E3716-E3724 [2016-06-28; online 2016-06-16]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.
Marques S, Zeisel A, Codeluppi S, ..., Linnarsson S, Castelo-Branco G
pii: 352/6291/1326 pmc: PMC5221728 mid: EMS70326
Science 352 (6291) 1326-1329 [2016-06-10; online 2016-06-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GPR44 is a pancreatic protein restricted to the human beta cell.
Hellström-Lindahl E, Danielsson A, Ponten F, ..., Johansson L, Eriksson O
pii: 10.1007/s00592-015-0811-3
Acta Diabetol 53 (3) 413-421 [2016-06-00; online 2015-10-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila.
Dantoft W, Lundin D, Esfahani SS, Engström Y
pii: 000446368
J Innate Immun 8 (4) 412-426 [2016-05-28; online 2016-05-28]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.
Caspeta L, Chen Y, Nielsen J
pii: srep27003 pmc: PMC4882594
Sci Rep 6 (-) 27003 [2016-05-27; online 2016-05-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.
Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B
pii: PONE-D-15-30061 pmc: PMC4890579 ENA: PRJEB8968
PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.
Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DG
pii: S0048-9697(16)30314-X
Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.
Hu YO, Karlson B, Charvet S, Andersson AF
pmc: PMC4864665
Front Microbiol 7 (-) 679 [2016-05-12; online 2016-05-12]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Determining breast cancer histological grade from RNA-sequencing data.
Wang M, Klevebring D, Lindberg J, ..., Grönberg H, Rantalainen M
pii: 10.1186/s13058-016-0710-8 pmc: PMC4862203
Breast Cancer Res. 18 (1) 48 [2016-05-10; online 2016-05-10]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.
Bertos-Fortis M, Farnelid HM, Lindh MV, ..., Pinhassi J, Legrand C
pmc: PMC4860504
Front Microbiol 7 (-) 625 [2016-05-09; online 2016-05-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.
Palkopoulou E, Baca M, Abramson NI, ..., Stankovic A, Dalén L
GENBANK: KT867379 GENBANK: KT867537
Glob Chang Biol 22 (5) 1710-1721 [2016-05-00; online 2016-02-27]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.
Hytönen MK, Arumilli M, Lappalainen AK, ..., Drögemüller C, Lohi H