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Started: -

Ended: Current

Year 2023

PubMed DOI Crossref
SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.
Gollnisch R, Wallenius J, Gribble KE, Ahrén D, Rengefors K
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-20]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.
Mosquera KD, Nilsson LKJ, de Oliveira MR, ..., de Souza AQL, Terenius O
Parasit Vectors 16 (1) 156 [2023-05-01; online 2023-05-01]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.
Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG
PLoS Pathog. 19 (5) e1011372 [2023-05-00; online 2023-05-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stratified Genetic Analysis Reveals Sex Differences In MPO-ANCA-associated Vasculitis.
Ekman D, Sennblad B, Knight A, ..., Lindblad-Toh K, Dahlqvist J
Rheumatology (Oxford) - (-) - [2023-04-02; online 2023-04-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.
Lindberg FA, Nordenankar K, Forsberg EC, Fredriksson R
Genes 14 (4) - [2023-03-30; online 2023-03-30]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.
Mainwaring OJ, Weishaupt H, Zhao M, ..., Hutter S, Swartling FJ
Nat Commun 14 (1) 1221 [2023-03-03; online 2023-03-03]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
Jun S, Toosi H, Mold J, ..., Roth A, Lagergren J
Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative.
Johannesson K, Leder EH, André C, ..., Thorndyke M, Blomberg A
Evol Appl 16 (2) 530-541 [2023-02-00; online 2023-01-07]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Migratory behaviour is positively associated with genetic diversity in butterflies.
García-Berro A, Talla V, Vila R, ..., Backström N, Talavera G
Mol. Ecol. 32 (3) 560-574 [2023-02-00; online 2022-11-23]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
BioImage Informatics [Collaborative] In Situ Sequencing (ISS) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).
Höök L, Näsvall K, Vila R, Wiklund C, Backström N
Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.
Wang B, Hu H, Bishop K, ..., Bertilsson S, Bravo AG
J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.
Nishimura K, Yang S, Lee KW, ..., Linnarsson S, Arenas E
Stem Cell Reports 18 (1) 337-353 [2023-01-10; online 2022-11-17]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.
Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M
Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genetic history of Scandinavia from the Roman Iron Age to the present.
Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, ..., Helgason A, Götherström A
Cell 186 (1) 32-46.e19 [2023-01-05; online 2023-01-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Solid-phase capture and profiling of open chromatin by spatial ATAC.
Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL
Nat. Biotechnol. - (-) - [2023-01-05; online 2023-01-05]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.
Weishaupt H, Čančer M, Rosén G, ..., Ameur A, Swartling FJ
Neuro-oncology 25 (1) 97-107 [2023-01-05; online 2022-06-24]
Bioinformatics Compute and Storage [Service] NGI Short read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.
Alaei Kakhki N, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R
Mol. Biol. Evol. 40 (1) - [2023-01-04; online 2022-12-30]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The path to immortalization of cells starts by managing stress through gene duplications.
Lewerentz J, Johansson AM, Stenberg P
Exp. Cell Res. 422 (1) 113431 [2023-01-01; online 2022-11-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.
Wen J, Trost B, Engchuan W, ..., Yuen RKC, Szatkiewicz JP
Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.
Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B
Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref
Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.
Cholleti H, de Jong J, Blomström AL, Berg M
Pathogens 12 (1) - [2022-12-21; online 2022-12-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.
Najafi M, Guo Y, Andersson G, Humblot P, Bongcam-Rudloff E
Genes 13 (12) - [2022-12-12; online 2022-12-12]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).
Hempel E, Bibi F, Faith JT, ..., Hofreiter M, Westbury MV
Mol. Biol. Evol. 39 (12) - [2022-12-05; online 2022-11-03]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Screening patients with autoimmune endocrine disorders for cytokine autoantibodies reveals monogenic immune deficiencies.
Sjøgren T, Bratland E, Røyrvik EC, ..., Husebye ES, Wolff ASB
J. Autoimmun. 133 (-) 102917 [2022-12-00; online 2022-09-30]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.
Akhter S, Westrin KJ, Zivi N, ..., Emanuelsson O, Sundström JF
New Phytol. 236 (5) 1951-1963 [2022-12-00; online 2022-09-16]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Endosperm cellularization failure induces a dehydration stress response leading to embryo arrest.
Xu W, Sato H, Bente H, Santos-González J, Köhler C
Plant Cell - (-) - [2022-11-25; online 2022-11-25]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.
Osbeck CMG, Lundin D, Karlsson C, ..., Moran MA, Pinhassi J
PLoS ONE 17 (11) e0243406 [2022-11-17; online 2022-11-17]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades</i>.
Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H
Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2208575119 [2022-11-16; online 2022-11-07]
Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus).
Cockerill CA, Hasselgren M, Dussex N, ..., Sokolova N, Norén K
Genes 13 (11) - [2022-11-15; online 2022-11-15]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Early changes in gene expression profiles in AML patients during induction chemotherapy.
Jakobsen I, Sundkvist M, Björn N, Gréen H, Lotfi K
BMC Genomics 23 (1) 752 [2022-11-14; online 2022-11-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic trajectories of a near-extinction event in the Chatham Island black robin.
von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N
BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.
Altınışık NE, Kazancı DD, Aydoğan A, ..., Erim Özdoğan A, Somel M
Sci Adv 8 (44) eabo3609 [2022-11-04; online 2022-11-04]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.
Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R
Mol. Biol. Evol. 39 (11) - [2022-11-03; online 2022-11-06]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Population dynamics and demographic history of Eurasian collared lemmings.
Lord E, Marangoni A, Baca M, ..., Fedorov VB, Dalén L
BMC Ecol Evol 22 (1) 126 [2022-11-03; online 2022-11-03]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).
Michell CT, Pohjoismäki JLO, Spong G, Thulin C
Sci Data 9 (1) 667 [2022-11-03; online 2022-11-03]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.
Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A
Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.
Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, ..., Leonard D, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (11) 1842-1850 [2022-11-00; online 2022-10-07]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.
Murach KA, Liu Z, Jude B, ..., Vechetti IJ, von Walden F
J. Biol. Chem. 298 (11) 102515 [2022-11-00; online 2022-09-21]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.
Yavuz S, Pucholt P, Sandling JK, ..., Lindblad-Toh K, Rönnblom L
Lupus Sci Med 9 (1) - [2022-11-00; online 2022-11-05]
Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly.
Shipilina D, Näsvall K, Höök L, ..., Talavera G, Backström N
Genomics 114 (6) 110481 [2022-11-00; online 2022-09-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
Butler-Laporte G, Povysil G, Kosmicki JA, ..., Ferreira MAR, Richards JB
PLoS Genet. 18 (11) e1010367 [2022-11-00; online 2022-11-03]
NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.
Banijamali M, Höjer P, Nagy A, ..., Viktorsson K, Ahmadian A
J Extracell Vesicles 11 (11) e12277 [2022-11-00; online 2022-11-05]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N
Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.
Lovrić A, Rassolie A, Alam S, ..., Gustafsson T, Rullman E
Commun Biol 5 (1) 1121 [2022-10-22; online 2022-10-22]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.
Behra PRK, Pettersson BMF, Ramesh M, ..., Dasgupta S, Kirsebom LA
BMC Genomics 23 (1) 704 [2022-10-15; online 2022-10-15]
Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Soil Microbiome Influences on Seedling Establishment and Growth of Prosopis chilensis and Prosopis tamarugo from Northern Chile.
Castro D, Concha C, Jamett F, Ibáñez C, Hurry V
Plants (Basel) 11 (20) - [2022-10-14; online 2022-10-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.
Hill J, Lillie M, Pettersson ME, ..., Andersson L, Jern P
Nat Commun 13 (1) 6033 [2022-10-13; online 2022-10-13]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.
Kahsay A, Rodriguez-Marquez E, López-Pérez A, Hörnblad A, von Hofsten J
Sci Rep 12 (1) 17149 [2022-10-13; online 2022-10-13]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.
Liu T, Li X, Yekta SS, ..., Schnürer A, Enrich-Prast A
Sci Rep 12 (1) 16570 [2022-10-04; online 2022-10-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system.
Pontiller B, Martínez-García S, Joglar V, ..., Teira E, Pinhassi J
ISME J 16 (10) 2360-2372 [2022-10-00; online 2022-07-08]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?
Arnqvist G, Sayadi A
Ecol Evol 12 (10) e9440 [2022-10-00; online 2022-10-27]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.
Tsirigoti C, Ali MM, Maturi V, Heldin CH, Moustakas A
Cell Death Dis 13 (9) 832 [2022-09-28; online 2022-09-28]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.
Sigeman H, Zhang H, Ali Abed S, Hansson B
J. Evol. Biol. - (-) - [2022-09-26; online 2022-09-26]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.
Capo E, Feng C, Bravo AG, ..., Hawkes J, Björn E
Environ. Sci. Technol. 56 (18) 13119-13130 [2022-09-20; online 2022-09-07]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.
Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J
Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]
NGI Short read [Service] NGI Spatial omics [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.
Stenberg H, Hellman S, Lindström L, ..., Hayer J, Malmberg M
BMC Vet Res 18 (1) 348 [2022-09-16; online 2022-09-16]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R
Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination.
Gao Y, Cai C, Wullimann D, ..., Aleman S, Buggert M
Immunity 55 (9) 1732-1746.e5 [2022-09-13; online 2022-07-19]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).
Thureborn O, Razafimandimbison SG, Wikström N, Rydin C
Front Plant Sci 13 (-) 967456 [2022-09-08; online 2022-09-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.
Hases L, Birgersson M, Indukuri R, Archer A, Williams C
Int J Mol Sci 23 (18) - [2022-09-08; online 2022-09-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial profiling of chromatin accessibility in mouse and human tissues.
Deng Y, Bartosovic M, Ma S, ..., Castelo-Branco G, Fan R
Nature 609 (7926) 375-383 [2022-09-00; online 2022-08-17]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.
Parrett JM, Chmielewski S, Aydogdu E, ..., Konczal M, Radwan J
Nat Ecol Evol 6 (9) 1330-1342 [2022-09-00; online 2022-07-18]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Uncovering the genomic basis of an extraordinary plant invasion.
Bieker VC, Battlay P, Petersen B, ..., Hodgins KA, Martin MD
Sci Adv 8 (34) eabo5115 [2022-08-26; online 2022-08-24]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.
Ericson PGP, Irestedt M, Zuccon D, ..., Werdelin L, Qu Y
Commun Biol 5 (1) 857 [2022-08-23; online 2022-08-23]
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Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.
Zufia JA, Legrand C, Farnelid H
Sci Rep 12 (1) 14330 [2022-08-22; online 2022-08-22]
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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
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Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.
Bier RL, Vass M, Székely AJ, Langenheder S
ISME J 16 (12) 2635-2643 [2022-08-18; online 2022-08-18]
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Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.
Osterholz H, Turner S, Alakangas LJ, ..., Kalinowski BE, Dopson M
Nat Commun 13 (1) 4837 [2022-08-17; online 2022-08-17]
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PubMed DOI Crossref
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
Ambikan AT, Yang H, Krishnan S, ..., Benfeitas R, Neogi U
Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
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Isolated Grauer's gorilla populations differ in diet and gut microbiome.
Michel A, Minocher R, Niehoff PP, ..., Caillaud D, Guschanski K
Mol. Ecol. - (-) - [2022-08-17; online 2022-08-17]
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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.
Broman E, Izabel-Shen D, Rodríguez-Gijón A, ..., Garcia SL, Nascimento FJA
Microbiome 10 (1) 126 [2022-08-15; online 2022-08-15]
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PubMed DOI Crossref
Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation.
Liu R, Pisco AO, Braun E, Linnarsson S, Zou J
J. Mol. Biol. 434 (15) 167606 [2022-08-15; online 2022-04-27]
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Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S
Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]
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Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.
Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H
Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]
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Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.
Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]
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Ageing desexualizes the Drosophila brain transcriptome.
Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U
Proc. Biol. Sci. 289 (1980) 20221115 [2022-08-10; online 2022-08-10]
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Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
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A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.
Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS
Genome Biol Evol 14 (8) - [2022-08-03; online 2022-07-26]
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A relationship between phages and organic carbon in wastewater treatment plant effluents.
Modin O, Fuad N, Abadikhah M, ..., Persson F, Wilén BM
Water Res X 16 (-) 100146 [2022-08-01; online 2022-06-16]
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Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]
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PubMed DOI Crossref
Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.
Latz MAC, Grujcic V, Brugel S, ..., Andersson A, Andersson AF
Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]
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Mosaic Deletions of Known Genes Explain Skeletal Dysplasias With High and Low Bone Mass.
Muurinen M, Taylan F, Tournis S, ..., Mäkitie O, Costantini A
JBMR Plus 6 (8) e10660 [2022-08-00; online 2022-07-05]
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PubMed DOI Crossref
Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.
Lundtoft C, Pucholt P, Martin M, ..., Svenungsson E, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (8) 1440-1450 [2022-08-00; online 2022-06-27]
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PubMed DOI Crossref
A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.
Gramlich S, Liu X, Favre A, Buerkle CA, Karrenberg S
New Phytol. 235 (4) 1641-1652 [2022-08-00; online 2022-06-23]
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PubMed DOI Crossref
Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.
Cholleti H, de Jong J, Blomström AL, Berg M
Viruses 14 (8) - [2022-07-28; online 2022-07-28]
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Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.
Swaegers J, Sánchez-Guillén RA, Chauhan P, Wellenreuther M, Hansson B
Proc. Biol. Sci. 289 (1979) 20220968 [2022-07-27; online 2022-07-20]
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PubMed DOI Crossref
Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.
Rodríguez J, Andersson A, Björn E, ..., Skrobonja A, Rowe O
Front Microbiol 13 (-) 809166 [2022-07-27; online 2022-07-27]
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Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma.
Costa Svedman F, Das I, Tuominen R, ..., Höiom V, Egyhazi Brage S
Cancers (Basel) 14 (15) - [2022-07-22; online 2022-07-22]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.
Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
Elife 11 (-) - [2022-07-21; online 2022-07-21]
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Lipoxins reduce obesity-induced adipose tissue inflammation in 3D-cultured human adipocytes and explant cultures.
Soták M, Rajan MR, Clark M, ..., Lange S, Börgeson E
iScience 25 (7) 104602 [2022-07-15; online 2022-06-11]
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Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.
Kuhl H, Du K, Schartl M, ..., Stöck M, Lamatsch DK
Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]
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PubMed DOI Crossref
Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.
Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR
Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.
Hardt U, Carlberg K, Af Klint E, ..., Ståhl PL, Malmström V
Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]
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An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.
Ballarino R, Bouwman BAM, Agostini F, ..., Bienko M, Crosetto N
Sci Data 9 (1) 400 [2022-07-12; online 2022-07-12]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees.
André D, Marcon A, Lee KC, ..., Schmid M, Nilsson O
Curr. Biol. 32 (13) 2988-2996.e4 [2022-07-11; online 2022-06-03]
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Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes.
Hoffman T, Sjödin A, Öhrman C, ..., Lundkvist Å, Olsen B
Microorganisms 10 (7) - [2022-07-11; online 2022-07-11]
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Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.
Varg JE, Outomuro D, Kunce W, ..., Svanbäck R, Johansson F
Environ Microbiome 17 (1) 36 [2022-07-06; online 2022-07-06]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.
Petitpré C, Faure L, Uhl P, ..., Hadjab S, Lallemend F
Nat Commun 13 (1) 3878 [2022-07-05; online 2022-07-05]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.
Martínez-García S, Bunse C, Pontiller B, ..., Legrand C, Pinhassi J
Front Microbiol 13 (-) 834675 [2022-07-05; online 2022-07-05]
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PubMed DOI Crossref
High-throughput muscle fiber typing from RNA sequencing data.
Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O
Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]
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Practical application of a Bayesian network approach to poultry epigenetics and stress.
Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, ..., Jensen P, Smith VA
BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.
Ellerstrand SJ, Choudhury S, Svensson K, ..., Hansson B, Runemark A
Ecol Evol 12 (7) e9078 [2022-07-00; online 2022-07-06]
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PubMed DOI Crossref
Grey wolf genomic history reveals a dual ancestry of dogs.
Bergström A, Stanton DWG, Taron UH, ..., Dalén L, Skoglund P
Nature 607 (7918) 313-320 [2022-07-00; online 2022-06-29]
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PubMed DOI Crossref
Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]
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Allorecognition genes drive reproductive isolation in Podospora anserina.
Ament-Velásquez SL, Vogan AA, Granger-Farbos A, ..., Clavé C, Johannesson H
Nat Ecol Evol 6 (7) 910-923 [2022-07-00; online 2022-05-12]
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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.
Novotny A, Jan KMG, Dierking J, Winder M
Sci Rep 12 (1) 10952 [2022-06-29; online 2022-06-29]
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Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.
Blixt MKE, Hellsand M, Konjusha D, ..., Ring H, Hallböök F
Oncogenesis 11 (1) 34 [2022-06-21; online 2022-06-21]
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Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.
Petrus-Reurer S, Lederer AR, Baqué-Vidal L, ..., La Manno G, Lanner F
Stem Cell Reports 17 (6) 1458-1475 [2022-06-14; online 2022-06-16]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation.
Konstantinidis E, Molisak A, Perrin F, ..., Berezovska O, Ingelsson M
Mol Ther Nucleic Acids 28 (-) 450-461 [2022-06-14; online 2022-03-28]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently.
Seidel L, Broman E, Ståhle M, ..., Hylander S, Dopson M
Front Microbiol 13 (-) 873281 [2022-06-10; online 2022-06-10]
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PubMed DOI Crossref
Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.
Suarez C, Sedlacek CJ, Gustavsson DJI, ..., Hermansson M, Persson F
NPJ Biofilms Microbiomes 8 (1) 47 [2022-06-08; online 2022-06-08]
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Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.
Srigyan M, Bolívar H, Ureña I, ..., Günther T, Valdiosera C
Commun Biol 5 (1) 554 [2022-06-07; online 2022-06-07]
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PubMed DOI Crossref
Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.
van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G
Dev. Cell 57 (11) 1421-1436.e5 [2022-06-06; online 2022-05-05]
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Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.
Alekseenko Z, Dias JM, Adler AF, ..., Parmar M, Ericson J
Nat Commun 13 (1) 3046 [2022-06-01; online 2022-06-01]
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The mosaic oat genome gives insights into a uniquely healthy cereal crop.
Kamal N, Tsardakas Renhuldt N, Bentzer J, ..., Spannagl M, Sirijovski N
Nature 606 (7912) 113-119 [2022-06-00; online 2022-05-18]
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PubMed DOI Crossref
The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.
Ma L, Bryce NS, Turner AW, ..., Björkegren JLM, Kovacic JC
PLoS Genet. 18 (6) e1010261 [2022-06-00; online 2022-06-17]
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PubMed DOI Crossref
Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.
Gunnarsson R, Yang M, Biloglav A, ..., Paulsson K, Johansson B
Leukemia 36 (6) 1681-1684 [2022-06-00; online 2022-04-01]
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PubMed DOI Crossref
Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.
Dahlin M, Singleton SS, David JA, ..., Mazumder R, Prast-Nielsen S
EBioMedicine 80 (-) 104061 [2022-06-00; online 2022-05-19]
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PubMed DOI Crossref
Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.
Rodrigues Soares AE, Boroffka N, Schröder O, ..., Benecke N, Günther T
R. Soc. open sci. 9 (6) 220104 [2022-06-00; online 2022-06-15]
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PubMed DOI Crossref
Development of gut microbiota during the first 2 years of life.
Wernroth ML, Peura S, Hedman AM, ..., Dicksved J, Fall T
Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]
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An empirical evaluation of genotype imputation of ancient DNA.
Ausmees K, Sanchez-Quinto F, Jakobsson M, Nettelblad C
G3 (Bethesda) 12 (6) - [2022-05-30; online 2022-04-29]
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PubMed DOI Crossref
Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.
Fineschi S, Klar J, Gustafsson KA, ..., Karlsson B, Dahl N
Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]
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Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.
Hellman M, Valhondo C, Martínez-Landa L, ..., Juhanson J, Hallin S
Front Microbiol 13 (-) 877990 [2022-05-24; online 2022-05-24]
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Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines-THP-1 and Mono Mac 6-Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation.
Akula S, Lara S, Olsson AK, Hellman L
Int J Mol Sci 23 (10) - [2022-05-22; online 2022-05-22]
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PubMed DOI Crossref
Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways.
Darwish E, Ghosh R, Ontiveros-Cisneros A, ..., Khan K, Van Aken O
Sci Adv 8 (20) eabm2091 [2022-05-20; online 2022-05-20]
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PubMed DOI Crossref
Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.
Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T
iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
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Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.
Laber CP, Pontiller B, Bunse C, ..., Pinhassi J, Farnelid H
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Kierczak M, Rafati N, Höglund J, ..., Karlsson T, Johansson Å
Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]
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Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.
Faucillion M, Johansson A, Larsson J
Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]
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Delgado LF, Andersson AF
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Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Dube F, Hinas A, Roy S, ..., Svärd S, Tydén E
Parasit Vectors 15 (1) 158 [2022-05-05; online 2022-05-05]
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FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.
Peña-Pérez L, Kharazi S, Frengen N, ..., Luc S, Månsson R
Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]
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Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.
Darolti I, Almeida P, Wright AE, Mank JE
J. Evol. Biol. 35 (12) 1646-1658 [2022-05-04; online 2022-05-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genomic Impact of Whaling in North Atlantic Fin Whales.
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Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L
Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.
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Eroglu E, Yen CYT, Tsoi Y, ..., Simon A, Chien KR
Nat Cell Biol 24 (5) 645-658 [2022-05-00; online 2022-05-12]
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Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.
Rojas L, Grüttner J, Ma'ayeh S, Xu F, Svärd SG
Front. Cell. Infect. Microbiol. 12 (-) 862211 [2022-04-27; online 2022-04-27]
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Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.
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Nat Commun 13 (1) 2236 [2022-04-25; online 2022-04-25]
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Zenere A, Rundquist O, Gustafsson M, Altafini C
iScience 25 (4) 104048 [2022-04-15; online 2022-03-11]
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Shakeri Yekta S, Elreedy A, Liu T, ..., Fujii M, Schnürer A
Sci. Total Environ. 817 (-) 152967 [2022-04-15; online 2022-01-10]
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.
Dehasque M, Pečnerová P, Kempe Lagerholm V, ..., Vartanyan S, Dalén L
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Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.
Lewerentz J, Johansson A, Larsson J, Stenberg P
BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]
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Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.
von Grothusen C, Frisendahl C, Modhukur V, ..., Boggavarapu NR, Gemzell-Danielsson K
Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]
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Ferreira PdL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
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STAR Protoc 3 (1) 101202 [2022-03-18; online 2022-03-03]
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Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
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Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]
Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.
Viluma A, Flagstad Ø, Åkesson M, ..., Wabakken P, Ellegren H
Genome Res. 32 (3) 449-458 [2022-03-00; online 2022-02-08]
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Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]
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Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]
NGI Short read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
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Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.
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Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.
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Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
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Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]
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The spatial transcriptomic landscape of the healing mouse intestine following damage.
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Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]
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Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.
Hou XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C
BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]
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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.
Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A
Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.
Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]
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The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.
Oliver C, Annacondia ML, Wang Z, ..., Köhler C, Martinez G
Plant Cell 34 (2) 784-801 [2022-02-03; online 2021-11-11]
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Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.
Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ
PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.
Edvardsen RB, Wallerman O, Furmanek T, ..., Norberg B, Rubin CJ
PLoS Genet. 18 (2) e1010011 [2022-02-00; online 2022-02-08]
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [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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A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene.
Rafiei V, Ruffino A, Persson Hodén K, ..., Dubey M, Tzelepis G
Mol. Plant Pathol. 23 (2) 291-303 [2022-02-00; online 2021-11-26]
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Occasional paternal inheritance of the germline-restricted chromosome in songbirds.
Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B
Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]
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Massive genome inversion drives coexistence of divergent morphs in common quails.
Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, ..., Leonard JA, Vilà C
Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]
NGI Short read [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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Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.
Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A
Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]
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Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.
Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström AL
Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.
Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR
Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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The formation of avian montane diversity across barriers and along elevational gradients.
Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA
Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]
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Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.
Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L
Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]
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Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.
Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M
Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]
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PubMed DOI Crossref
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
Chachoua I, Tzelepis I, Dai H, ..., Mehmood R, Göndör A
Nat Commun 13 (1) 204 [2022-01-11; online 2022-01-11]
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PubMed DOI Crossref
Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
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PubMed DOI Crossref
Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.
Romdhane S, Spor A, Banerjee S, ..., Saghai A, Philippot L
Environ Microbiome 17 (1) 1 [2022-01-06; online 2022-01-06]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.
Mennuni M, Filograna R, Felser A, ..., Lytovchenko O, Larsson N
EMBO Rep. 23 (1) e53054 [2022-01-05; online 2021-11-15]
CRISPR Functional Genomics [Service] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.
Skaftason A, Qu Y, Abdulla M, ..., Rosenquist R, Mansouri L
Genes Chromosomes Cancer 61 (1) 27-36 [2022-01-00; online 2021-10-23]
Clinical Genomics Uppsala [Service] NGI Short read [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.
Benz C, Ali M, Krystkowiak I, ..., Davey NE, Ivarsson Y
Mol. Syst. Biol. 18 (1) e10584 [2022-01-00; online 2022-01-20]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2021

PubMed DOI Crossref
Genome-wide spatial expression profiling in formalin-fixed tissues.
Gracia Villacampa E, Larsson L, Mirzazadeh R, ..., Carlson J, Lundeberg J
Cell Genomics 1 (3) 100065 [2021-12-08; online 2021-12-08]
NGI Short read [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis.
Mäkinen A, Nikkilä A, Mehtonen J, ..., Paavonen T, Lohi O
Pathology 53 (7) 875-882 [2021-12-00; online 2021-05-26]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of EM-seq and PBAT methylome library methods for low-input DNA.
Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, ..., Needhamsen M, Jagodic M
Epigenetics 17 (10) 1195-1204 [2021-11-17; online 2021-11-17]
NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Year 2010

PubMed DOI Crossref
Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.
Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J
J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]
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Publications 9.2.2