Publications

Why is COVID‐19 so mild in children?

Brodin P

Acta Paediatr - (-) - [2020-04-15; online 2020-04-15]

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.

Berglund E, Saarenpää S, Jemt A, ..., Lundeberg J, Giacomello S

pmc

BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.

Petrus-Reurer S, Winblad N, Kumar P, ..., Kvanta A, Lanner F

pmc

Stem Cell Reports 14 (4) 648-662 [2020-04-14; online 2020-03-19]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles

Thomen A, Najafinobar N, Penen F, ..., Kurczy ME, Ewing AG

ACS Nano - (-) - [2020-04-08; online 2020-04-08]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Optimization of Tetrahydroindazoles as Inhibitors of Human Dihydroorotate Dehydrogenase and Evaluation of Their Activity and In Vitro Metabolic Stability

Popova G, Ladds MJGW, Johansson L, ..., Yngve U, Lain S

J. Med. Chem. 63 (-) 3915-3934 [2020-04-08; online 2020-04-08]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Building blocks are synthesized on demand during the yeast cell cycle

Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J

Proc Natl Acad Sci USA 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.

Shafeeq S, Wang X, Lünsdorf H, Brauner A, Römling U

Microorganisms 8 (4) - [2020-04-05; online 2020-04-05]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.

Andersson N, Bakker B, Karlsson J, ..., Foijer F, Gisselsson D

Cancer Res. 80 (7) 1512-1523 [2020-04-01; online 2020-02-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.

Mahajan M, Yee B, Hägglund E, ..., Fuerst JA, Andersson SGE

Mol. Biol. Evol. 37 (4) 1020-1040 [2020-04-01; online 2019-12-07]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.

Andersson K, Malmgren B, Åström E, ..., Taylan F, Dahllöf G

pmc

Orphanet J Rare Dis 15 (1) 80 [2020-03-31; online 2020-03-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comparative analysis of genome-wide DNA methylation in Neurospora

Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H

Epigenetics - (-) 1-16 [2020-03-31; online 2020-03-31]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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

pmc

Nanomaterials (Basel) 10 (4) - [2020-03-31; online 2020-03-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comparative analysis of genome-wide DNA methylation in Neurospora

Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H

Epigenetics - (-) 1-16 [2020-03-31; online 2020-03-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines their Interactions with G-Quadruplex DNA

Prasad B, Das RN, Jamroskovic J, ..., Sabouri N, Chorell E

Chem. Eur. J. - (-) - [2020-03-18; online 2020-03-18]

Determining the Genetic Regulation and Coordination of Lignification in Stem Tissues of Arabidopsis Using Semiquantitative Raman Microspectroscopy

Blaschek L, Nuoendagula , Bacsik Z, Kajita S, Pesquet E

ACS Sustainable Chem. Eng. - (-) - [2020-03-18; online 2020-03-18]

Intravital Microscopy Facility [Technology development]

Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.

Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F

pmc

Genes 11 (3) - [2020-03-14; online 2020-03-14]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.

Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF

pmc

Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

pmc

Front Genet 11 (-) 218 [2020-03-13; online 2020-03-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.

Forsberg A, Huoman J, Söderholm S, ..., Gustafsson M, Jenmalm MC

Pediatr Allergy Immunol - (-) - [2020-03-09; online 2020-03-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly

Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A

NPLANTS - (-) - [2020-03-09; online 2020-03-09]

Cryo-EM [Service] Proteogenomics [Service]

MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.

Scaletti ER, Vallin KS, Bräutigam L, ..., Stenmark P, Jemth AS

J. Biol. Chem. - (-) - [2020-03-06; online 2020-03-06]

Uncovering diversity and metabolic spectrum of animals in dead zone sediments.

Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA

pmc

Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Brain Region Specific Amyloid Plaque Associated Myelin Lipid Loss, APOE Deposition and Disruption of the Myelin Sheath in Familial Alzheimer's Disease Mice

Kaya I, Jennische E, Lange S, ..., Malmberg P, Fletcher JS

J. Neurochem. - (-) - [2020-03-05; online 2020-03-05]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Interplay between Cocaine, Drug Removal, and Methylphenidate Reversal on Phospholipid Alterations in Drosophila Brain Determined by Imaging Mass Spectrometry

Philipsen MH, Phan NTN, Fletcher JS, Ewing AG

ACS Chem Neurosci 11 (5) 806-813 [2020-03-04; online 2020-02-11]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.

Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I

Nutrients 12 (3) - [2020-03-03; online 2020-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomic resources for evolutionary studies in flat periwinkles and related species.

Marques JP, Sotelo G, Galindo J, ..., Hollander J, Faria R

Sci Data 7 (1) 73 [2020-03-03; online 2020-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structure of a minimal photosystem I from the green alga Dunaliella salina

Perez-Boerema A, Klaiman D, Caspy I, ..., Amunts A, Nelson N

NPLANTS - (-) - [2020-03-02; online 2020-03-02]

Cellular and Genetic Regulation of Coniferaldehyde Incorporation in Lignin of Herbaceous and Woody Plants by Quantitative Wiesner Staining

Blaschek L, Champagne A, Dimotakis C, ..., Kajita S, Pesquet E

Front Plant Sci 11 (-) - [2020-03-02; online 2020-03-02]

Intravital Microscopy Facility [Technology development]

Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs

Wille M, Wensman JJ, Larsson S, ..., Hayer J, Malmberg M

Infection, Genetics and Evolution - (-) 104290 [2020-03-00; online 2020-03-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.

Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK

GENBANK

Mol. Ecol. 29 (6) 1120-1136 [2020-03-00; online 2020-03-09]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stressful Beginnings with Long-Term Consequences

Consiglio CR, Brodin P

Cell 180 (5) 820-821 [2020-03-00; online 2020-03-00]

Mass Cytometry [Collaborative]

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

pmc

Sci Adv 6 (11) eaay0456 [2020-03-00; online 2020-03-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.

Marisca R, Hoche T, Agirre E, ..., Castelo-Branco G, Czopka T

pmc mid

Nat. Neurosci. 23 (3) 363-374 [2020-03-00; online 2020-02-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

Fenton TM, Jørgensen PB, Niss K, ..., Johansson-Lindbom B, Agace WW

Immunity 52 (3) 557-570.e6 [2020-03-00; online 2020-03-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The nf-core framework for community-curated bioinformatics pipelines

Ewels PA, Peltzer A, Fillinger S, ..., Di Tommaso P, Nahnsen S

Nat Biotechnol 38 (3) 276-278 [2020-03-00; online 2020-02-13]

NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]

Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro‐Oxindole Dihydroquinazolinones as IRAP Inhibitors

Engen K, Vanga SR, Lundbäck T, ..., Larhed M, Rosenström U

ChemistryOpen 9 (3) 325-337 [2020-03-00; online 2020-03-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia.

Richards AL, Pardiñas AF, Frizzati A, ..., O'Donovan MC, Walters JTR

Schizophr Bull 46 (2) 336-344 [2020-02-26; online 2019-06-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles

Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM

Proc Natl Acad Sci USA - (-) 201918232 [2020-02-25; online 2020-02-25]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Patterns of African and Asian admixture in the Afrikaner population of South Africa.

Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM

BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Achieving symptom relief in patients with Myalgic encephalomyelitis by targeting the neuro-immune interface and inducing disease tolerance

Rodriguez LST, Pou C, Lakshmikanth T, ..., Julin P, Brodin P

- - (-) - [2020-02-21; online 2020-02-21]

Mass Cytometry [Collaborative]

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

pmc

Front Microbiol 11 (-) 252 [2020-02-21; online 2020-02-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

pmc

Commun Biol 3 (1) 84 [2020-02-21; online 2020-02-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.

Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M

Pharmacogenomics J. - (-) - [2020-02-21; online 2020-02-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes

Kumar R, Chand K, Bhowmik S, ..., Hedenström M, Chorell E

Nucleic Acids Res 48 (3) 1108-1119 [2020-02-20; online 2020-01-08]

Genome-Wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.

Li C, Stoma S, Lotta LA, ..., Langenberg C, Codd V

Am. J. Hum. Genet. - (-) - [2020-02-20; online 2020-02-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.

Munn-Chernoff MA, Johnson EC, Chou YL, ..., Bulik CM, Agrawal A

Addict Biol - (-) e12880 [2020-02-16; online 2020-02-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi.

Lynikienė J, Marčiulynienė D, Marčiulynas A, ..., Vaičiukynė M, Menkis A

Microorganisms 8 (2) - [2020-02-15; online 2020-02-15]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

Scaletti E, Claesson M, Helleday T, Jemth AS, Stenmark P

J. Mol. Biol. 432 (4) 1126-1142 [2020-02-14; online 2020-01-15]

Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.

Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N

Scand. J. Immunol. - (-) e12864 [2020-02-13; online 2020-02-13]

Autoimmunity Profiling [Service]

Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.

Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S

pmc

Elife 9 (-) - [2020-02-11; online 2020-02-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

New approaches to the study of immune responses in humans

Brodin P

Hum Genet - (-) - [2020-02-10; online 2020-02-10]

Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.

Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A

pmc

PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.

Grönroos T, Mäkinen A, Laukkanen S, ..., Heinäniemi M, Lohi O

pmc

Sci Rep 10 (1) 2043 [2020-02-06; online 2020-02-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Capsid Structure of a Marine Algal Virus of the Order Picornavirales

Munke A, Kimura K, Tomaru Y, Okamoto K

J Virol 94 (9) - [2020-02-05; online 2020-04-16]

A chromosome-scale reference genome for Giardia intestinalis WB.

Xu F, Jex A, Svärd SG

Sci Data 7 (1) 38 [2020-02-04; online 2020-02-04]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Thermal proteome profiling identifies oxidative-dependent inhibition of the transcription of major oncogenes as a new therapeutic mechanism for select anticancer compounds

Peuget S, Zhu J, Sanz G, ..., Zubarev R, Selivanova G

Cancer Res - (-) canres.2069.2019 [2020-02-04; online 2020-02-04]

Chemical Proteomics [Collaborative]

Glycogenin is Dispensable for Glycogen Synthesis in Human Muscle, and Glycogenin Deficiency Causes Polyglucosan Storage.

Visuttijai K, Hedberg-Oldfors C, Thomsen C, ..., Roach P, Oldfors A

J. Clin. Endocrinol. Metab. 105 (2) - [2020-02-01; online 2019-10-20]

Exosomes influence the behavior of human mesenchymal stem cells on titanium surfaces.

Wang X, Shah FA, Vazirisani F, ..., Ekström K, Thomsen P

Biomaterials 230 (-) 119571 [2020-02-00; online 2019-10-24]

The Molecular Anatomy of Mouse Skin during Hair Growth and Rest

Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M

Cell Stem Cell - (-) - [2020-02-00; online 2020-02-00]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

pmc

Cells 9 (2) - [2020-01-30; online 2020-01-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.

Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K

pmc

Viruses 12 (2) - [2020-01-30; online 2020-01-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization

Jamroskovic J, Doimo M, Chand K, ..., Chorell E, Sabouri N

J. Am. Chem. Soc. - (-) - [2020-01-28; online 2020-01-28]

Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin.

Roemhild R, Linkevicius M, Andersson DI

PLoS Biol. 18 (1) e3000612 [2020-01-27; online 2020-01-27]

Image-Based Morphological Profiling Identifies a Lysosomotropic, Iron-Sequestering Autophagy Inhibitor

Laraia L, Garivet G, Foley DJ, ..., Rodriguez R, Waldmann H

Angew. Chem. Int. Ed. - (-) - [2020-01-24; online 2020-01-24]

CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.

Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D

pmc

Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly.

Pinese M, Lacaze P, Rath EM, ..., Dinger ME, Thomas DM

pmc

Nat Commun 11 (1) 435 [2020-01-23; online 2020-01-23]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Human immune system variation during one year

Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P

- - (-) - [2020-01-23; online 2020-01-23]

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

pmc

BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Loss of centromere function drives karyotype evolution in closely related Malassezia species.

Sankaranarayanan SR, Ianiri G, Coelho MA, ..., Heitman J, Sanyal K

Elife 9 (-) - [2020-01-20; online 2020-01-20]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.

Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M

Pharmacogenomics J. - (-) - [2020-01-17; online 2020-01-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica

Redl S, Poehlein A, Esser C, ..., Dürre P, Nielsen AT

Front Microbiol 10 (-) - [2020-01-17; online 2020-01-17]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Proteomic analysis of follicular fluid during human ovulation.

Zakerkish F, Brännström M, Carlsohn E, ..., van der Post S, Thoroddsen A

Acta Obstet Gynecol Scand - (-) - [2020-01-16; online 2020-01-16]

Evolution of a new function by fusion between phage DNA and a bacterial gene.

Warsi O, Knopp M, Surkov S, Hultqvist JJ, Andersson DI

Mol. Biol. Evol. - (-) - [2020-01-16; online 2020-01-16]

Discovery of species-unique peptide biomarkers of bacterial pathogens by tandem mass spectrometry-based proteotyping.

Karlsson R, Thorsell A, Gomila M, ..., Kristiansson E, Moore E

Mol. Cell Proteomics - (-) - [2020-01-15; online 2020-01-15]

Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.

Bonomi A, Veglia F, Baldassarre D, ..., Gigante B, on behalf of the IMPROVE study group

Genes Immun. - (-) - [2020-01-14; online 2020-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

BMC Plant Biol. 20 (1) 18 [2020-01-13; online 2020-01-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.

Rugiu L, Panova M, Pereyra RT, Jormalainen V

pmc

BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.

Nunes L, Aasebø K, Mathot L, ..., Sjöblom T, Glimelius B

Acta Oncol - (-) 1-10 [2020-01-10; online 2020-01-10]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

A regulatory role for CHD2 in myelopoiesis.

Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A

Epigenetics - (-) 1-13 [2020-01-10; online 2020-01-10]

High-throughput Genome Engineering (HTGE) [Service]

DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.

Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG

pmc

Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]

Chemical Proteomics [Service]

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.

Shah S, Henry A, Roselli C, ..., Swerdlow DI, Lumbers RT

Nat Commun 11 (1) 163 [2020-01-09; online 2020-01-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Simultaneous mass spectrometry imaging of multiple neuropeptides in the brain and alterations induced by experimental parkinsonism and L-DOPA therapy.

Hulme H, Fridjonsdottir E, Gunnarsdottir H, ..., Svenningsson P, Andrén PE

Neurobiol. Dis. - (-) 104738 [2020-01-09; online 2020-01-09]

National Resource for Mass Spectrometry Imaging [Service]

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

pmc

Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Light-up Logic Platform for Selective Recognition of Parallel G-Quadruplex Structures via Disaggregation-Induced Emission

Deiana M, Chand K, Jamroskovic J, ..., Chorell E, Sabouri N

Angew. Chem. Int. Ed. 59 (2) 896-902 [2020-01-07; online 2019-11-22]

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

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]

Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum

Khoomrung S, Nookaew I, Sen P, ..., Harandi AM, Nielsen J

J. Proteome Res. 19 (1) 269-278 [2020-01-03; online 2019-10-18]

Integrative discovery of treatments for high-risk neuroblastoma.

Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S

pmc

Nat Commun 11 (1) 71 [2020-01-03; online 2020-01-03]

Spatial Lipidomics Reveals Region and Long Chain Base Specific Accumulations of Monosialogangliosides in Amyloid Plaques in Familial Alzheimer’s Disease Mice (5xFAD) Brain

Kaya I, Jennische E, Dunevall J, ..., Baykal AT, Fletcher JS

ACS Chem Neurosci 11 (1) 14-24 [2020-01-02; online 2019-11-27]

Gothenburg Imaging Mass Spectrometry [Collaborative]

PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.

Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L

Circ. Res. - (-) - [2020-01-02; online 2020-01-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

van der Valk T, Gonda CM, Silegowa H, ..., Detwiler KM, Guschanski K

- 37 (1) 183-194 [2020-01-01; online 2019-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A dual-action peptide-containing hydrogel targets wound infection and inflammation

Puthia M, Butrym M, Petrlova J, ..., Kjellström S, Schmidtchen A

Sci. Transl. Med. 12 (524) eaax6601 [2020-01-01; online 2020-01-01]

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M

Nat Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]

In Situ Sequencing (ISS) [Technology development]

Metabolic response patterns in brain microdialysis fluids and serum during interstitial cisplatin treatment of high-grade glioma

Björkblom B, Jonsson P, Tabatabaei P, ..., Bergenheim AT, Antti H

Br J Cancer 122 (2) 221-232 [2020-01-00; online 2019-12-10]

Regulation of α-synuclein by chaperones in mammalian cells

Burmann BM, Gerez JA, Matečko-Burmann I, ..., Riek R, Hiller S

Nature 577 (7788) 127-132 [2020-01-00; online 2019-12-04]

NMR Spectroscopic Analysis to Evaluate the Quality of Insulin: Concentration, Variability, and Excipient Content

Malmodin D, Pedersen A, Karlsson BG, Forsander G

J Diabetes Sci Technol 14 (1) 180-184 [2020-01-00; online 2019-02-19]

Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies.

Mehdipour T, Tohidkia MR, Ata Saei A, ..., Zubarev RA, Nouri M

pmc

Immunology 159 (1) 96-108 [2020-01-00; online 2019-11-08]

Chemical Proteomics [Service]

Effect of sample preparation techniques upon single cell chemical imaging: A practical comparison between synchrotron radiation based X-ray fluorescence (SR-XRF) and Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS)

De Samber B, De Rycke R, De Bruyne M, ..., Polerecky L, Vincze L

Analytica Chimica Acta - (-) - [2020-01-00; online 2020-01-00]

Cryo-EM [Technology development]

Copper nanoparticles have negligible direct antibacterial impact

Bastos CAP, Faria N, Wills J, ..., Rees P, Powell JJ

NanoImpact 17 (-) 100192 [2020-01-00; online 2020-01-00]

Gothenburg Imaging Mass Spectrometry [Collaborative]

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

De Leoz MLA, Duewer DL, Fung A, ..., Yuan H, Stein SE

pmc

Mol. Cell Proteomics 19 (1) 11-30 [2020-01-00; online 2019-10-07]

Mesoporous silica with precisely controlled pores reduces food efficiency and suppresses weight gain in mice

Rinde M, Kupferschmidt N, Iqbal MN, ..., Lindgren M, Bengtsson T

Nanomedicine 15 (2) 131-144 [2020-01-00; online 2020-01-00]

Intravital Microscopy Facility [Service]

Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.

Yuan S, Larsson SC

pmc

Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.

Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K

pmc

Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome

Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M

RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-07]

Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.

Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S

Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]

Proteogenomics [Collaborative]

Developmental exposure to a human relevant mixture of endocrine disruptors alters metabolism and adipogenesis in zebrafish (Danio rerio)

Mentor A, Brunström B, Mattsson A, Jönsson M

Chemosphere 238 (-) 124584 [2020-01-00; online 2020-01-00]

Identification of novel diagnostic and prognostic biomarkers for abdominal aortic aneurysm

Memon AA, Zarrouk M, Ågren-Witteschus S, ..., Gottsäter A, Sundquist K

Eur J Prev Cardiolog 27 (2) 132-142 [2020-01-00; online 2019-08-29]

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions—Insights from transcription factors

Millard PS, Bugge K, Marabini R, ..., Burow M, Kragelund BB

Protein Science 29 (1) 169-183 [2020-01-00; online 2019-11-11]

Circadian regulation of phosphodiesterase 6 genes in zebrafish differs between cones and rods: Implications for photopic and scotopic vision.

Abalo XM, Lagman D, Heras G, ..., Eggert J, Larhammar D

Vision Res. 166 (-) 43-51 [2020-01-00; online 2019-12-16]

Screening for bioactive secondary metabolites in Sri Lankan medicinal plants by microfractionation and targeted isolation of antimicrobial flavonoids from Derris scandens

Mohotti S, Rajendran S, Muhammad T, ..., Hettiarachchi CM, Gunasekera S

Journal of Ethnopharmacology 246 (-) 112158 [2020-01-00; online 2020-01-00]

Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions.

Ingvarsson PK, Bernhardsson C

pmc

Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Hepatitis E virus genotype 3 strains and a plethora of other viruses detected in raw and still in tap water

Wang H, Kjellberg I, Sikora P, ..., Bergstedt O, Norder H

Water Research 168 (-) 115141 [2020-01-00; online 2020-01-00]

Clinical Genomics Gothenburg [Collaborative]

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds.

Elfstrand M, Zhou L, Baison J, ..., Stenlid J, García-Gil MR

Mol. Ecol. 29 (1) 199-213 [2020-01-00; online 2019-12-09]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

In-plate toxicometabolomics of single zebrafish embryos

Ribbenstedt A, Posselt M, Brunius C, Benskin JP

Mol Omics - (-) - [2020-00-00; online 2020-00-00]

Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil

Blomström AL, Luz HR, Öhlund P, ..., Labruna MB, Berg M

Viruses 12 (1) 48 [2019-12-31; online 2019-12-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil.

Blomström AL, Luz HR, Öhlund P, ..., Labruna MB, Berg M

pmc

Viruses 12 (1) - [2019-12-31; online 2019-12-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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. - (-) - [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]

Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling.

Ahi EP, Brunel M, Tsakoumis E, Schmitz M

pmc

Sci Rep 9 (1) 20166 [2019-12-27; online 2019-12-27]

Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components.

Mazurkewich S, Poulsen JN, Lo Leggio L, Larsbrink J

pmc PDB PDB PDB PDB PDB PDB PDB PDB PDB PDB PDB PDB

J. Biol. Chem. 294 (52) 19978-19987 [2019-12-27; online 2019-11-18]

Identification of a C2-symmetric diol based human immunodeficiency virus protease inhibitor targeting Zika virus NS2B-NS3 protease.

Akaberi D, Chinthakindi PK, Båhlström A, ..., Lundkvist Å, Lennerstrand J

J. Biomol. Struct. Dyn. - (-) 1-11 [2019-12-27; online 2019-12-27]

Dynamic Chirality in the Mechanism of Action of Allosteric CD36 Modulators of Macrophage-Driven Inflammation

Danelius E, Ohm RG, Ahsanullah , ..., Erdelyi M, Lubell WD

J. Med. Chem. 62 (24) 11071-11079 [2019-12-26; online 2019-11-27]

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.

Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N

Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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]

Estimating Detection Limits of Potentiometric DNA Sensors Using Surface Plasmon Resonance Analyses

Xu X, Makaraviciute A, Abdurakhmanov E, ..., Nyholm L, Zhang Z

ACS Sens. - (-) - [2019-12-23; online 2019-12-23]

Drug Discovery and Development (DDD) [Technology development]

Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste

Moestedt J, Westerholm M, Isaksson S, Schnürer A

Bioengineering 7 (1) 3 [2019-12-23; online 2019-12-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.

Josefsson A, Larsson K, Freyhult E, Damber J, Welén K

Cancers (Basel) 12 (1) - [2019-12-21; online 2019-12-21]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.

Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P

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]

Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.

Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A

Brain Sci 10 (1) - [2019-12-20; online 2019-12-20]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Lipid Droplet-Associated Kinase STK25 Regulates Peroxisomal Activity and Metabolic Stress Response in Steatotic Liver.

Nerstedt A, Kurhe Y, Cansby E, ..., Hoy AJ, Mahlapuu M

J. Lipid Res. - (-) - [2019-12-19; online 2019-12-19]

Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.

Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB

Epigenetics - (-) 1-18 [2019-12-19; online 2019-12-19]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Levels of caspase-3 and histidine-rich glycoprotein in the embryo secretome as biomarkers of good-quality day-2 embryos and high-quality blastocysts

Kaihola H, Yaldir FG, Bohlin T, ..., Hreinsson J, Åkerud H

PLoS ONE 14 (12) e0226419 [2019-12-19; online 2019-12-19]

PLA and Single Cell Proteomics [Service]

Apolipoprotein B48 metabolism in chylomicrons and very low-density lipoproteins and its role in triglyceride transport in normo- and hypertriglyceridemic human subjects.

Björnson E, Packard CJ, Adiels M, ..., Taskinen MR, Borén J

J. Intern. Med. - (-) - [2019-12-17; online 2019-12-17]

A transposable element insertion is associated with an alternative life history strategy.

Woronik A, Tunström K, Perry MW, ..., Käkelä R, Wheat CW

pmc

Nat Commun 10 (1) 5757 [2019-12-17; online 2019-12-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.

Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S

pmc

Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]

Plasma Profiling [Service]

Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production

Liu Y, Liu Q, Krivoruchko A, Khoomrung S, Nielsen J

Nat Chem Biol - (-) - [2019-12-16; online 2019-12-16]

SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes.

Nordin J, Ameur A, Lindblad-Toh K, Gyllensten U, Meadows JRS

Eur. J. Hum. Genet. - (-) - [2019-12-16; online 2019-12-16]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.

Ueberschär M, Wang H, Zhang C, ..., Wen J, Dai Q

pmc

Nat Commun 10 (1) 5700 [2019-12-13; online 2019-12-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J

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]

High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.

Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. - (-) - [2019-12-11; online 2019-12-11]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion

van der Woude LC, Perrella G, Snoek BL, ..., Kaiserli E, van Zanten M

Proc Natl Acad Sci USA 116 (50) 25343-25354 [2019-12-10; online 2019-11-25]

A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.

Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L

Sci Rep 9 (1) 18633 [2019-12-09; online 2019-12-09]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes.

Betancourt LH, Szasz AM, Kuras M, ..., Sanchez A, Marko-Varga G

Cancers (Basel) 11 (12) - [2019-12-09; online 2019-12-09]

Comprehensive longitudinal study of epigenetic mutations in aging.

Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S

Clin Epigenetics 11 (1) 187 [2019-12-09; online 2019-12-09]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort

Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O

Dia Care - (-) dc191199 [2019-12-08; online 2019-12-08]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.

Ignjatovic V, Geyer PE, Palaniappan KK, ..., Deutsch EW, Schwenk JM

pmc mid

J. Proteome Res. 18 (12) 4085-4097 [2019-12-06; online 2019-10-11]

Depression, GABA, and Age Correlate with Plasma Levels of Inflammatory Markers

Bhandage AK, Cunningham JL, Jin Z, ..., Ekselius L, Birnir B

Int J Mol Sci 20 (24) 6172 [2019-12-06; online 2019-12-06]

PLA and Single Cell Proteomics [Collaborative]

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.

Jia T, Chu C, Liu Y, ..., Schumann G, Desrivières S

Mol. Psychiatry - (-) - [2019-12-06; online 2019-12-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

GLUL Ablation Can Confer Drug Resistance to Cancer Cells via a Malate-Aspartate Shuttle-Mediated Mechanism

Muthu M, Kumar R, Syed Khaja AS, ..., Persson JL, Nordström A

Cancers (Basel) 11 (12) 1945 [2019-12-05; online 2019-12-05]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.

Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM

Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]

Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]

Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Dahl Aslan AK

Int J Obes (Lond) - (-) - [2019-12-04; online 2019-12-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.

Tsagiopoulou M, Papakonstantinou N, Moysiadis T, ..., Rosenquist R, Stamatopoulos K

Clin Epigenetics 11 (1) 177 [2019-12-02; online 2019-12-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High throughput barcoding method for genome-scale phasing.

Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A

pmc

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]

Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.

Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K

Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]

BioImage Informatics [Service]

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

Batista RA, Moreno-Romero J, Qiu Y, ..., Figueiredo DD, Köhler C

Elife 8 (-) - [2019-12-02; online 2019-12-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.

Vicente M, Priehodová E, Diallo I, ..., Černý V, Schlebusch CM

BMC Genomics 20 (1) 915 [2019-12-02; online 2019-12-02]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats

Dong Y, Sanford RA, Inskeep WP, ..., Fried GA, Fouke BW

Astrobiology 19 (12) 1442-1458 [2019-12-01; online 2019-12-01]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mitochondrial protein enriched extracellular vesicles discovered in human melanoma tissues can be detected in patient plasma

Jang SC, Crescitelli R, Cvjetkovic A, ..., Kalluri R, Lötvall J

J Extracell Vesicles 8 (1) 1635420 [2019-12-01; online 2019-08-27]

Centre for Cellular Imaging [Service] Glycoproteomics [Service]

Arteria: An automation system for a sequencing core facility

Dahlberg J, Hermansson J, Sturlaugsson S, ..., Hofmann O, Larsson P

Gigascience 8 (12) - [2019-12-01; online 2019-12-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Endosomal signalling via exosome surface TGFβ-1

Shelke GV, Yin Y, Jang SC, ..., Nilsson JA, Lötvall J

J Extracell Vesicles 8 (1) 1650458 [2019-12-01; online 2019-09-20]

Centre for Cellular Imaging [Service] Glycoproteomics [Service]

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) - [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]

Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS

Zhu S, Wuolikainen A, Wu J, ..., Forsgren L, Trupp M

J Mol Neurosci 69 (4) 643-657 [2019-12-00; online 2019-11-12]

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T

GEO

Nat Commun 10 (1) - [2019-12-00; online 2019-02-04]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Collaborative]

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]

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Rojas-Macias MA, Mariethoz J, Andersson P, ..., Lisacek F, Karlsson NG

Nat Commun 10 (1) - [2019-12-00; online 2019-07-22]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Glycoproteomics [Technology development]

Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.

Morales HE, Faria R, Johannesson K, ..., Westram AM, Butlin RK

pmc

Sci Adv 5 (12) eaav9963 [2019-12-00; online 2019-12-04]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.

Ross JM, Coppotelli G, Branca RM, ..., Sinclair DA, Olson L

pmc

Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]

Proteogenomics [Collaborative]

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]

Breast cancer quantitative proteome and proteogenomic landscape

Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]

Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes

Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C

Sci Rep 9 (1) - [2019-12-00; online 2019-06-03]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads

Shakeri Yekta S, Liu T, Axelsson Bjerg M, ..., Björn A, Schnürer A

Biotechnol Biofuels 12 (1) - [2019-12-00; online 2019-11-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The genomic footprint of sexual conflict.

Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G

Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Meckel syndrome: Clinical and mutation profile in six fetuses.

Radhakrishnan P, Nayak SS, Shukla A, Lindstrand A, Girisha KM

Clin. Genet. 96 (6) 560-565 [2019-12-00; online 2019-08-21]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

The genomics of major psychiatric disorders in a large pedigree from Northern Sweden

Szatkiewicz J, Crowley JJ, Adolfsson AN, ..., Adolfsson R, Sullivan PF

Transl Psychiatry 9 (1) - [2019-12-00; online 2019-02-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida

Stairs CW, Kokla A, Ástvaldsson Á, ..., Svärd S, Ettema TJG

BMC Biol. 17 (1) - [2019-12-00; online 2019-03-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide

Wu M, Farkas D, Eriksson LA, Strid Å

Sci Rep 9 (1) - [2019-12-00; online 2019-01-28]

Acute β-adrenoceptor mediated glucose clearance in brown adipose tissue; a distinct pathway independent of functional insulin signaling

Olsen JM, Åslund A, Bokhari MH, Hutchinson DS, Bengtsson T

Mol Metab 30 (-) 240-249 [2019-12-00; online 2019-12-00]

Intravital Microscopy Facility [Service]

The potential of magnetisation transfer NMR to monitor the dissolution process of cellulose in cold alkali

Gunnarsson M, Hasani M, Bernin D

Cellulose 26 (18) 9403-9412 [2019-12-00; online 2019-09-12]

The 1H NMR serum metabolomics response to a two meal challenge: a cross-over dietary intervention study in healthy human volunteers

Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A

Nutr J 18 (1) - [2019-12-00; online 2019-04-08]

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

Carow B, Hauling T, Qian X, ..., Nilsson M, Rottenberg ME

Nat Commun 10 (1) - [2019-12-00; online 2019-04-23]

In Situ Sequencing (ISS) [Collaborative]

The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway

Gul N, Karlsson J, Tängemo C, ..., Bergö MO, Lindahl P

Sci Rep 9 (1) - [2019-12-00; online 2019-10-11]

Mercury methylating microbial communities of boreal forest soils

Xu J, Buck M, Eklöf K, ..., Bertilsson S, Bravo AG

Sci Rep 9 (1) - [2019-12-00; online 2019-01-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family

Lindholm Carlström E, Halvardson J, Etemadikhah M, ..., Gustavson KH, Feuk L

BMC Med Genomics 12 (1) - [2019-12-00; online 2019-11-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations

Filppula AM, Parvizi R, Mateus A, Baranczewski P, Artursson P

Sci Rep 9 (1) - [2019-12-00; online 2019-04-10]

Drug Discovery and Development (DDD) [Technology development]

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]

Biochemical Imaging Centre Umeå [Service] Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C

Genome Biol. 20 (1) - [2019-12-00; online 2019-02-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

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] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cardiovascular organ damage in type 2 diabetes mellitus: the role of lipids and inflammation

Kozakova M, Morizzo C, Goncalves I, ..., Nilsson J, Palombo C

Cardiovasc Diabetol 18 (1) - [2019-12-00; online 2019-05-10]

The associations of self-rated health with cardiovascular risk proteins: a proteomics approach

Bao X, Borné Y, Yin S, ..., Melander O, Engström G

Clin Proteomics 16 (1) - [2019-12-00; online 2019-11-18]

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

Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]

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]

Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

Diamanti K, Cavalli M, Pan G, ..., Komorowski J, Wadelius C

Sci Rep 9 (1) - [2019-12-00; online 2019-07-04]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile

Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F

J. Pathol 249 (4) 425-434 [2019-12-00; online 2019-08-27]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

Cavalli M, Baltzer N, Pan G, ..., Komorowski J, Wadelius C

Hum Genomics 13 (1) - [2019-12-00; online 2019-04-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly

Suarez C, Piculell M, Modin O, ..., Persson F, Hermansson M

Sci Rep 9 (1) - [2019-12-00; online 2019-03-25]

Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity

Hajheidari M, Wang Y, Bhatia N, ..., Gan X, Tsiantis M

Current Biology 29 (24) 4183-4192.e6 [2019-12-00; online 2019-12-00]

Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis

van der Post S, Jabbar KS, Birchenough G, ..., Johansson MEV, Hansson GC

Gut 68 (12) 2142-2151 [2019-12-00; online 2019-03-26]

The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

Baião GC, Schneider DI, Miller WJ, Klasson L

BMC Genomics 20 (1) - [2019-12-00; online 2019-06-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry

Rende U, Niittylä T, Moritz T

Plant Methods 15 (1) - [2019-12-00; online 2019-11-07]

ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery

Saei AA, Beusch CM, Chernobrovkin A, ..., Végvári Á, Zubarev RA

Nat Commun 10 (1) - [2019-12-00; online 2019-12-16]

Morphological analysis of Apolipoprotein E binding to Aβ Amyloid using a combination of Surface Plasmon Resonance, Immunogold Labeling and Scanning Electron Microscopy

Islam T, Gharibyan AL, Lee CC, Olofsson A

BMC Biotechnol. 19 (1) - [2019-12-00; online 2019-12-11]

Biochemical Imaging Centre Umeå [Collaborative] Cryo-EM [Technology development]

ToF-SIMS mediated analysis of human lung tissue reveals increased iron deposition in COPD (GOLD IV) patients

Najafinobar N, Venkatesan S, von Sydow L, ..., Cloonan SM, Malmberg P

Sci Rep 9 (1) - [2019-12-00; online 2019-07-11]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) - [2019-12-00; online 2019-02-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone

Gidlöf O, Evander M, Rezeli M, ..., Laurell T, Erlinge D

Sci Rep 9 (1) - [2019-12-00; online 2019-06-20]

A microfluidic platform towards automated multiplexed in situ sequencing

Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M

Sci Rep 9 (1) - [2019-12-00; online 2019-03-05]

In Situ Sequencing (ISS) [Technology development]

Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder

Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S

Sci Rep 9 (1) - [2019-12-00; online 2019-07-08]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

Publisher Correction: Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) - [2019-12-00; online 2019-08-22]

Polymer gels with tunable ionic Seebeck coefficient for ultra-sensitive printed thermopiles

Zhao D, Martinelli A, Willfahrt A, ..., Fabiano S, Crispin X

Nat Commun 10 (1) - [2019-12-00; online 2019-03-06]

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA

Sci Rep 9 (1) - [2019-12-00; online 2019-12-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas

Backman S, Åkerström T, Maharjan R, ..., Hellman P, Björklund P

Sci Rep 9 (1) - [2019-12-00; online 2019-04-18]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement

Schwarz A, Möller-Hackbarth K, Ebarasi L, ..., Lal M, Patrakka J

Sci Rep 9 (1) - [2019-12-00; online 2019-06-20]

Advanced Light Microscopy (ALM) [Collaborative]

A bacterial assay for rapid screening of IAA catabolic enzymes

Brunoni F, Collani S, Šimura J, ..., Bellini C, Ljung K

Plant Methods 15 (1) - [2019-12-00; online 2019-11-04]

Genomic regions of speciation and adaptation among three species of grouse

Kozma R, Rödin-Mörch P, Höglund J

Sci Rep 9 (1) - [2019-12-00; online 2019-01-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA

BMC Evol. Biol. 19 (1) - [2019-12-00; online 2019-06-18]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.

Yuan S, Jiang X, Michaëlsson K, Larsson SC

Diabetes Care 42 (12) 2197-2203 [2019-12-00; online 2019-09-23]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

Bergman A, Hellgren J, Moritz T, ..., Nielsen J, Chen Y

Microb. Cell Fact. 18 (1) - [2019-12-00; online 2019-02-01]

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M

Nat Commun 10 (1) - [2019-12-00; online 2019-04-09]

Advanced FISH Technologies [Technology development] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Genetic variation in CADM2 as a link between psychological traits and obesity

Morris J, Bailey MES, Baldassarre D, ..., Smith DJ, Strawbridge RJ

Sci Rep 9 (1) - [2019-12-00; online 2019-05-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Angioimmunoblastic T-cell lymphoma and myelodysplastic syndrome with mutations in TET2, DNMT3 and CUX1 - azacitidine induces only lymphoma remission.

Tobiasson M, Pandzic T, Cavelier L, Sander B, Wahlin BE

Leuk. Lymphoma 60 (13) 3316-3319 [2019-12-00; online 2019-06-17]

Clinical Genomics Uppsala [Collaborative]

Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum

Rajan MR, Sotak M, Barrenäs F, ..., Lange S, Börgeson E

Sci Rep 9 (1) - [2019-12-00; online 2019-10-28]

Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

Nakamura M, Köhler C, Hennig L

BMC Genomics 20 (1) - [2019-12-00; online 2019-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model

Velie BD, Lillie M, Fegraeus KJ, ..., Strand E, Lindgren G

BMC Genomics 20 (1) - [2019-12-00; online 2019-02-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants

Wang P, Calvo-Polanco M, Reyt G, ..., Boursiac Y, Salt DE

Sci Rep 9 (1) - [2019-12-00; online 2019-03-12]

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows

Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J

BMC Bioinformatics 20 (1) - [2019-12-00; online 2019-10-15]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML

Sci Rep 9 (1) - [2019-12-00; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

A Cell-Free Approach Based on Phospholipid Characterization for Determination of the Cell Specific Unbound Drug Fraction (fu,cell)

Treyer A, Walday S, Boriss H, Matsson P, Artursson P

Pharm Res 36 (12) - [2019-12-00; online 2019-11-07]

Drug Discovery and Development (DDD) [Technology development]

Mesenchymal stromal cell-derived nanovesicles ameliorate bacterial outer membrane vesicle-induced sepsis via IL-10

Park KS, Svennerholm K, Shelke GV, ..., Gribonika I, Lötvall J

Stem Cell Res Ther 10 (1) - [2019-12-00; online 2019-08-01]

Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells

Mehmeti M, Bergenfelz C, Källberg E, ..., André I, Leandersson K

Commun Biol 2 (1) - [2019-12-00; online 2019-05-09]

Growth performance and nutrient removal of a Chlorella vulgaris-Rhizobium sp. co-culture during mixotrophic feed-batch cultivation in synthetic wastewater

Ferro L, Gojkovic Z, Muñoz R, Funk C

Algal Research 44 (-) 101690 [2019-12-00; online 2019-12-00]

Influence of urea on methyl $$\upbeta$$β-D-glucopyranoside in alkali at different temperatures

Gunnarsson M, Hasani M, Bernin D

Cellulose 26 (18) 9413-9422 [2019-12-00; online 2019-09-14]

Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening

Tükenmez H, Edström I, Ummanni R, ..., Elofsson M, Larsson C

Sci Rep 9 (1) - [2019-12-00; online 2019-01-10]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference

Ny S, Sandegren L, Salemi M, Giske CG

Sci Rep 9 (1) - [2019-12-00; online 2019-07-16]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection

Zhao H, Chen M, Valdés A, Lind SB, Pettersson U

BMC Microbiol. 19 (1) - [2019-12-00; online 2019-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) - [2019-12-00; online 2019-01-23]

Inhibition of translation termination by small molecules targeting ribosomal release factors

Ge X, Oliveira A, Hjort K, ..., Sanyal S, Åqvist J

Sci Rep 9 (1) - [2019-12-00; online 2019-10-28]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]

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]

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]

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach

Zan Y, Payen T, Lillie M, ..., Siegel PB, Carlborg Ö

Genet. Sel. Evol. 51 (1) - [2019-12-00; online 2019-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment

Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N

Neurobiology of Disease 132 (-) 104583 [2019-12-00; online 2019-12-00]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K

Nat Commun 10 (1) - [2019-12-00; online 2019-04-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Proteogenomics [Technology development]

A Mitochondrial LYR Protein Is Required for Complex I Assembly.

Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW

pmc

Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]

Proteogenomics [Collaborative]

Amyloid fibrils prepared using an acetylated and methyl amidated peptide model of the α-Synuclein NAC 71–82 amino acid stretch contain an additional cross-β structure also found in prion proteins

Näsström T, Andersson PO, Lejon C, Karlsson BCG

Sci Rep 9 (1) - [2019-12-00; online 2019-11-04]

Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC

Nirwan N, Itoh Y, Singh P, ..., Amunts A, Saikrishnan K

Nat Commun 10 (1) - [2019-12-00; online 2019-07-11]

Biomarkers of blood cadmium and incidence of cardiovascular events in non-smokers: results from a population-based proteomics study

Borné Y, Fagerberg B, Sallsten G, ..., Barregard L, Engström G

Clin Proteomics 16 (1) - [2019-12-00; online 2019-05-15]

Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model

Kampfraath AA, Klasson L, Anvar SY, ..., Kraaijeveld K, Ellers J

BMC Genomics 20 (1) - [2019-12-00; online 2019-02-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden

Bai X, Zhang J, Ambikan A, ..., Xiong Y, Matussek A

Sci Rep 9 (1) - [2019-12-00; online 2019-04-04]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

Programmed DNA elimination of germline development genes in songbirds.

Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, ..., Forstmeier W, Suh A

pmc

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]

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells

Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M

Front Immunol 10 (-) - [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cell Profiling [Collaborative] Proteogenomics [Technology development]

Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Raethong N, Wang H, Nielsen J, Vongsangnak W

Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Plasma Profiling [Collaborative]

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]

The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.

Tractenberg RE, Lindvall JM, Attwood TK, Via A

pmc

PLoS ONE 14 (11) e0225256 [2019-11-26; online 2019-11-26]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Uncovering microbial inter-domain interactions in complex communities

Florenza J, Tamminen M, Bertilsson S

Phil. Trans. R. Soc. B 374 (1786) 20190087 [2019-11-25; online 2019-10-07]

Microbial Single Cell Genomics [Technology development]

MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.

Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M

pmc

iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]

Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.

Pisanu C, Williams MJ, Ciuculete DM, ..., Squassina A, Schiöth HB

Transl Psychiatry 9 (1) 315 [2019-11-21; online 2019-11-21]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.

Čančer M, Drews LF, Bengtsson J, ..., Weishaupt H, Swartling FJ

Cell Death Dis 10 (12) 881 [2019-11-21; online 2019-11-21]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The Swedish Twin Registry: Content and Management as a Research Infrastructure.

Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE

Twin Res Hum Genet - (-) 1-9 [2019-11-21; online 2019-11-21]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Interaction between Copper Chaperone Atox1 and Parkinson’s Disease Protein α-Synuclein Includes Metal-Binding Sites and Occurs in Living Cells

Horvath I, Blockhuys S, Šulskis D, ..., Burmann BM, Wittung-Stafshede P

ACS Chem Neurosci 10 (11) 4659-4668 [2019-11-20; online 2019-10-10]

Genetic predisposition to mosaic Y chromosome loss in blood

Thompson DJ, None , Genovese G, ..., None , None

Nature 575 (7784) 652-657 [2019-11-20; online 2019-11-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).

Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK

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]

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

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]

Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.

Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y

Mol. Psychiatry - (-) - [2019-11-19; online 2019-11-19]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors

Xu X, Makaraviciute A, Kumar S, ..., Nyholm L, Zhang Z

Anal. Chem. 91 (22) 14697-14704 [2019-11-19; online 2019-10-25]

Drug Discovery and Development (DDD) [Technology development]

Boldness in Male and Female Zebrafish ( Danio rerio) Is Dependent on Strain and Test.

Mustafa A, Roman E, Winberg S

pmc

Front. Behav. Neurosci. 13 (-) 248 [2019-11-19; online 2019-11-19]

A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1–12): Synthesis and NMR Ensemble Analysis of Nisin(1–12) and Analogues

Dickman R, Danelius E, Mitchell SA, ..., Erdélyi M, Tabor AB

Chem. Eur. J. 25 (64) 14572-14582 [2019-11-18; online 2019-10-10]

Synthesis of Indomorphan Pseudo-Natural Product Inhibitors of Glucose Transporters GLUT-1 and -3

Ceballos J, Schwalfenberg M, Karageorgis G, ..., Ziegler S, Waldmann H

Angew. Chem. Int. Ed. 58 (47) 17016-17025 [2019-11-18; online 2019-10-07]

Structure of a mitochondrial ATP synthase with bound native cardiolipin

Mühleip A, McComas SE, Amunts A

Elife 8 (-) - [2019-11-18; online 2019-11-18]

Cryo-EM [Service] Proteogenomics [Service]

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

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]

Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.

Sundberg I, Rasmusson AJ, Ramklint M, ..., Ekselius L, Cunningham JL

Psychoneuroendocrinology - (-) 104514 [2019-11-14; online 2019-11-14]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Biomarkers [Service]

Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K

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]

The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension

Morikawa M, Mitani Y, Holmborn K, ..., Heldin CH, Miyazono K

Sci. Signal. 12 (607) eaay4430 [2019-11-12; online 2019-11-12]

Genome Engineering Zebrafish [Collaborative]

A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels

Van Moerkercke A, Duncan O, Zander M, ..., Millar AH, Van Aken O

Proc Natl Acad Sci USA 116 (46) 23345-23356 [2019-11-12; online 2019-10-29]

On-demand virtual research environments using microservices

Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O

- 5 (-) e232 [2019-11-11; online 2019-11-11]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PIRIN2 suppresses S‐type lignin accumulation in a noncell‐autonomous manner in Arabidopsis xylem elements

Zhang B, Sztojka B, Escamez S, ..., Boerjan W, Tuominen H

New Phytol - (-) - [2019-11-11; online 2019-11-11]

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy M, Foster R, Barbera P, ..., Bass D, Burki F

Mol Ecol Resour - (-) - [2019-11-09; online 2019-11-09]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid biophysical characterization and NMR structural analysis of small proteins from bacteria and archaea

Kubatova N, Pyper DJ, Jonker HRA, ..., Schmitz-Streit R, Schwalbe H

ChemBioChem - (-) - [2019-11-09; online 2019-11-09]

Calcium-activated chloride channel regulator 1 (CLCA1) forms non-covalent oligomers in colonic mucus and has mucin 2–processing properties

Nyström EEL, Arike L, Ehrencrona E, Hansson GC, Johansson MEV

J. Biol. Chem. 294 (45) 17075-17089 [2019-11-08; online 2019-09-29]

Carnivores, competition and genetic connectivity in the Anthropocene.

Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C

pmc

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]

Comparative distribution of extended-spectrum beta-lactamase–producing Escherichia coli from urine infections and environmental waters

Fagerström A, Mölling P, Khan FA, ..., Jass J, Söderquist B

PLoS ONE 14 (11) e0224861 [2019-11-07; online 2019-11-07]

Cell‐of‐origin determined by both gene expression profiling and immunohistochemistry is the strongest predictor of survival in patients with diffuse large B‐cell lymphoma

Abdulla M, Hollander P, Pandzic T, ..., Rosenquist R, Amini R

Am J Hematol - (-) - [2019-11-07; online 2019-11-07]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.

Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M

pmc

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]

Counting the Number of Glutamate Molecules in Single Synaptic Vesicles

Wang Y, Fathali H, Mishra D, ..., Skibicka KP, Cans AS

J. Am. Chem. Soc. 141 (44) 17507-17511 [2019-11-06; online 2019-10-23]

Gothenburg Imaging Mass Spectrometry [Service]

Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.

Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL

Viruses 11 (11) - [2019-11-05; online 2019-11-05]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Myc‐dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF receptor‐2

Testini C, Smith RO, Jin Y, ..., Hellström M, Claesson‐Welsh L

EMBO rep 20 (11) - [2019-11-05; online 2019-09-23]

Proteogenomics [Service]

Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Balliu B, Durrant M, Goede O, ..., Ingelsson E, Montgomery SB

pmc

Genome Biol. 20 (1) 230 [2019-11-04; online 2019-11-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function

Volk JK, Nyström EEL, van der Post S, ..., Hansson GC, Birchenough GMH

- 216 (11) 2602-2618 [2019-11-04; online 2019-08-16]

EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia

Kosalai ST, Morsy MHA, Papakonstantinou N, ..., Rosenquist R, Kanduri M

Epigenetics 14 (11) 1125-1140 [2019-11-02; online 2019-06-26]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.

Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA

J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]

Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.

Melhus H, Michaëlsson K, Larsson SC

J. Clin. Endocrinol. Metab. 104 (11) 5595-5600 [2019-11-01; online 2019-07-17]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A genomic inference of the White Plymouth Rock genealogy

Guo Y, Lillie M, Zan Y, ..., Siegel PB, Carlborg Ö

Poult. Sci. 98 (11) 5272-5280 [2019-11-01; online 2019-07-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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]

Diagnostic pitfalls in vitamin B6-dependent epilepsy caused by mutations in the PLPBP gene.

Jensen KV, Frid M, Stödberg T, ..., Darin N, Grønborg S

pmc

JIMD Rep 50 (1) 1-8 [2019-11-00; online 2019-09-30]

PIN-driven auxin transport emerged early in streptophyte evolution

Skokan R, Medvecká E, Viaene T, ..., Petrášek J, Friml J

NPLANTS 5 (11) 1114-1119 [2019-11-00; online 2019-11-11]

Influence of blue mussel (Mytilus edulis) intake on fatty acid composition in erythrocytes and plasma phospholipids and serum metabolites in women with rheumatoid arthritis

Lindqvist HM, Gjertsson I, Andersson S, Calder PC, Bärebring L

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 150 (-) 7-15 [2019-11-00; online 2019-11-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, ..., Blomberg N, Scollen S

Nat. Rev. Genet. 20 (11) 693-701 [2019-11-00; online 2019-08-27]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers.

Chatterjee S, Lee LY, Kawahara R, ..., Palmisano G, Thaysen-Andersen M

Proteomics 19 (21-22) e1900010 [2019-11-00; online 2019-10-16]

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area

Nilsson LKJ, de Oliveira MR, Marinotti O, ..., de Souza AQL, Terenius O

Microb Ecol 78 (4) 781-791 [2019-11-00; online 2019-04-15]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching

Gustavsson E, Isaksson L, Persson C, ..., Orekhov V, Westenhoff S

Biophysical Journal - (-) - [2019-11-00; online 2019-11-00]

Mass transport during coagulation of cellulose-ionic liquid solutions in different non-solvents

Hedlund A, Theliander H, Köhnke T

Cellulose 26 (16) 8525-8541 [2019-11-00; online 2019-08-19]

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.

Papoutsoglou G, Lagani V, Schmidt A, ..., Tegnér J, Tsamardinos I

Cytometry A 95 (11) 1178-1190 [2019-11-00; online 2019-11-06]

Mass Cytometry [Service]

Electrochemical Evaluation of a Napthalene Diimide Derivative for Potential Application in Aqueous Organic Redox Flow Batteries

Wiberg C, Owusu F, Wang E, Ahlberg E

Energy Technol. 7 (11) 1900843 [2019-11-00; online 2019-08-23]

A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning

Ossinger A, Bajic A, Pan S, ..., Hailer NP, Schizas N

Journal of Neuroscience Methods - (-) 108522 [2019-11-00; online 2019-11-00]

BioImage Informatics [Service] Bioinformatics Compute and Storage [Service]

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis

Dobie R, Wilson-Kanamori JR, Henderson BEP, ..., Marioni JC, Henderson NC

Cell Rep 29 (7) 1832-1847.e8 [2019-11-00; online 2019-11-00]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Genetic differentiation between and within ecotypes of pike ( Esox lucius ) in the Baltic Sea

Nordahl O, Koch‐Schmidt P, Sunde J, ..., Forsman A, Larsson P

Aquatic Conserv: Mar Freshw Ecosyst 29 (11) 1923-1935 [2019-11-00; online 2019-08-16]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Molecular imaging identifies age-related attenuation of acetylcholine in retrosplenial cortex in response to acetylcholinesterase inhibition.

Vallianatou T, Shariatgorji M, Nilsson A, ..., Svenningsson P, Andrén PE

pmc

Neuropsychopharmacology 44 (12) 2091-2098 [2019-11-00; online 2019-04-22]

National Resource for Mass Spectrometry Imaging [Service]

Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy

Čančer M, Hutter S, Holmberg KO, ..., Weishaupt H, Swartling FJ

Cell Stem Cell - (-) - [2019-11-00; online 2019-11-00]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Identification of two abundant Aerococcus urinae cell wall-anchored proteins.

Senneby E, Sunnerhagen T, Hallström B, ..., Karlsson C, Rasmussen M

Int. J. Med. Microbiol. 309 (7) 151325 [2019-11-00; online 2019-06-24]

Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden

Stenmark B, Hellmark B, Söderquist B

Eur J Clin Microbiol Infect Dis 38 (11) 2069-2075 [2019-11-00; online 2019-08-09]

Association of PTHrP levels in CSF with Alzheimer’s disease biomarkers

Kushnir MM, Michno W, Rockwood AL, ..., Strathmann FG, Hanrieder J

Clinical Mass Spectrometry 14 (-) 124-129 [2019-11-00; online 2019-11-00]

Gothenburg Imaging Mass Spectrometry [Service]

Physical activity is associated with a large number of cardiovascular-specific proteins: Cross-sectional analyses in two independent cohorts

Stattin K, Lind L, Elmståhl S, ..., Michaëlsson K, Byberg L

Eur J Prev Cardiolog 26 (17) 1865-1873 [2019-11-00; online 2019-08-14]

A revised solid-state NMR method to assess the crystallinity of cellulose

Sparrman T, Svenningsson L, Sahlin-Sjövold K, ..., Westman G, Bernin D

Cellulose 26 (17) 8993-9003 [2019-11-00; online 2019-09-03]

Tuning drug release from polyoxazoline-drug conjugates

Harris JM, Bentley MD, Moreadith RW, ..., Dizman B, Nordstierna L

European Polymer Journal 120 (-) 109241 [2019-11-00; online 2019-11-00]

Mice exposed to maternal androgen excess and diet-induced obesity have altered phosphorylation of catechol-O-methyltransferase in the placenta and fetal liver.

Fornes R, Manti M, Qi X, ..., Benrick A, Stener-Victorin E

Int J Obes (Lond) 43 (11) 2176-2188 [2019-11-00; online 2019-01-22]

The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C

pmc

Sci Rep 9 (1) 15753 [2019-10-31; online 2019-10-31]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Associations of autozygosity with a broad range of human phenotypes.

Clark DW, Okada Y, Moore KHS, ..., Kubo M, Wilson JF

pmc

Nat Commun 10 (1) 4957 [2019-10-31; online 2019-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Perspective on CETSA Literature: Toward More Quantitative Data Interpretation

Seashore-Ludlow B, Axelsson H, Lundbäck T

SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521988452 [2019-10-30; online 2019-10-30]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Viral antigens elicit augmented immune responses in primary Sjögren’s syndrome

Björk A, Thorlacius GE, Mofors J, ..., Kvarnström M, Wahren-Herlenius M

- - (-) - [2019-10-30; online 2019-10-30]

CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation.

Cook NL, Pjanic M, Emmerich AG, ..., Castillejo-López C, Ingelsson E

pmc

BMC Endocr Disord 19 (1) 115 [2019-10-29; online 2019-10-29]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

High-grade progression confers poor survival in pancreatic neuroendocrine tumors.

Botling J, Lamarca A, Bajic D, ..., Skogseid B, Crona J

Neuroendocrinology - (-) - [2019-10-29; online 2019-10-29]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.

Tiukova IA, Jiang H, Dainat J, ..., Gu Z, Passoth V

Microorganisms 7 (11) - [2019-10-26; online 2019-10-26]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.

Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

Eur. J. Hum. Genet. - (-) - [2019-10-25; online 2019-10-25]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detection of a High-Turnover Serotonin Circuit in the Mouse Brain Using Mass Spectrometry Imaging.

Sugiyama E, Guerrini MM, Honda K, ..., Suematsu M, Sugiura Y

pmc

iScience 20 (-) 359-372 [2019-10-25; online 2019-09-27]

National Resource for Mass Spectrometry Imaging [Service]

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Pettersson ME, Rochus CM, Han F, ..., Folkvord A, Andersson L

Genome Res. - (-) - [2019-10-24; online 2019-10-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Mining the Proteome Associated with Rheumatic and Autoimmune Diseases.

Ruiz-Romero C, Lam MPY, Nilsson P, ..., Watt FE, Blanco FJ

J. Proteome Res. - (-) - [2019-10-23; online 2019-10-23]

Autoimmunity Profiling [Technology development]

Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G

Leukemia & Lymphoma - (-) 1-10 [2019-10-22; online 2019-10-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity

Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR

- - (-) - [2019-10-22; online 2019-10-22]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Genetic architecture of subcortical brain structures in 38,851 individuals

Satizabal CL, Adams HHH, Hibar DP, ..., Seshadri S, Ikram MA

Nat Genet - (-) - [2019-10-21; online 2019-10-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

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]

DPI Selectively Inhibits Intracellular NADPH Oxidase Activity in Human Neutrophils.

Buck A, Sanchez Klose FP, Venkatakrishnan V, ..., Christenson K, Bylund J

Immunohorizons 3 (10) 488-497 [2019-10-18; online 2019-10-18]

Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State

Diab J, Hansen T, Goll R, ..., Florholmen J, Forsdahl G

- 25 (11) 1780-1787 [2019-10-18; online 2019-05-11]

The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell–specific adapter protein

Andersen TCB, Kristiansen PE, Huszenicza Z, ..., Andreotti AH, Spurkland A

J. Biol. Chem. 294 (42) 15480-15494 [2019-10-18; online 2019-09-04]

Considerations and Implications in the Purification of Extracellular Vesicles – A Cautionary Tale

Lee YXF, Johansson H, Wood MJA, El Andaloussi S

Front. Neurosci. 13 (-) - [2019-10-18; online 2019-10-18]

Bioinformatics Compute and Storage [Service] Proteogenomics [Service]

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

- - (-) - [2019-10-17; online 2019-10-17]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Microbe-host interplay in atopic dermatitis and psoriasis.

Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H

pmc

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]

Root distribution in intercropping systems – a comparison of DNA based methods and visual distinction of roots

Hassan A, Dresbøll DB, Rasmussen CR, ..., Lund OS, Thorup-Kristensen K

Archives of Agronomy and Soil Science - (-) 1-14 [2019-10-16; online 2019-10-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.

Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, ..., Engblom S, Dopson M

pmc

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]

Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.

Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H

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]

CSF levels of apolipoprotein C1 and autotaxin found to associate with neuropathic pain and fibromyalgia.

Lind AL, Just D, Mikus M, ..., Gordh T, Månberg A

pmc

J Pain Res 12 (-) 2875-2889 [2019-10-15; online 2019-10-15]

Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches.

Yao S, Kuja-Halkola R, Martin J, ..., Bulik CM, Larsson H

Biol. Psychiatry 86 (8) 577-586 [2019-10-15; online 2019-05-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Monitoring of Protein Biomarkers of Inflammation in Human Traumatic Brain Injury Using Microdialysis and Proximity Extension Assay Technology in Neurointensive Care.

Dyhrfort P, Shen Q, Clausen F, ..., Lewén A, Hillered L

pmc

J. Neurotrauma 36 (20) 2872-2885 [2019-10-15; online 2019-06-17]

PLA and Single Cell Proteomics [Technology development]

A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding

Fleming CL, Sandoz PA, Inghardt T, ..., Grøtli M, Andréasson J

Angew. Chem. Int. Ed. 58 (42) 15000-15004 [2019-10-14; online 2019-09-05]

Dynamic Nanocellulose Networks for Thermoset-like yet Recyclable Plastics with a High Melt Stiffness and Creep Resistance

Peterson A, Östergren I, Lotsari A, ..., Boldizar A, Müller C

Biomacromolecules 20 (10) 3924-3932 [2019-10-14; online 2019-09-17]

Cryo-EM [Technology development]

Sustained Egr-1 Response via p38 MAP Kinase Signaling Modulates Early Immune Responses of Dendritic Cells Parasitized by Toxoplasma gondii

ten Hoeve AL, Hakimi MA, Barragan A

Front. Cell. Infect. Microbiol. 9 (-) - [2019-10-11; online 2019-10-11]

Intravital Microscopy Facility [Service]

N-Trifluoromethylthiolated Sulfonimidamides and Sulfoximines: Anti-microbial, Anti-mycobacterial, and Cytotoxic Activity

Thota N, Makam P, Rajbongshi KK, ..., Naicker T, Arvidsson PI

ACS Med Chem Lett 10 (10) 1457-1461 [2019-10-10; online 2019-09-11]

Drug Discovery and Development (DDD) [Technology development]

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.

Sanchez A, Kuras M, Murillo JR, ..., Betancourt LH, Marko-Varga G

Cell Biol. Toxicol. - (-) - [2019-10-10; online 2019-10-10]

Associations Between Apolipoprotein A1, High-Density Lipoprotein Cholesterol, and Urinary Cytokine Levels in Elderly Males and Females

Fellström B, Helmersson-Karlqvist J, Lind L, ..., Ärnlöv J, Larsson A

Journal of Interferon & Cytokine Research - (-) - [2019-10-10; online 2019-10-10]

Apolipoprotein E impairs amyloid‐β fibril elongation and maturation

Islam T, Gharibyan AL, Golchin SA, ..., Olofsson L, Olofsson A

FEBS J - (-) - [2019-10-09; online 2019-10-09]

SynQuant: an automatic tool to quantify synapses from microscopy images

Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G

- - (-) - [2019-10-09; online 2019-10-09]

BioImage Informatics [Collaborative]

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon

Malmström H, Günther T, Svensson EM, ..., Storå J, Jakobsson M

Proc. R. Soc. B 286 (1912) 20191528 [2019-10-09; online 2019-10-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Intracrystalline Transport Barriers Affecting the Self-Diffusion of CH4 in Zeolites |Na12|-A and |Na12–xKx|-A

Hedin N, Rzepka P, Jasso-Salcedo AB, Church TL, Bernin D

Langmuir 35 (40) 12971-12978 [2019-10-08; online 2019-09-11]

Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.

Semo A, Gayà-Vidal M, Fortes-Lima C, ..., Schlebusch C, Rocha J

Mol. Biol. Evol. - (-) - [2019-10-08; online 2019-10-08]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Reduced sialyl-Lewis x on salivary MUC7 from patients with burning mouth syndrome.

Acharya S, Jin C, Bylund J, ..., Carlén A, Karlsson NG

Mol Omics 15 (5) 331-339 [2019-10-07; online 2019-08-16]

Glycoproteomics [Collaborative] PLA and Single Cell Proteomics [Collaborative]

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

pmc

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]

Proteomic Analysis of Longitudinal Changes in Blood Pressure

Lin YT, Fall T, Hammar U, ..., Engström G, Sundström J

J Clin Med 8 (10) 1585 [2019-10-02; online 2019-10-02]

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Tin A, Marten J, Halperin Kuhns VL, ..., Vitart V, Köttgen A

Nat. Genet. - (-) - [2019-10-02; online 2019-10-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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]

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

pmc

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]

Interoperable and scalable data analysis with microservices: applications in metabolomics

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

- 35 (19) 3752-3760 [2019-10-01; online 2019-03-09]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates

Debiais-Thibaud M, Simion P, Ventéo S, ..., Mazan S, Haitina T

- 36 (10) 2265-2276 [2019-10-01; online 2019-07-04]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities

Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N

Water Research 162 (-) 437-445 [2019-10-00; online 2019-10-00]

Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Upregulation of PBP1B and LpoB in cysB Mutants Confers Mecillinam (Amdinocillin) Resistance in Escherichia coli.

Thulin E, Andersson DI

pmc

Antimicrob. Agents Chemother. 63 (10) - [2019-10-00; online 2019-09-23]

Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation

Castillejo-Lopez C, Pjanic M, Pirona AC, ..., Arner E, Ingelsson E

iScience 20 (-) 42-59 [2019-10-00; online 2019-10-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genetic basis and timing of a major mating system shift in Capsella

Bachmann JA, Tedder A, Laenen B, ..., Castric V, Slotte T

New Phytol 224 (1) 505-517 [2019-10-00; online 2019-08-00]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra)

Papazian S, Girdwood T, Wessels BA, ..., Moritz T, Albrectsen BR

Metabolomics 15 (10) - [2019-10-00; online 2019-09-28]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Real time MRI to elucidate the functionality of coating films intended for modified release

Bernin D, Marucci M, Boissier C, ..., Olsson U, Abrahmsén-Alami S

Journal of Controlled Release 311-312 (-) 117-124 [2019-10-00; online 2019-10-00]

Molecular characterization of particulate organic matter in full scale anaerobic digesters: An NMR spectroscopy study

Shakeri Yekta S, Hedenström M, Svensson BH, ..., Hertkorn N, Björn A

Science of The Total Environment 685 (-) 1107-1115 [2019-10-00; online 2019-10-00]

Cell generation dynamics underlying naive T-cell homeostasis in adult humans.

Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J

PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Cappellini E, Welker F, Pandolfi L, ..., Lordkipanidze D, Willerslev E

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]

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Kurland S, Wheat CW, Paz Celorio Mancera M, ..., Ryman N, Laikre L

Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Isolation and characterization of microvesicles from mesenchymal stem cells

Mohammadi MR, Riazifar M, Pone EJ, ..., Lotvall J, Zhao W

Methods - (-) - [2019-10-00; online 2019-10-00]

Elevated IL-27 in patients with acute coronary syndrome is associated with adverse ventricular remodeling and increased risk of recurrent myocardial infarction and cardiovascular death

Grufman H, Yndigegn T, Gonçalves I, Nilsson J, Schiopu A

Cytokine 122 (-) 154208 [2019-10-00; online 2019-10-00]

Whole genome sequencing of apparently mutation-negative MEN1 patients

Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P

- - (-) - [2019-10-00; online 2019-10-00]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A

Wehrli PM, Uzelac I, Olsson T, ..., Tietze D, Gottfries J

Bioorganic & Medicinal Chemistry 27 (19) 115043 [2019-10-00; online 2019-10-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Glycoproteomics [Service] Swedish NMR Centre (SNC) [Service]

Implantable Organic Electronic Ion Pump Enables ABA Hormone Delivery for Control of Stomata in an Intact Tobacco Plant

Bernacka‐Wojcik I, Huerta M, Tybrandt K, ..., Berggren M, Stavrinidou E

Small 15 (43) 1902189 [2019-10-00; online 2019-09-12]

Cellular uptake of self-assembled phytantriol-based hexosomes is independent of major endocytic machineries

Rodrigues L, Schneider F, Zhang X, ..., Lundmark R, Hubert M

Journal of Colloid and Interface Science 553 (-) 820-833 [2019-10-00; online 2019-10-00]

Biochemical Imaging Centre Umeå [Collaborative]

Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus

Odqvist L, Jevnikar Z, Riise R, ..., Collins B, Vaarala O

Ann Rheum Dis 78 (10) 1363-1370 [2019-10-00; online 2019-07-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer

Svedlund J, Strell C, Qian X, ..., Sieuwerts AM, Nilsson M

EBioMedicine 48 (-) 212-223 [2019-10-00; online 2019-10-00]

In Situ Sequencing (ISS) [Technology development]

Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging.

Shariatgorji M, Nilsson A, Fridjonsdottir E, ..., Odell LR, Andrén PE

Nat. Methods 16 (10) 1021-1028 [2019-10-00; online 2019-09-23]

National Resource for Mass Spectrometry Imaging [Technology development]

Endocytic pathway of vascular cell adhesion molecule 1 in human umbilical vein endothelial cell identified in vitro by using functionalized nontoxic fluorescent quantum dots

Fu Y, Jussi J, Wang Q, ..., Yang X, Chen Y

Sensors and Actuators B: Chemical 297 (-) 126702 [2019-10-00; online 2019-10-00]

Advanced Light Microscopy (ALM) [Service]

Distribution of bacteria between different milk fractions, investigated using culture‐dependent methods and molecular‐based and fluorescent microscopy approaches

Sun L, Dicksved J, Priyashantha H, Lundh Å, Johansson M

J Appl Microbiol 127 (4) 1028-1037 [2019-10-00; online 2019-07-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL

pmc mid

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]

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

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]

A clonal expression biomarker associates with lung cancer mortality.

Biswas D, Birkbak NJ, Rosenthal R, ..., Swanton C, TRACERx Consortium

Nat. Med. 25 (10) 1540-1548 [2019-10-00; online 2019-10-07]

Clinical Genomics Uppsala [Collaborative]

Fam83F induces p53 stabilisation and promotes its activity.

Salama M, Benitez-Riquelme D, Elabd S, ..., Davidson G, Blattner C

pmc

Cell Death Differ. 26 (10) 2125-2138 [2019-10-00; online 2019-01-28]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Prognostic Impact of BRAF and KRAS Mutation in Patients with Colorectal and Appendiceal Peritoneal Metastases Scheduled for CRS and HIPEC.

Graf W, Cashin PH, Ghanipour L, ..., Terman A, Birgisson H

Ann. Surg. Oncol. - (-) - [2019-09-30; online 2019-09-30]

Clinical Genomics Uppsala [Collaborative]

Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole.

Rodriguez-Furlan C, Domozych D, Qian W, ..., Raikhel NV, Hicks GR

Proc. Natl. Acad. Sci. U.S.A. - (-) - [2019-09-30; online 2019-09-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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

Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cold Atmospheric Plasma Disarms M1 Protein, an Important Streptococcal Virulence Factor

Persson ST, Ekström S, Papareddy P, Herwald H

J Innate Immun - (-) 1-14 [2019-09-27; online 2019-09-27]

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 GEO GEO GEO GEO GEO

EMBO J. - (-) e101323 [2019-09-26; online 2019-09-26]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.

Seyfferth C, Wessels BA, Gorzsás A, ..., Sundberg B, Felten J

pmc

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]

Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.

Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C

pmc GEO

Elife 8 (-) - [2019-09-25; online 2019-09-25]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Discovery of Novel Sequences in 1,000 Swedish Genomes.

Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A

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 [Service]

Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.

Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A

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]

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

Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development

Johansson MM, Pottmeier P, Suciu P, ..., Peuckert C, Jazin E

Front Genet 10 (-) - [2019-09-24; online 2019-09-24]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

IGEMS: The Consortium on Interplay of Genes and Environment Across Multiple Studies - An Update.

Pedersen NL, Gatz M, Finch BK, ..., Sachdev P, Whitfield KE

Twin Res Hum Genet - (-) 1-8 [2019-09-23; online 2019-09-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.

Boström AE, Chatzittofis A, Ciuculete DM, ..., Schiöth HB, Jokinen J

Epigenetics - (-) 1-16 [2019-09-22; online 2019-09-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Microwave Synthesis of Alkali-Free Hexaniobate, Decaniobate, and Hexatantalate Polyoxometalate Ions

Rambaran MA, Pascual-Borràs M, Ohlin CA

Eur. J. Inorg. Chem. 2019 (35) 3913-3918 [2019-09-22; online 2019-09-05]

The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity.

Papoutsoglou P, Tsubakihara Y, Caja L, ..., Heldin CH, Moustakas A

Cell Rep 28 (12) 3182-3198.e11 [2019-09-17; online 2019-09-19]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method

Rajan SK, Lindqvist M, Brummer RJ, Schoultz I, Repsilber D

PLoS ONE 14 (9) e0222171 [2019-09-17; online 2019-09-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

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]

Nestin Regulates Neurogenesis in Mice Through Notch Signaling From Astrocytes to Neural Stem Cells

Wilhelmsson U, Lebkuechner I, Leke R, ..., Pekna M, Pekny M

- 29 (10) 4050-4066 [2019-09-13; online 2019-01-03]

Anticancer effect of deuterium depleted water - redox disbalance leads to oxidative stress.

Zhang X, Gaetani M, Chernobrovkin A, Zubarev RA

Mol. Cell Proteomics - (-) - [2019-09-13; online 2019-09-13]

Chemical Proteomics [Collaborative]

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

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]

Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture

Reddy HK, Carroni M, Hajdu J, Svenda M

Elife 8 (-) - [2019-09-12; online 2019-09-12]

Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.

Teumer A, Li Y, Ghasemi S, ..., Pattaro C, Köttgen A

pmc

Nat Commun 10 (1) 4130 [2019-09-11; online 2019-09-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota

Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C

MBio 10 (5) - [2019-09-10; online 2019-09-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin

Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L

Proc Natl Acad Sci USA 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease.

Stahel P, Nahmias A, Sud SK, ..., Batterham RL, Dash S

Diabetes - (-) - [2019-09-10; online 2019-09-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

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]

μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome

Milon N, Chantry-Darmon C, Satge C, ..., Bergès H, Bancaud A

Nucleic Acids Res 47 (15) 8050-8060 [2019-09-05; online 2019-07-25]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Chemical screening pipeline for identification of specific plant autophagy modulators

Dauphinee AN, Cardoso C, Dalman K, ..., Bozhkov P, Minina EA

Plant Physiol. - (-) pp.00647.2019 [2019-09-05; online 2019-09-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.

Pederson ERA, Warshan D, Rasmussen U

pmc

G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]

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]

Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.

Yuan S, Michaëlsson K, Wan Z, Larsson SC

Calcif. Tissue Int. - (-) - [2019-09-04; online 2019-09-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein prenylation restrains innate immunity by inhibiting Rac1 effector interactions.

Akula MK, Ibrahim MX, Ivarsson EG, ..., Sayin VI, Bergo MO

pmc

Nat Commun 10 (1) 3975 [2019-09-04; online 2019-09-04]

Chemical Changes On, and Through, The Bacterial Envelope in Escherichia coli Mutants Exhibiting Impaired Plasmid Transfer Identified Using Time-of-Flight Secondary Ion Mass Spectrometry

Dimovska Nilsson K, Palm M, Hood J, ..., Farewell A, Fletcher JS

Anal. Chem. 91 (17) 11355-11361 [2019-09-03; online 2019-07-30]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Association of Use of the Neonatal Early-Onset Sepsis Calculator With Reduction in Antibiotic Therapy and Safety: A Systematic Review and Meta-analysis.

Achten NB, Klingenberg C, Benitz WE, ..., van Rossum AMC, Plötz FB

JAMA Pediatr - (-) - [2019-09-03; online 2019-09-03]

Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle

Aliakbari A, Ehsani A, Vaez Torshizi R, ..., Jensen J, Sarup P

J. Anim. Sci. 97 (9) 3832-3844 [2019-09-03; online 2019-07-05]

Challenges for CLEM from a Light Microscopy Perspective." Book title: Correlative Imaging, focusing on the future

Anderson K, Nilsson T, Fernandez‐Rodriguez J

John Wiley & Sons Ltd 2 (-) 23-34 [2019-09-01]

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

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]

Vimentin Phosphorylation Is Required for Normal Cell Division of Immature Astrocytes

Pablo , Marasek , Pozo-Rodrigálvarez , ..., Pekna , Pekny

Cells 8 (9) 1016 [2019-09-01; online 2019-09-01]

The autoantibody response to cyclic citrullinated collagen type II peptides in rheumatoid arthritis.

Liang B, Ge C, Lönnblom E, ..., Zhao M, Holmdahl R

Rheumatology (Oxford) 58 (9) 1623-1633 [2019-09-01; online 2019-03-21]

Autoimmunity Profiling [Service]

Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.

Höök L, Leal L, Talla V, Backström N

pmc

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]

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW

pmc

Mol. Biol. Evol. 36 (9) 1975-1989 [2019-09-01; online 2019-06-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Global extracellular vesicle proteomic signature defines U87-MG glioma cell hypoxic status with potential implications for non-invasive diagnostics.

Indira Chandran V, Welinder C, Gonçalves de Oliveira K, ..., Marko-Varga G, Belting M

pmc

J. Neurooncol. 144 (3) 477-488 [2019-09-00; online 2019-08-14]

Targeted ultra-deep sequencing of a South African Bantu-speaking cohort to comprehensively map and characterize common and novel variants in 65 pharmacologically-related genes.

Tshabalala S, Choudhury A, Beeton-Kempen N, ..., Ramsay M, Mancama D

pmc mid

Pharmacogenet. Genomics 29 (7) 167-178 [2019-09-00; online 2019-06-05]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exploration of potential biochemical markers for persistence of patent ductus arteriosus in preterm infants at 22–27 weeks’ gestation

Olsson KW, Larsson A, Jonzon A, Sindelar R

Pediatr Res 86 (3) 333-338 [2019-09-00; online 2018-09-18]

A simultaneous assessment of organic matter and trace elements bio-accessibility in substrate and digestate from an anaerobic digestion plant

Laera A, Shakeri Yekta S, Hedenström M, ..., Esposito G, van Hullebusch ED

Bioresource Technology 288 (-) 121587 [2019-09-00; online 2019-09-00]

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 GENBANK

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]

Multiplexed analysis of the secretin-like GPCR-RAMP interactome.

Lorenzen E, Dodig-Crnković T, Kotliar IB, ..., Schwenk JM, Sakmar TP

pmc

Sci Adv 5 (9) eaaw2778 [2019-09-00; online 2019-09-18]

A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden

Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K

Journal of Global Antimicrobial Resistance - (-) - [2019-09-00; online 2019-09-00]

Whole exome sequencing identifies novel variant underlying hereditary spastic paraplegia in consanguineous Pakistani families.

Zulfiqar S, Tariq M, Ali Z, ..., Dahl N, Baig SM

J Clin Neurosci 67 (-) 19-23 [2019-09-00; online 2019-07-04]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Impact of demography on linked selection in two outcrossing Brassicaceae species

Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T

Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis

Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK

Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]

Clinical Genomics Lund [Service]

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.

Morais EB, Schönenberger J, Conti E, Antonelli A, Szövényi P

pmc

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]

Perturbed ovarian and uterine glucocorticoid receptor signaling accompanies the balanced regulation of mitochondrial function and NFκB-mediated inflammation under conditions of hyperandrogenism and insulin resistance

Hu M, Zhang Y, Guo X, ..., Shao LR, Billig H

Life Sciences 232 (-) 116681 [2019-09-00; online 2019-09-00]

Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil

Randewig D, Marshall JD, Näsholm T, Jämtgård S

Soil Biology and Biochemistry 136 (-) 107530 [2019-09-00; online 2019-09-00]

Fast time-resolved NMR with non-uniform sampling

Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K

Progress in Nuclear Magnetic Resonance Spectroscopy - (-) - [2019-09-00; online 2019-09-00]

Copy number variation and neuropsychiatric problems in females and males in the general population.

Martin J, Tammimies K, Karlsson R, ..., Lichtenstein P, Magnusson PKE

Am. J. Med. Genet. B Neuropsychiatr. Genet. 180 (6) 341-350 [2019-09-00; online 2018-10-11]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein kinase MST3 modulates lipid homeostasis in hepatocytes and correlates with nonalcoholic steatohepatitis in humans.

Cansby E, Kulkarni NM, Magnusson E, ..., Blüher M, Mahlapuu M

FASEB J. 33 (9) 9974-9989 [2019-09-00; online 2019-06-07]

Dimerization of 9,10-anthraquinone-2,7-Disulfonic acid (AQDS)

Wiberg C, Carney TJ, Brushett F, Ahlberg E, Wang E

Electrochimica Acta 317 (-) 478-485 [2019-09-00; online 2019-09-00]

Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.

Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP

Science 365 (6456) - [2019-08-30; online 2019-08-31]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The human transmembrane mucin MUC17 responds to TNFα by increased presentation at the plasma membrane

Schneider H, Berger E, Dolan B, ..., Pelaseyed T, Hansson GC

Biochemical Journal 476 (16) 2281-2295 [2019-08-30; online 2019-08-22]

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

pmc

Viruses 11 (9) - [2019-08-30; online 2019-08-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Neuroticism as a predictor of frailty in old age: a genetically informative approach.

Danielsdottir HB, Jylhävä J, Hägg S, ..., Mosing MA, Lehto K

Psychosom Med - (-) - [2019-08-28; online 2019-08-28]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC

Reimegård J, Danielsson M, Tarbier M, ..., Friedländer MR, Gallant CJ

- - (-) - [2019-08-28; online 2019-08-28]

Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Technology development]

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

pmc

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]

Profiling surface proteins on individual exosomes using a proximity barcoding assay.

Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M

pmc

Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]

Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Technology development]

Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.

Marquardt N, Kekäläinen E, Chen P, ..., Ljunggren HG, Michaëlsson J

pmc

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]

In search of causal pathways in diabetes: a study using proteomics and genotyping data from a cross-sectional study.

Beijer K, Nowak C, Sundström J, ..., Fall T, Lind L

Diabetologia - (-) - [2019-08-24; online 2019-08-24]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.

Pin E, Sjöberg R, Andersson E, ..., Nilsson P, Månberg A

Methods Mol. Biol. 2044 (-) 303-318 [2019-08-23; online 2019-08-23]

Autoimmunity Profiling [Technology development]

Yeast Volatomes Differentially Affect Larval Feeding in an Insect Herbivore

Ljunggren J, Borrero-Echeverry F, Chakraborty A, ..., Witzgall P, Bengtsson M

Appl Environ Microbiol 85 (21) - [2019-08-23; online 2019-10-16]

Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk.

Tengvall K, Huang J, Hellström C, ..., Olsson T, Kockum I

pmc

Proc. Natl. Acad. Sci. U.S.A. 116 (34) 16955-16960 [2019-08-20; online 2019-08-02]

Autoimmunity Profiling [Collaborative]

Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography-Mass Spectrometry.

Jin C, Harvey DJ, Struwe WB, Karlsson NG

Anal. Chem. 91 (16) 10604-10613 [2019-08-20; online 2019-08-01]

Glycoproteomics [Technology development]

Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats

Heinrich K, Leslie DJ, Morlock M, Bertilsson S, Jonas K

MBio 10 (4) - [2019-08-20; online 2019-08-20]

Proteogenomics [Service]

Genome-wide systematic identification of methyltransferase recognition and modification patterns.

Jensen TØ, Tellgren-Roth C, Redl S, ..., Pedersen LE, Nielsen AT

pmc

Nat Commun 10 (1) 3311 [2019-08-19; online 2019-08-19]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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

pmc

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]

Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis.

Elowsson Rendin L, Löfdahl A, Åhrman E, ..., Malmström J, Westergren-Thorsson G

pmc

Int J Mol Sci 20 (16) - [2019-08-17; online 2019-08-17]

Complete Genome Sequence of Hydrocarbon-Degrading Halotolerant Acinetobacter radioresistens DD78, Isolated from the Aconcagua River Mouth in Central Chile.

Macaya CC, Méndez V, Durán RE, ..., Moore ERB, Seeger M

Microbiol Resour Announc 8 (33) - [2019-08-15; online 2019-08-15]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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

pmc

MBio 10 (4) - [2019-08-13; online 2019-08-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Nucleation of an Activating Conformational Change by a Cation−π Interaction

Rogne P, Andersson D, Grundström C, ..., Linusson A, Wolf-Watz M

Biochemistry 58 (32) 3408-3412 [2019-08-13; online 2019-07-24]

Functional Identification of Target by Expression Proteomics (FITExP)

Gaetani M, Zubarev RA

- - (-) 257-266 [2019-08-13; online 2019-07-26]

Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila.

Bonzom C, Hüttner S, Mirgorodskaya E, ..., Verhaert RMD, Olsson L

pmc

AMB Express 9 (1) 126 [2019-08-12; online 2019-08-12]

The bio.tools registry of software tools and data resources for the life sciences.

Ison J, Ienasescu H, Chmura P, ..., Løngreen P, Brunak S

pmc

Genome Biol. 20 (1) 164 [2019-08-12; online 2019-08-12]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.

Costa TDF, Zhuang T, Lorent J, ..., Defilippi P, Strömblad S

pmc

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]

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

Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]

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] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin.

Flowers SA, Lane CS, Karlsson NG

Anal. Chem. 91 (15) 9819-9827 [2019-08-06; online 2019-07-11]

Glycoproteomics [Technology development]

Selective Enrichment of Phosphorylated Peptides by Monolithic Polymers Surface Imprinted with bis-Imidazolium Moieties by UV-Initiated Cryopolymerization

Liu M, Torsetnes SB, Wierzbicka C, ..., Sellergren B, Irgum K

Anal. Chem. 91 (15) 10188-10196 [2019-08-06; online 2019-06-25]

Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.

Glanville KP, Coleman JRI, Hanscombe KB, ..., O'Reilly PF, Lewis CM

Biol. Psychiatry - (-) - [2019-08-05; online 2019-08-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

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]

Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells.

Amaral PP, Engström PG, Robson SC, ..., Kouzarides T, Castelo-Branco G

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]

Trophic transfer of CuO NPs and dissolved Cu from sediment to worms to fish - a proof-of-concept study

Lammel T, Jensen A, Mouneyrac C, ..., Sturve J, Selck H

Environmental Science: Nano 2019 (4) - [2019-08-01]

The Critical Role of Dysregulated RhoB Signaling Pathway in Radioresistance of Colorectal Cancer.

Liu N, Cui W, Jiang X, ..., Wang X, Sun XF

Int. J. Radiat. Oncol. Biol. Phys. 104 (5) 1153-1164 [2019-08-01; online 2019-04-27]

Mass Cytometry [Service]

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.

Herlemann DPR, Markert S, Meeske C, ..., Jürgens K, Schweder T

pmc

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]

Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells

Li H, Lim HC, Zacharaki D, ..., Hansson J, Scheding S

Haematologica - (-) haematol.2019.216648 [2019-08-01; online 2019-08-01]

Clinical Genomics Lund [Service]

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

pmc

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]

Viral mimetic priming enhances α-synuclein-induced degeneration: Implications for Parkinson’s disease

Olsen LK, Cairns AG, Ådén J, ..., Dowd E, McKernan DP

Brain, Behavior, and Immunity 80 (-) 525-535 [2019-08-00; online 2019-08-00]

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

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]

Contact allergy to beeswax and propolis among patients with cheilitis or facial dermatitis

Nyman GSA, Tang M, Inerot A, ..., Malmberg P, Hagvall L

Contact Dermatitis 81 (2) 110-116 [2019-08-00; online 2019-05-27]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Syntaxin 5 Is Required for the Formation and Clearance of Protein Inclusions during Proteostatic Stress

Babazadeh R, Ahmadpour D, Jia S, ..., Liu B, Nystrom T

Cell Rep 28 (8) 2096-2110.e8 [2019-08-00; online 2019-08-00]

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.

Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA

pmc GENBANK

Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.

Kawakami T, Wallberg A, Olsson A, ..., Rundlöf M, Webster MT

pmc

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]

Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.

Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

In-hospital metabolite changes in infective endocarditis—a longitudinal 1H NMR-based study

Klein CF, Holle SLK, Andersen MH, ..., Iversen KK, Malmendal A

Eur J Clin Microbiol Infect Dis 38 (8) 1553-1560 [2019-08-00; online 2019-05-22]

A role for the auxin precursor anthranilic acid in root gravitropism via regulation of PIN ‐ FORMED protein polarity and relocalisation in Arabidopsis

Doyle SM, Rigal A, Grones P, ..., Novák O, Robert S

New Phytol 223 (3) 1420-1432 [2019-08-00; online 2019-06-07]

Molecular insights into hypomineralized enamel

Malmberg P, Norén JG, Bernin D

Eur J Oral Sci 127 (4) 340-346 [2019-08-00; online 2019-04-29]

Reply to "CRISPR screens are feasible in TP53 wild-type cells".

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

pmc

Mol. Syst. Biol. 15 (8) e9059 [2019-08-00; online 2019-08-30]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]

Layer formation mechanism of K-feldspar in bubbling fluidized bed combustion of phosphorus-lean and phosphorus-rich residual biomass

Wagner K, Häggström G, Skoglund N, ..., Öhman M, Hofbauer H

Applied Energy 248 (-) 545-554 [2019-08-00; online 2019-08-00]

Role of apolipoprotein C-III overproduction in diabetic dyslipidaemia.

Adiels M, Taskinen MR, Björnson E, ..., Packard C, Borén J

Diabetes Obes Metab 21 (8) 1861-1870 [2019-08-00; online 2019-05-08]

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]

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]

Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma.

Mohlin S, Hansson K, Radke K, ..., von Stedingk K, Bexell D

pmc GEO

EMBO Mol Med 11 (8) e10058 [2019-08-00; online 2019-07-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Targeted and Structural Proteomics [Service]

Clinical protein science in translational medicine targeting malignant melanoma.

Gil J, Betancourt LH, Pla I, ..., Malm J, Marko-Varga G

pmc

Cell Biol. Toxicol. 35 (4) 293-332 [2019-08-00; online 2019-03-21]

Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.

Frisk S, Taylan F, Blaszczyk I, ..., Laurell T, Nordgren A

pmc

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]

31° South: The physiology of adaptation to arid conditions in a passerine bird.

Ribeiro ÂM, Puetz L, Pattinson NB, ..., Smit B, Gilbert MTP

GENBANK

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]

sTRAIL-R2 (Soluble TNF [Tumor Necrosis Factor]-Related Apoptosis-Inducing Ligand Receptor 2) a Marker of Plaque Cell Apoptosis and Cardiovascular Events

Gonçalves I, Singh P, Tengryd C, ..., Nilsson J, Edsfeldt A

Stroke 50 (8) 1989-1996 [2019-08-00; online 2019-08-00]

Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures

Segura JH, Nilsson MB, Schleucher J, ..., Bertilsson S, Öquist MG

Soil Biology and Biochemistry 135 (-) 438-448 [2019-08-00; online 2019-08-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Goodbye reference, hello genome graphs.

Ameur A

Nat. Biotechnol. 37 (8) 866-868 [2019-08-00; online 2019-08-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Systematic Development of Sandwich Immunoassays for the Plasma Secretome.

Häussler RS, Bendes A, Iglesias M, ..., Qundos U, Schwenk JM

Proteomics 19 (15) e1900008 [2019-08-00; online 2019-07-22]

Plasma Profiling [Technology development]

Circulating HER2/ErbB2 Levels Are Associated With Increased Incidence of Diabetes: A Population-Based Cohort Study

Muhammad IF, Borné Y, Bao X, ..., Nilsson J, Engström G

Dia Care 42 (8) 1582-1588 [2019-08-00; online 2019-06-14]

Molecular insights into hypomineralized enamel

Malmberg P, Norén JG, Bernin D

Eur J Oral Sci 127 (4) 340-346 [2019-08-00; online 2019-04-29]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Joint Image Deconvolution and Separation Using Mixed Dictionaries

Siadat M, Aghazadeh N, Akbarifard F, Brismar H, Oktem O

IEEE Trans. on Image Process. 28 (8) 3936-3945 [2019-08-00; online 2019-08-00]

Advanced Light Microscopy (ALM) [Technology development]

Mixture toxicity effects and uptake of titanium dioxide (TiO2) nanoparticles and 3,3′,4,4′-tetrachlorobiphenyl (PCB77) in juvenile brown trout following co-exposure via the diet

Lammel T, Wassmur B, Mackevica A, Chen CEL, Sturve J

Aquatic Toxicology 213 (-) 105195 [2019-08-00; online 2019-08-00]

Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates

Segura JH, Nilsson MB, Sparrman T, ..., Tolu J, Öquist MG

Plant Soil 441 (1-2) 173-190 [2019-08-00; online 2019-05-24]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Computational and Experimental Druggability Assessment of Human DNA Glycosylases

Michel M, Visnes T, Homan EJ, ..., Warpman Berglund U, Helleday T

ACS Omega 4 (7) 11642-11656 [2019-07-31; online 2019-07-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

Revealing the Regional Localization and Differential Lung Retention of Inhaled Compounds by Mass Spectrometry Imaging.

Hamm GR, Bäckström E, Brülls M, ..., Fridén M, Goodwin RJA

J Aerosol Med Pulm Drug Deliv - (-) - [2019-07-31; online 2019-07-31]

National Resource for Mass Spectrometry Imaging [Service]

Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.

Imgenberg-Kreuz J, Almlöf JC, Leonard D, ..., Sandling JK, Nordmark G

pmc

Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

pmc

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]

Multiplex plasma protein profiling identifies novel markers to discriminate patients with adenocarcinoma of the lung.

Djureinovic D, Pontén V, Landelius P, ..., Micke P, Ståhle E

pmc

BMC Cancer 19 (1) 741 [2019-07-29; online 2019-07-29]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

Combinations of Spok genes create multiple meiotic drivers in Podospora.

Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H

pmc Dryad

Elife 8 (-) - [2019-07-26; online 2019-07-26]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Estrogen deprivation triggers an immunosuppressive phenotype in breast cancer cells

Hühn D, Martí-Rodrigo P, Mouron S, ..., Carreras-Puigvert J, Fernandez-Capetillo O

- - (-) - [2019-07-25; online 2019-07-25]

Chemical Biology Consortium Sweden (CBCS) [Service]

Analysis of the behaviour of confined molecules using 2H T1 nuclear magnetic relaxation dispersion

Shamshir A, Sparrman T, Westlund PO

Molecular Physics - (-) 1-10 [2019-07-24; online 2019-07-24]

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

pmc

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]

Annotations, Ontologies, and Whole Slide Images - Development of an Annotated Ontology-Driven Whole Slide Image Library of Normal and Abnormal Human Tissue.

Lindman K, Rose JF, Lindvall M, Lundström C, Treanor D

pmc

J Pathol Inform 10 (-) 22 [2019-07-23; online 2019-07-23]

AIDA Data Hub [Collaborative]

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]

α-synuclein-lipoprotein interactions and elevated ApoE level in cerebrospinal fluid from Parkinson's disease patients.

Paslawski W, Zareba-Paslawska J, Zhang X, ..., Andrén PE, Svenningsson P

pmc

Proc. Natl. Acad. Sci. U.S.A. 116 (30) 15226-15235 [2019-07-23; online 2019-07-03]

National Resource for Mass Spectrometry Imaging [Service]

Vitamin D and Phenylbutyrate Supplementation Does Not Modulate Gut Derived Immune Activation in HIV-1

Missailidis C, Sørensen N, Ashenafi S, ..., Brighenti S, Bergman P

Nutrients 11 (7) 1675 [2019-07-21; online 2019-07-21]

Evolved for success in novel environments: The round goby genome

Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S

- - (-) - [2019-07-19; online 2019-07-19]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Anti‐tumor effects of PIM / PI 3K/ mTOR triple kinase inhibitor IBL ‐302 in neuroblastoma

Mohlin S, Hansson K, Radke K, ..., Stedingk K, Bexell D

EMBO Mol Med - (-) - [2019-07-16; online 2019-07-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation.

Miller DSJ, Schmierer B, Hill CS

pmc

J. Cell. Sci. 132 (14) - [2019-07-15; online 2019-07-15]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]

Post‐metaphase correction of aberrant kinetochore‐microtubule attachments in mammalian eggs

Kouznetsova A, Kitajima TS, Brismar H, Höög C

EMBO rep - (-) - [2019-07-10; online 2019-07-10]

Advanced Light Microscopy (ALM) [Collaborative]

Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations.

Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM

Mol. Biol. Evol. - (-) - [2019-07-09; online 2019-07-09]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak

Bikkarolla SK, Nordberg V, Rajer F, ..., Sandegren L, Westerlund F

MBio 10 (4) - [2019-07-09; online 2019-07-09]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Systems-level immunomonitoring using self-sampled capillary blood

Josyula VS, Lakshmikanth T, Mikes J, Chen Y, Brodin P

- - (-) - [2019-07-08; online 2019-07-08]

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]

GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files

Wik E, Olin H, Haughey C, Klasson L, Dainat J

JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.

Ranade SS, Delhomme N, García-Gil MR

pmc

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]

Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.

Edfors F, Forsström B, Vunk H, ..., Schwenk JM, Uhlen M

J. Proteome Res. 18 (7) 2706-2718 [2019-07-05; online 2019-06-07]

Plasma Profiling [Technology development]

Seeking the ultimate challenge.

Brodin P

Nat Med - (-) - [2019-07-03; online 2019-07-03]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.

Christel S, Yu C, Wu X, ..., Åström ME, Dopson M

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]

Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification

Pértille F, Da Silva VH, Johansson AM, ..., Jensen P, Guerrero-Bosagna C

Epigenetics 14 (7) 685-707 [2019-07-03; online 2019-05-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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]

Serum metabolite profiles of habitual diet: evaluation by 1H-nuclear magnetic resonance analysis

Lindqvist HM, Rådjursöga M, Malmodin D, Winkvist A, Ellegård L

Am J Clin Nutr 110 (1) 53-62 [2019-07-01; online 2019-05-25]

Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis.

Naegeli A, Bratanis E, Karlsson C, ..., Malmström J, Collin M

pmc

J. Exp. Med. 216 (7) 1615-1629 [2019-07-01; online 2019-05-15]

Androgen Receptor Burden and Poor Response to Abiraterone or Enzalutamide in TP53 Wild-Type Metastatic Castration-Resistant Prostate Cancer.

De Laere B, Rajan P, Grönberg H, ..., Lindberg J, CORE-ARV-CTC and ProBIO Investigators

pmc

JAMA Oncol 5 (7) 1060-1062 [2019-07-01; online 2019-05-03]

Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.

Sen BC, Wasserstrom S, Findlay K, ..., von Wachenfeldt C, Flärdh K

Mol Microbiol 112 (1) 184-198 [2019-07-00; online 2019-05-17]

Biochemical Imaging Centre Umeå [Service] Cryo-EM [Collaborative]

Epigenome-wide association study of lung function level and its change.

Imboden M, Wielscher M, Rezwan FI, ..., Jarvis D, Probst-Hensch NM

pmc

Eur. Respir. J. 54 (1) - [2019-07-00; online 2019-07-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

1H NMR profiling of the 6-OHDA parkinsonian rat brain reveals metabolic alterations and signs of recovery after N-acetylcysteine treatment

Virel A, Dudka I, Laterveer R, af Bjerkén S

Molecular and Cellular Neuroscience 98 (-) 131-139 [2019-07-00; online 2019-07-00]

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon.

Martijn J, Lind AE, Schön ME, ..., Pettersson OV, Ettema TJG

Environ. Microbiol. 21 (7) 2485-2498 [2019-07-00; online 2019-05-07]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.

Andersson A, Remnestål J, Nellgård B, ..., Nilsson P, Fredolini C

Clin. Chim. Acta 494 (-) 79-93 [2019-07-00; online 2019-03-09]

Plasma Profiling [Technology development]

Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments.

Clewemar P, Hailer NP, Hailer Y, ..., Ljunggren Ö, Stattin EL

pmc

Mol Genet Genomic Med 7 (7) e00723 [2019-07-00; online 2019-05-16]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The autoimmune targets in IPEX are dominated by gut epithelial proteins

Eriksson D, Bacchetta R, Gunnarsson HI, ..., Kämpe O, Landegren N

Journal of Allergy and Clinical Immunology 144 (1) 327-330.e8 [2019-07-00; online 2019-07-00]

Autoimmunity Profiling [Service]

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]

The molecular pathogenesis of superoxide dismutase 1-linked ALS is promoted by low oxygen tension

Keskin I, Forsgren E, Lehmann M, ..., Marklund SL, Gilthorpe JD

Acta Neuropathol 138 (1) 85-101 [2019-07-00; online 2019-03-12]

OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis

Wang W, Zhang X, Niittylä T

Plant Cell 31 (7) 1446-1465 [2019-07-00; online 2019-04-25]

Biochemical Imaging Centre Umeå [Service] Cryo-EM [Service]

Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain

Bigalke JM, Aibara S, Roth R, ..., Amunts A, Sandmark J

Sci Adv 5 (7) eaau4202 [2019-07-00; online 2019-07-31]

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS G13D mutation.

Charitou T, Srihari S, Lynn MA, ..., Kolch W, Lynn DJ

pmc

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]

Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.

Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL

J Psychiatr Res 114 (-) 41-47 [2019-07-00; online 2019-04-02]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis

Laraia L, Friese A, Corkery DP, ..., Wu YW, Waldmann H

Nat Chem Biol 15 (7) 710-720 [2019-07-00; online 2019-06-20]

<p>Investigation of psoriasis skin tissue by label-free multi-modal imaging: a case study on a phototherapy-treated patient</p>

Agarwal NR, Dowlatshahi Pour M, Vandikas MS, ..., Osmancevic A, Malmberg P

PTT Volume 9 (-) 43-57 [2019-07-00; online 2019-07-00]

Gothenburg Imaging Mass Spectrometry [Collaborative]

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]

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]

Transcriptome analysis of shade avoidance and shade tolerance in conifers.

Ranade SS, Delhomme N, García-Gil MR

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]

TRAF6 function as a novel co-regulator of Wnt3a target genes in prostate cancer

Aripaka K, Gudey SK, Zang G, ..., von Hofsten J, Landström M

EBioMedicine 45 (-) 192-207 [2019-07-00; online 2019-07-00]

PLA and Single Cell Proteomics [Service]

BACH1 Stabilization by Antioxidants Stimulates Lung Cancer Metastasis

Wiel C, Le Gal K, Ibrahim MX, ..., Sayin VI, Bergo MO

Cell 178 (2) 330-345.e22 [2019-07-00; online 2019-07-00]

Choroid plexus transcriptome and ultrastructure analysis reveals a TLR2-specific chemotaxis signature and cytoskeleton remodeling in leukocyte trafficking

Mottahedin A, Joakim Ek C, Truvé K, Hagberg H, Mallard C

Brain, Behavior, and Immunity 79 (-) 216-227 [2019-07-00; online 2019-07-00]

Surface activated polyethylene separator promoting Li+ ion transport in gel polymer electrolytes and cycling stability of Li-metal anode

Qiu Z, Shi L, Wang Z, ..., Zhao Y, Yuan S

Chemical Engineering Journal 368 (-) 321-330 [2019-07-00; online 2019-07-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes.

Pujol-Moix N, Martinez-Perez A, Sabater-Lleal M, ..., Souto JC, Soria JM

Int J Mol Sci 20 (13) - [2019-06-30; online 2019-06-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Insights into the Exfoliation Process of V2O5·nH2O Nanosheet Formation Using Real-Time 51V NMR

Etman AS, Pell AJ, Svedlindh P, ..., Sun J, Bernin D

ACS Omega 4 (6) 10899-10905 [2019-06-30; online 2019-06-24]

Allelic Variation in Taste Genes Is Associated with Taste and Diet Preferences and Dental Caries.

Eriksson L, Esberg A, Haworth S, Holgerson PL, Johansson I

pmc

Nutrients 11 (7) - [2019-06-29; online 2019-06-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.

Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A

pmc

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]

Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.

Landegren N, Rosen LB, Freyhult E, ..., Anderson M, Kämpe O

pmc

Elife 8 (-) - [2019-06-27; online 2019-06-27]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication

Yau WL, Nguyen-Dinh V, Larsson E, ..., Överby AK, Lundmark R

J Virol 93 (18) - [2019-06-26; online 2019-08-28]

Biochemical Imaging Centre Umeå [Collaborative] Bioinformatics Compute and Storage [Service] Cryo-EM [Service]

Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.

Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE

PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.

Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B

pmc

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]

Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.

Shungin D, Haworth S, Divaris K, ..., Timpson NJ, Johansson I

pmc

Nat Commun 10 (1) 2773 [2019-06-24; online 2019-06-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.

Happonen L, Hauri S, Svensson Birkedal G, ..., Malmström L, Malmström J

pmc

Nat Commun 10 (1) 2727 [2019-06-21; online 2019-06-21]

Targeted and Structural Proteomics [Technology development]

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

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]

Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations

Papathanou M, Björklund ÅK, Martis-Thiele MM, Wallén-Mackenzie Å

- - (-) - [2019-06-20; online 2019-06-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B

Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Correlative STED super-resolution light and electron microscopy on resin sections

Wurm CA, Schwarz H, Jans DC, ..., Humbel B, Jakobs S

J. Phys. D: Appl. Phys. - (-) - [2019-06-19; online 2019-06-19]

Advanced Light Microscopy (ALM) [Technology development]

Peptide-Loaded Cubosomes Functioning as an Antimicrobial Unit against Escherichia coli

Boge L, Browning KL, Nordström R, ..., Ringstad L, Andersson M

ACS Appl. Mater. Interfaces 11 (24) 21314-21322 [2019-06-19; online 2019-05-23]

A Call for Blood-In Human Immunology.

Brodin P, Duffy D, Quintana-Murci L

Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes

Bomkamp C, Tripathy SJ, Bengtsson Gonzales C, ..., Craig AM, Pavlidis P

PLoS Comput. Biol. 15 (6) e1007113 [2019-06-18; online 2019-06-18]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival

Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A

The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J

PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.

Smythe AB, Holovachov O, Kocot KM

pmc

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]

Modeling Motor Neuron Resilience in ALS Using Stem Cells.

Allodi I, Nijssen J, Benitez JA, ..., Kiehn O, Hedlund E

pmc

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]

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]

Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP‐1

Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, ..., Höglund J, Laurila A

Mol Ecol - (-) - [2019-06-07; online 2019-06-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM

pmc

Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]

Autoimmunity Profiling [Technology development] Bioinformatics Compute and Storage [Service] Plasma Profiling [Technology development] Proteogenomics [Technology development]

Dietary Pattern Specific Protein Biomarkers for Cardiovascular Disease: A Cross‐Sectional Study in 2 Independent Cohorts

Warensjö Lemming E, Byberg L, Stattin K, ..., Wolk A, Michaëlsson K

J Am Heart Assoc 8 (11) - [2019-06-04; online 2019-06-04]

Serum Metabolite Markers of Dementia Through Quantitative NMR Analysis: The Importance of Threonine-Linked Metabolic Pathways

Figueira J, Adolfsson R, Nordin Adolfsson A, Nyberg L, Öhman A

JAD 69 (3) 763-774 [2019-06-04; online 2019-06-04]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Staphylococcus aureus isolates from nares of orthopaedic patients in Sweden are mupirocin susceptible

Magnusson C, Stegger M, Hellmark B, Stenmark B, Söderquist B

Infectious Diseases 51 (6) 475-478 [2019-06-03; online 2019-04-15]

E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.

Anandapadamanaban M, Kyriakidis NC, Csizmók V, ..., Wahren-Herlenius M, Sunnerhagen M

J. Biol. Chem. - (-) - [2019-06-03; online 2019-06-03]

Protein Science Facility (PSF) [Collaborative]

Recombinant dermatan sulfate is a potent activator of heparin cofactor II-dependent inhibition of thrombin

Tykesson E, Maccarana M, Thorsson H, ..., Ellervik U, Westergren-Thorsson G

- 29 (6) 446-451 [2019-06-01; online 2019-04-23]

Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species

Baskaran P, Ekblad A, Soucémarianadin LN, ..., Schleucher J, Lindahl BD

FEMS Microbiol. Ecol. 95 (6) - [2019-06-01; online 2019-04-25]

Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011–16

Gianecini RA, Golparian D, Zittermann S, ..., Gonzalez V, None

- 74 (6) 1551-1559 [2019-06-01; online 2019-02-28]

Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions

de Vries PS, Brown MR, Bentley AR, ..., Rao DC, Morrison AC

Am. J. Epidemiol. 188 (6) 1033-1054 [2019-06-01; online 2019-01-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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 - (-) - [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]

Assembly mechanisms of the bacterial cytoskeletal protein FilP

Javadi A, Söderholm N, Olofsson A, Flärdh K, Sandblad L

Life Sci. Alliance 2 (3) e201800290 [2019-06-00; online 2019-06-26]

Cryo-EM [Collaborative]

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

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]

Can markers of biological age predict dependency in old age?

Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S

pmc

Biogerontology 20 (3) 321-329 [2019-06-00; online 2019-01-21]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.

Hill J, Rastas P, Hornett EA, ..., Nylin S, Wheat CW

pmc

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]

Alterations in the metabolism of phospholipids, bile acids and branched-chain amino acids predicts development of type 2 diabetes in black South African women: a prospective cohort study

Zeng Y, Mtintsilana A, Goedecke JH, ..., Olsson T, Chorell E

Metabolism 95 (-) 57-64 [2019-06-00; online 2019-06-00]

The effects of male social environment on sperm phenotype and genome integrity

Silva WTAF, Sáez‐Espinosa P, Torijo‐Boix S, ..., Gómez‐Torres MJ, Immler S

J Evol Biol 32 (6) 535-544 [2019-06-00; online 2019-03-25]

Circulating mast cell progenitors correlate with reduced lung function in allergic asthma

Salomonsson M, Malinovschi A, Kalm‐Stephens P, ..., Alving K, Hallgren J

Clin Exp Allergy 49 (6) 874-882 [2019-06-00; online 2019-06-03]

A catalog of genetic loci associated with kidney function from analyses of a million individuals

Wuttke M, None , Li Y, ..., Pattaro C, None

Nat Genet 51 (6) 957-972 [2019-06-00; online 2019-05-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

β-Mannosidosis caused by a novel homozygous intragenic inverted duplication in MANBA

Blomqvist M, Smeland MF, Lindgren J, ..., Riise Stensland HMF, Asin-Cayuela J

Cold Spring Harb Mol Case Stud 5 (3) a003954 [2019-06-00; online 2019-03-18]

Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Service]

DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures

Zhang H, Söderholm N, Sandblad L, Wiklund K, Andersson M

Microsc Microanal 25 (3) 711-719 [2019-06-00; online 2019-03-21]

Cryo-EM [Technology development]

A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.

Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M

pmc

EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] Glycoproteomics [Collaborative] PLA and Single Cell Proteomics [Technology development]

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.

Das J, Verma D, Gustafsson M, Lerm M

pmc

Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx

Awad W, Al-Eryani Y, Ekström S, Logan DT, von Wachenfeldt C

Structure 27 (6) 923-936.e6 [2019-06-00; online 2019-06-00]

Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.

Maffezzini C, Laine I, Dallabona C, ..., Wredenberg A, Wedell A

pmc

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]

Gene fusion involving the insulin‐like growth factor 1 receptor in an ALK ‐negative inflammatory myofibroblastic tumour

Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F

Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Bax to the future – A novel, high-yielding approach for purification and expression of full-length Bax protein for structural studies

Dingeldein APG, Lindberg MJ, Ådén J, ..., Stoll R, Gröbner G

Protein Expression and Purification 158 (-) 20-26 [2019-06-00; online 2019-06-00]

Toxic Activation of an AAA+ Protease by the Antibacterial Drug Cyclomarin A

Maurer M, Linder D, Franke KB, ..., Bukau B, Mogk A

Cell Chem Biol - (-) - [2019-06-00; online 2019-06-00]

Lipopolysaccharide‐induced alteration of mitochondrial morphology induces a metabolic shift in microglia modulating the inflammatory response in vitro and in vivo

Nair S, Sobotka KS, Joshi P, ..., Mallard C, Hagberg H

Glia 67 (6) 1047-1061 [2019-06-00; online 2019-01-13]

Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time

Klemm AH, Thomae AW, Wachal K, Dietzel S

Microsc Microanal 25 (3) 699-704 [2019-06-00; online 2019-02-06]

BioImage Informatics [Technology development]

Somatic alterations detected in diagnostic prostate biopsies provide an inadequate representation of multifocal prostate cancer.

Kristiansen A, Bergström R, Delahunt B, ..., Egevad L, Lindberg J

Prostate 79 (8) 920-928 [2019-06-00; online 2019-03-25]

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers

Nadachowska‐Brzyska K, Burri R, Ellegren H

Mol Ecol 28 (9) 2290-2304 [2019-05-29; online 2019-05-29]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.

Bedri SK, Nilsson OB, Fink K, ..., Grönlund H, Glaser A

pmc

PLoS ONE 14 (5) e0217208 [2019-05-29; online 2019-05-29]

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing

Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y

PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]

Clinical Genomics Lund [Service]

The viral protein corona directs viral pathogenesis and amyloid aggregation.

Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S

pmc

Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]

Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs

Scaletti E, Jemth A, Helleday T, Stenmark P

FEBS Lett - (-) - [2019-05-25; online 2019-05-25]

Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.

Di Martino ML, Ek V, Hardt WD, Eriksson J, Sellin ME

pmc

MBio 10 (3) - [2019-05-21; online 2019-05-21]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Crystal structure of the catalytic domain of the Weissela oryzae botulinum-like toxin

Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P

FEBS Lett - (-) - [2019-05-20; online 2019-05-20]

Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]

Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients

Idborg H, Zandian A, Ossipova E, ..., Svenungsson E, Jakobsson PJ

Front Immunol 10 (-) - [2019-05-17; online 2019-05-17]

Drug Discovery and Development (DDD) [Collaborative] Plasma Profiling [Collaborative]

Distinct glycosylation in membrane proteins within neonatal versus adult myocardial tissue.

Contessotto P, Ellis BW, Jin C, ..., Kilcoyne M, Pandit A

Matrix Biol. - (-) - [2019-05-17; online 2019-05-17]

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

pmc Dryad

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]

Metabolic profiling of zebrafish embryo development from blastula period to early larval stages

Dhillon SS, Torell F, Donten M, ..., Trygg J, Lundstedt T

PLoS ONE 14 (5) e0213661 [2019-05-14; online 2019-05-14]

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

pmc

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]

Protic Ionic Liquids Based on the Alkyl-Imidazolium Cation: Effect of the Alkyl Chain Length on Structure and Dynamics

Abdurrokhman I, Elamin K, Danyliv O, ..., Swenson J, Martinelli A

J. Phys. Chem. B 123 (18) 4044-4054 [2019-05-09; online 2019-04-17]

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.

Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T

pmc

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]

Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.

Nicoletti P, Barrett S, McEvoy L, ..., Alfirevic A, Pirmohamed M

Clin. Pharmacol. Ther. - (-) - [2019-05-07; online 2019-05-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetical Genomics of Tonic Immobility in the Chicken.

Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D

Genes 10 (5) - [2019-05-07; online 2019-05-07]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mass Cytometry Identifies Distinct Subsets of Regulatory T Cells and Natural Killer Cells Associated With High Risk for Type 1 Diabetes.

Barcenilla H, Åkerman L, Pihl M, Ludvigsson J, Casas R

pmc

Front Immunol 10 (-) 982 [2019-05-03; online 2019-05-03]

Mass Cytometry [Service]

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.

Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA

pmc

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]

SpotLight Proteomics—A IgG-Enrichment Phenotype Profiling Approach with Clinical Implications

Lundström SL, Heyder T, Wiklundh E, ..., Grunewald J, Zubarev RA

Int J Mol Sci 20 (9) 2157 [2019-05-01; online 2019-05-01]

Software engineering for scientific big data analysis

Grüning BA, Lampa S, Vaudel M, Blankenberg D

Gigascience 8 (5) - [2019-05-01; online 2019-05-23]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.

Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M

pmc

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]

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

pmc

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]

Prompt apoptotic response to high glucose in SGLT-expressing renal cells

Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A

American Journal of Physiology-Renal Physiology 316 (5) F1078-F1089 [2019-05-01; online 2019-05-01]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service]

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Lampa S, Dahlö M, Alvarsson J, Spjuth O

Gigascience 8 (5) - [2019-05-01; online 2019-04-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Identification of a non-canonical chondroitin sulfate linkage region trisaccharide.

Persson A, Nilsson J, Vorontsov E, Noborn F, Larson G

Glycobiology 29 (5) 366-371 [2019-05-01; online 2019-03-03]

Helicobacter suis infection alters glycosylation and decreases the pathogen growth inhibiting effect and binding avidity of gastric mucins.

Padra M, Adamczyk B, Flahou B, ..., Karlsson NG, Lindén SK

Mucosal Immunol 12 (3) 784-794 [2019-05-00; online 2019-03-07]

Elevated circulating effector memory T cells but similar levels of regulatory T cells in patients with type 2 diabetes mellitus and cardiovascular disease

Rattik S, Engelbertsen D, Wigren M, ..., Nilsson J, Björkbacka H

Diabetes and Vascular Disease Research 16 (3) 270-280 [2019-05-00; online 2018-12-21]

GM1 locates to mature amyloid structures implicating a prominent role for glycolipid-protein interactions in Alzheimer pathology

Michno W, Wehrli PM, Zetterberg H, Blennow K, Hanrieder J

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1867 (5) 458-467 [2019-05-00; online 2019-05-00]

Gothenburg Imaging Mass Spectrometry [Service]

Interferon signature in patients with STAT1 gain‐of‐function mutation is epigenetically determined

Kaleviste E, Saare M, Leahy TR, ..., Peterson P, Kisand K

Eur. J. Immunol. 49 (5) 790-800 [2019-05-00; online 2019-03-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Axonemal doublet microtubules can split into two complete singlets in human sperm flagellum tips

Zabeo D, Croft JT, Höög JL

FEBS Lett 593 (9) 892-902 [2019-05-00; online 2019-04-19]

Molecular orientation distribution of regenerated cellulose fibers investigated with rotor synchronized solid state NMR spectroscopy

Svenningsson L, Sparrman T, Bialik E, Bernin D, Nordstierna L

Cellulose 26 (8) 4681-4692 [2019-05-00; online 2019-04-17]

Pervasive hybridizations in the history of wheat relatives.

Glémin S, Scornavacca C, Dainat J, ..., David J, Ranwez V

pmc

Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Investigation of human apoB48 metabolism using a new, integrated non-steady-state model of apoB48 and apoB100 kinetics.

Björnson E, Packard CJ, Adiels M, ..., Taskinen MR, Borén J

pmc

J. Intern. Med. 285 (5) 562-577 [2019-05-00; online 2019-03-12]

Comparisons of analysis of fatty acid methyl ester (FAME) of microalgae by chromatographic techniques

Niemi C, Lage S, Gentili FG

Algal Research 39 (-) 101449 [2019-05-00; online 2019-05-00]

How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers

Rettelbach A, Nater A, Ellegren H

Genetics 212 (1) 277-285 [2019-05-00; online 2019-03-14]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mineralogical investigations of Jamaican hematite-rich and goethite-rich bauxites using XRD and solid state 27Al and 31P MAS NMR spectroscopy

Young NJ, Coley MD, Greenaway AM

Journal of Geochemical Exploration 200 (-) 54-76 [2019-05-00; online 2019-05-00]

Interannual variation in seasonal diatom sedimentation reveals the importance of late winter processes and their timing for sediment signal formation

Maier DB, Diehl S, Bigler C

Limnol Oceanogr 64 (3) 1186-1199 [2019-05-00; online 2019-01-31]

An Atlas of Vagal Sensory Neurons and Their Molecular Specialization

Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P

Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]

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]

FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex.

Lindén M, Thomsen C, Grundevik P, ..., Ståhlberg A, Åman P

pmc

EMBO Rep. 20 (5) - [2019-05-00; online 2019-04-08]

Imaging of vitamin D in psoriatic skin using time-of-flight secondary ion mass spectrometry (ToF-SIMS): A pilot case study

Siekkeri Vandikas M, Hellström E, Malmberg P, Osmancevic A

The Journal of Steroid Biochemistry and Molecular Biology 189 (-) 154-160 [2019-05-00; online 2019-05-00]

Gothenburg Imaging Mass Spectrometry [Collaborative]

Spatial proteomics: a powerful discovery tool for cell biology

Lundberg E, Borner GHH

Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-18]

Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]

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]

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]

PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model

Zang G, Mu Y, Gao L, Bergh A, Landström M

Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Endocytosis, intracellular fate, accumulation, and agglomeration of titanium dioxide (TiO2) nanoparticles in the rainbow trout liver cell line RTL-W1

Lammel T, Mackevica A, Johansson BR, Sturve J

Environ Sci Pollut Res 26 (15) 15354-15372 [2019-05-00; online 2019-03-31]

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q

Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dynamic pH‐induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen

Carius AB, Rogne P, Duchoslav M, ..., Samuelsson G, Shutova T

Physiol Plantarum 166 (1) 288-299 [2019-05-00; online 2019-03-18]

AdipoR1 and AdipoR2 maintain membrane fluidity in most human cell types and independently of adiponectin

Ruiz M, Ståhlman M, Borén J, Pilon M

J. Lipid Res. 60 (5) 995-1004 [2019-05-00; online 2019-03-19]