Publications 2020

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]

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]

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]

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]

The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.

Yañez O, Chávez-Galarza J, Tellgren-Roth C, ..., Neumann P, de Miranda JR

pmc

Sci Rep 10 (1) 5956 [2020-04-06; online 2020-04-06]

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

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]

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]

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

José Miguel de la Rosa-Trevín PAHVJOaEL

Acta Crystallographica Section D (v. 76 pp. 350–356) - (-) - [2020-04-01]

Cryo-EM [Technology development]

Substantial intrinsic variability in chemoradiosensitivity of newly established anaplastic thyroid cancer cell-lines.

Gretarsson S, Nygren A, Rosendahl AH, ..., Wennerberg J, Ekblad L

Acta Otolaryngol. 140 (4) 337-343 [2020-04-00; online 2020-01-10]

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

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]

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

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]

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]

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]

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]

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]

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 6 (3) 314-320 [2020-03-09; online 2020-03-09]

Cryo-EM [Service] Proteogenomics [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]

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]

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]

Protein Science Facility (PSF) [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]

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]

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]

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]

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

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

NPLANTS 6 (3) 321-327 [2020-03-02; online 2020-03-02]

Cryo-EM [Service]

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 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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

Protein Science Facility (PSF) [Service]

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]

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]

New approaches to the study of immune responses in humans

Brodin P

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

Mass Cytometry [Technology development]

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]

Cryo-EM [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]

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]

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]

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]

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]

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]

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]

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B

F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]

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

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]

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]

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]

Biochemical Imaging Centre Umeå [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]

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]

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]

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]

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]

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]

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]

Glycoproteomics [Collaborative]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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

Biochemical Imaging Centre Umeå [Service]

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]

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]

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]

Swedish Metabolomics Centre (SMC) [Service]

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]

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]

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants

Sullivan AR, Eldfjell Y, Schiffthaler B, ..., Street NR, Wang XR

Genome Biol Evol 12 (1) 3586-3598 [2020-01-01; online 2019-11-27]

NGI Uppsala (Uppsala Genome Center) [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]

Targeted and Structural Proteomics [Collaborative]

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]

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]

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]

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]

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]

Swedish NMR Centre (SNC) [Service]

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]

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]

Swedish NMR Centre (SNC) [Service]

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]

Clinical Biomarkers [Service]

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]

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]

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]

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]

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]

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]

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]

Glycoproteomics [Collaborative]

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]

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]

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]

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]

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]

Swedish NMR Centre (SNC) [Service]

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]

Swedish Metabolomics Centre (SMC) [Service]

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]

In-plate toxicometabolomics of single zebrafish embryos

Ribbenstedt A, Posselt M, Brunius C, Benskin JP

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