Bioinformatics Compute and Storage

Do different growth rates of trees cause distinct habitat qualities for saproxylic assemblages?

Runnel K, Stephan JG, Jonsell M, ..., Tamm H, Ranius T

Oecologia 197 (3) 807-816 [2021-11-00; online 2021-10-17]

Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.

Öhlund P, Hayer J, Hesson JC, Blomström AL

Viruses 13 (11) - [2021-10-29; online 2021-10-29]

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

Microbial Plankton Community Structure and Function Responses to Vitamin B12 and B1 Amendments in an Upwelling System.

Joglar V, Pontiller B, Martínez-García S, ..., Fernández E, Teira E

Appl. Environ. Microbiol. 87 (22) e0152521 [2021-10-28; online 2021-09-08]

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

Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.

Wallander K, Thonberg H, Nilsson D, Tham E

Hered Cancer Clin Pract 19 (1) 46 [2021-10-28; online 2021-10-28]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.

Iburg S, Izabel-Shen D, Austin ÅN, ..., Eklöf JS, Nascimento FJA

mSphere 6 (5) e0012721 [2021-10-27; online 2021-09-01]

Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).

Rendón-Anaya M, Wilson J, Sveinsson S, ..., Street NR, Ingvarsson PK

Mol. Biol. Evol. 38 (11) 5034-5050 [2021-10-27; online 2021-07-31]

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

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.

Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L

Mol. Ecol. - (-) - [2021-10-26; online 2021-10-26]

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]

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.

Brealey JC, Leitão HG, Hofstede T, Kalthoff DC, Guschanski K

Curr. Biol. 31 (20) 4650-4658.e6 [2021-10-25; online 2021-08-25]

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

Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8.

Paulsson JO, Rafati N, DiLorenzo S, ..., Zedenius J, Juhlin CC

J. Clin. Endocrinol. Metab. 106 (11) 3265-3282 [2021-10-21; online 2021-06-26]

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

Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.

Tang Q, Burri R, Liu Y, ..., Heckel G, Schweizer M

Mol. Ecol. - (-) - [2021-10-21; online 2021-10-21]

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

Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.

Brouwer SM, Brus-Szkalej M, Saripella GV, ..., Liljeroth E, Grenville-Briggs LJ

Plants (Basel) 10 (10) - [2021-10-18; online 2021-10-18]

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

Frailty and the risk of dementia: is the association explained by shared environmental and genetic factors?

Bai G, Wang Y, Kuja-Halkola R, ..., Hägg S, Jylhävä J

BMC Med 19 (1) 248 [2021-10-18; online 2021-10-18]

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

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.

Andersson A, Larsson L, Stenbeck L, ..., Engblom C, Lundeberg J

Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]

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

Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.

Li J, Lee MO, Chen J, ..., Chuong CM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (41) - [2021-10-12; online 2021-10-06]

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

Philippine Ayta possess the highest level of Denisovan ancestry in the world.

Larena M, McKenna J, Sanchez-Quinto F, ..., Endicott P, Jakobsson M

Curr. Biol. 31 (19) 4219-4230.e10 [2021-10-11; online 2021-08-12]

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

HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.

Chatzittofis A, Boström ADE, Ciuculete DM, ..., Schiöth HB, Jokinen J

Sci Rep 11 (1) 20134 [2021-10-11; online 2021-10-11]

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

Comparison of sequencing data processing pipelines and application to underrepresented African human populations.

Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M

BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]

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

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery.

Hakim R, Zachariadis V, Sankavaram SR, ..., Enge M, Svensson M

J. Neurosci. 41 (40) 8441-8459 [2021-10-06; online 2021-08-20]

Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.

Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S

BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]

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

Spatiotemporally flexible subnetworks reveal the quasi-cyclic nature of integration and segregation in the human brain.

Strindberg M, Fransson P, Cabral J, Ådén U

Neuroimage 239 (-) 118287 [2021-10-01; online 2021-06-18]

Bioaugmentation as a strategy for tailor-made volatile fatty acid production.

Atasoy M, Cetecioglu Z

J Environ Manage 295 (-) 113093 [2021-10-01; online 2021-06-23]

The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.

Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J

Sci Adv 7 (40) eabh4390 [2021-10-00; online 2021-10-01]

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

Serum 25-hydroxyvitamin D is associated with fracture risk only during periods of seasonally high levels in women with a high body mass index.

Michaëlsson K, Byberg L, Svennblad B, ..., Baron JA, Melhus H

J. Bone Miner. Res. 36 (10) 1957-1966 [2021-10-00; online 2021-07-10]

Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance.

Kaufmann P, Wolak ME, Husby A, Immonen E

Nat Ecol Evol 5 (10) 1394-1402 [2021-10-00; online 2021-08-19]

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

Amiel Castro R, Kunovac Kallak T, Sundström Poromaa I, ..., Ehlert U, Skalkidou A

Psychoneuroendocrinology 132 (-) 105361 [2021-10-00; online 2021-07-17]

Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

Twort VG, Minet J, Wheat CW, Wahlberg N

Systematic Entomology 46 (4) 926-937 [2021-10-00; online 2021-07-08]

Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.

Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M

Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]

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]

High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.

Hammarsjö A, Pettersson M, Chitayat D, ..., Lindstrand A, Grigelioniene G

J. Hum. Genet. 66 (10) 995-1008 [2021-10-00; online 2021-04-20]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.

Sundbaum JK, Baecklund E, Eriksson N, ..., Wadelius M, Hallberg P

Pharmacogenomics 22 (15) 973-982 [2021-10-00; online 2021-09-15]

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

Ecologically coherent population structure of uncultivated bacterioplankton.

Sjöqvist C, Delgado LF, Alneberg J, Andersson AF

ISME J 15 (10) 3034-3049 [2021-10-00; online 2021-05-05]

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

DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha.

Lagercrantz U, Billhardt A, Rousku SN, ..., Reza SH, Eklund DM

New Phytol. 232 (2) 595-609 [2021-10-00; online 2021-08-19]

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

In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A

Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]

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

Composition and Seasonality of Membrane Transporters in Marine Picoplankton.

Hagström Å, Zweifel UL, Sundh J, ..., Müller-Karulis B, Pinhassi J

Front Microbiol 12 (-) 714732 [2021-09-28; online 2021-09-28]

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]

Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.

Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E

Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]

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

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.

Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K

Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]

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

Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.

Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B

Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]

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

Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.

Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N

J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]

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

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP

Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]

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

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.

Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T

Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]

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

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.

Sandholt AKS, Wattrang E, Lilja T, ..., Svärd SG, Söderlund R

BMC Genomics 22 (1) 660 [2021-09-14; online 2021-09-14]

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

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.

Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]

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]

A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.

Powell D, Groβe-Wilde E, Krokene P, ..., Andersson MN, Schlyter F

Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]

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

Selection on accessible chromatin regions in Capsella grandiflora.

Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T

Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]

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

Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.

Bedoya-Reina OC, Li W, Arceo M, ..., Kogner P, Schlisio S

Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]

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]

Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.

Zhao Y, Lindberg BG, Esfahani SS, ..., Piazza S, Engström Y

BMC Biol. 19 (1) 185 [2021-09-03; online 2021-09-03]

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

Anorexia and Fat Aversion Induced by Vertical Sleeve Gastrectomy Is Attenuated in Neurotensin Receptor 1-Deficient Mice.

Ratner C, Shin JH, Dwibedi C, ..., Seeley RJ, Holst B

Endocrinology 162 (9) - [2021-09-01; online 2021-07-01]

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.

Xiao W, Ren L, Chen Z, ..., Wang C, Shi L

Nat. Biotechnol. 39 (9) 1141-1150 [2021-09-00; online 2021-09-09]

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

The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.

Axelsson E, Ljungvall I, Bhoumik P, ..., Häggström J, Lindblad-Toh K

PLoS Genet. 17 (9) e1009726 [2021-09-00; online 2021-09-02]

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

Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.

Chase MA, Ellegren H, Mugal CF

Evolution 75 (9) 2179-2196 [2021-09-00; online 2021-05-03]

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]

Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.

Reid S, Hagberg N, Sandling JK, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. 80 (9) 1183-1189 [2021-09-00; online 2021-03-25]

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

Genomic and transcriptomic characterization of desmoplastic small round cell tumors.

Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F

Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]

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

Drought legacy affects microbial community trait distributions related to moisture along a savannah grassland precipitation gradient

Leizeaga A, Hicks LC, Manoharan L, Hawkes CV, Rousk J

J Ecol 109 (9) 3195-3210 [2021-09-00; online 2020-11-26]

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

Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak.

Faticov M, Abdelfattah A, Roslin T, ..., Lindahl BD, Tack AJM

New Phytol. 231 (5) 1770-1783 [2021-09-00; online 2021-06-18]

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

Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.

Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E

International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]

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]

Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.

Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB

Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]

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

Amnion signals are essential for mesoderm formation in primates.

Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR

Nat Commun 12 (1) 5126 [2021-08-26; online 2021-08-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.

Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A

J Leukoc Biol - (-) - [2021-08-25; online 2021-08-25]

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

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.

Mahboubi A, Delhomme N, Häggström S, Hanson J

Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]

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

Transcriptomic markers of fungal growth, respiration and carbon-use efficiency.

Hasby FA, Barbi F, Manzoni S, Lindahl BD

FEMS Microbiol. Lett. 368 (15) - [2021-08-19; online 2021-08-03]

Community composition of aquatic fungi across the thawing Arctic.

Kluge M, Wurzbacher C, Wauthy M, ..., Stenlid J, Peura S

Sci Data 8 (1) 221 [2021-08-19; online 2021-08-19]

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

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.

Houtman M, Hesselberg E, Rönnblom L, ..., Malmström V, Padyukov L

Front Immunol 12 (-) 707217 [2021-08-17; online 2021-08-17]

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

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.

Singh A, Moestedt J, Berg A, Schnürer A

Front Microbiol 12 (-) 700256 [2021-08-16; online 2021-08-16]

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

Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.

Rahimi Y, Ingvarsson PK, Bihamta MR, ..., Taleei A, Khoshnoodi Jabar Abadi S

Front Plant Sci 12 (-) 710867 [2021-08-16; online 2021-08-16]

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

Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.

Lindholm Carlström E, Niazi A, Etemadikhah M, ..., Nilsson B, Feuk L

Genes 12 (8) - [2021-08-13; online 2021-08-13]

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

Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.

Ma J, Tibbitt CA, Georén SK, ..., Bachert C, Coquet JM

Sci Immunol 6 (62) - [2021-08-13; online 2021-08-15]

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]

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.

Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S

Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]

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

Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.

Bellenberg S, Salas B, Ganji S, ..., Dopson M, Vera M

Sci Rep 11 (1) 16275 [2021-08-11; online 2021-08-11]

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

Genome assemblies of three closely related leaf beetle species (Galerucella spp.).

Yang X, Slotte T, Dainat J, Hambäck PA

G3 (Bethesda) 11 (8) - [2021-08-07; online 2021-12-02]

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

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.

Sayyab S, Lundmark A, Larsson M, ..., Nordlund J, Syvänen A

Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]

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]

Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae.

Tellgren-Roth C, Thorell K, Galperin MY, ..., Sjöling Å, Martín-Rodríguez AJ

Microbiol Resour Announc 10 (31) e0055921 [2021-08-05; online 2021-08-05]

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

Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.

Natarajan K, Eisfeldt J, Hammond M, ..., Öijerstedt L, Graff C

Acta Neuropathol Commun 9 (1) 132 [2021-08-03; online 2021-08-03]

Affinity Proteomics Uppsala [Technology development] 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]

PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.

Seyfferth C, Wessels BA, Vahala J, ..., Tuominen H, Lundberg-Felten J

Cells 10 (8) 1971 [2021-08-03; online 2021-08-03]

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

Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.

Indukuri R, Jafferali MH, Song D, ..., Archer A, Williams C

Int. J. Cancer 149 (3) 692-706 [2021-08-01; online 2021-04-05]

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

The Babytwins Study Sweden (BATSS): A Multi-Method Infant Twin Study of Genetic and Environmental Factors Influencing Infant Brain and Behavioral Development.

Falck-Ytter T, Hamrefors L, Siqueiros Sanches M, ..., Tammimies K, Ronald A

Twin Res Hum Genet 24 (4) 217-227 [2021-08-00; online 2021-09-15]

Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).

Figueroa D, Capo E, Lindh MV, ..., Pinhassi J, Andersson A

Environ. Microbiol. 23 (8) 4200-4213 [2021-08-00; online 2021-06-01]

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

Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.

Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M

Mol Ecol Resour 21 (6) 1833-1849 [2021-08-00; online 2021-05-06]

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

Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).

Nadachowska-Brzyska K, Dutoit L, Smeds L, ..., Gustafsson L, Ellegren H

Mol. Ecol. 30 (16) 3965-3973 [2021-08-00; online 2021-07-01]

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

Founder effects facilitate the use of a genotyping-based approach to molecular diagnosis in Swedish patients with familial hypercholesterolaemia.

Benedek P, Jiao H, Duvefelt K, ..., Eriksson M, Angelin B

J. Intern. Med. 290 (2) 404-415 [2021-08-00; online 2021-05-06]

Dynamics of Baltic Sea phages driven by environmental changes.

Hoetzinger M, Nilsson E, Arabi R, ..., Middelboe M, Holmfeldt K

Environ. Microbiol. 23 (8) 4576-4594 [2021-08-00; online 2021-07-07]

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

Cystatin B-deficiency triggers ectopic histone H3 tail cleavage during neurogenesis.

Daura E, Tegelberg S, Yoshihara M, ..., Lehesjoki AE, Joensuu T

Neurobiol. Dis. 156 (-) 105418 [2021-08-00; online 2021-06-05]

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.

Christmas MJ, Jones JC, Olsson A, ..., Geib JC, Webster MT

Mol. Biol. Evol. 38 (8) 3126-3143 [2021-07-29; online 2021-04-07]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure

Complex population structure of the Atlantic puffin revealed by whole genome analyses.

Kersten O, Star B, Leigh DM, ..., Jakobsen KS, Boessenkool S

Commun Biol 4 (1) 922 [2021-07-29; online 2021-07-29]

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

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.

Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC

Elife 10 (-) - [2021-07-28; online 2021-07-28]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] Microbial Single Cell Genomics NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-scale metabolic network reconstruction of model animals as a platform for translational research.

Wang H, Robinson JL, Kocabas P, ..., Zetterberg H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 118 (30) e2102344118 [2021-07-27; online 2021-07-21]

Bioinformatics Compute and Storage [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Technology development]

Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.

Mattisson J, Danielsson M, Hammond M, ..., Halvardson J, Forsberg LA

Sci Rep 11 (1) 15160 [2021-07-26; online 2021-07-26]

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

Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.

Svensson E, Günther T, Hoischen A, ..., Netea MG, Jakobsson M

Curr. Biol. 31 (14) 2973-2983.e9 [2021-07-26; online 2021-05-18]

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

Bifidobacteria-mediated immune system imprinting early in life.

Henrick BM, Rodriguez L, Lakshmikanth T, ..., Frese SA, Brodin P

Cell 184 (15) 3884-3898.e11 [2021-07-22; online 2021-06-17]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A search for modifying genetic factors in CHEK2:c.1100delC breast cancer patients.

Wendt C, Muranen TA, Mielikäinen L, ..., Borg Å, Lindblom A

Sci Rep 11 (1) 14763 [2021-07-20; online 2021-07-20]

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

DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.

Imgenberg-Kreuz J, Sandling JK, Norheim KB, ..., Eloranta ML, Nordmark G

Front Immunol 12 (-) 702037 [2021-07-16; online 2021-07-16]

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

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.

Mehrshad M, Lopez-Fernandez M, Sundh J, ..., Bertilsson S, Dopson M

Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]

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]

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.

Calleja-Rodriguez A, Chen Z, Suontama M, Pan J, Wu HX

Front Plant Sci 12 (-) 666820 [2021-07-07; online 2021-07-07]

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

Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.

Kundu S, Ali MA, Handin N, ..., Globisch D, Sjöblom T

J. Exp. Clin. Cancer Res. 40 (1) 225 [2021-07-07; online 2021-07-07]

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

The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades.

Hiltunen M, Ament-Velásquez SL, Johannesson H

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-05-30]

High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.

Zhang L, Steward RA, Wheat CW, Reed RD

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-07-21]

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

Comparative Genomics Reveals Factors Associated with Phenotypic Expression of Wolbachia.

Baião GC, Janice J, Galinou M, Klasson L

Genome Biol Evol 13 (7) - [2021-07-06; online 2021-05-19]

Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.

Haas JC, Vergara A, Serrano AR, ..., Hurry V, Street NR

Tree Physiol 41 (7) 1230-1246 [2021-07-05; online 2021-01-09]

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

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.

Jensen A, Lillie M, Bergström K, Larsson P, Höglund J

Heredity (Edinb) 127 (1) 79-91 [2021-07-00; online 2021-05-07]

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

Variants in BANK1 are associated with lupus nephritis of European ancestry.

Bolin K, Imgenberg-Kreuz J, Leonard D, ..., Rönnblom L, Nordmark G

Genes Immun. 22 (3) 194-202 [2021-07-00; online 2021-06-14]

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

The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.

Bakovic V, Martin Cerezo ML, Höglund A, ..., Hargeby A, Wright D

Mol. Ecol. 30 (14) 3530-3547 [2021-07-00; online 2021-06-08]

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

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.

Bartosovic M, Kabbe M, Castelo-Branco G

Nat. Biotechnol. 39 (7) 825-835 [2021-07-00; online 2021-04-12]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.

Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA

Mol. Ecol. 30 (14) 3515-3529 [2021-07-00; online 2021-06-11]

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

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).

Bachmann JA, Tedder A, Fracassetti M, ..., Köhler C, Slotte T

Heredity (Edinb) 127 (1) 124-134 [2021-07-00; online 2021-04-19]

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]

Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.

Lepzien R, Liu S, Czarnewski P, ..., Grunewald J, Smed-Sörensen A

Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]

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

Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.

Veerman RE, Teeuwen L, Czarnewski P, ..., Gabrielsson S, Eldh M

J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development]

Mammuthus sp. (Early and Middle Pleistocene Mammoths).

Pečnerová P, Díez-Del-Molino D, van der Valk T, ..., Götherström A, Dalén L

Trends Genet. 37 (7) 682-683 [2021-07-00; online 2021-05-11]

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

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.

Broman E, Bonaglia S, Norkko A, Creer S, Nascimento FJA

Mol. Ecol. 30 (13) 3023-3039 [2021-07-00; online 2020-08-19]

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

Genomic signatures of rapid adaptive divergence in a tropical montane species.

Ericson PGP, Irestedt M, She H, Qu Y

Biol. Lett. 17 (7) 20210089 [2021-07-00; online 2021-07-28]

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

An ARHGAP25 variant links aberrant Rac1 function to early-onset skeletal fragility.

Mäkitie RE, Henning P, Jiu Y, ..., Lappalainen P, Mäkitie O

JBMR Plus 5 (7) e10509 [2021-07-00; online 2021-06-07]

A single-cell type transcriptomics map of human tissues.

Karlsson M, Zhang C, Méar L, ..., Uhlén M, Lindskog C

Sci Adv 7 (31) eabh2169 [2021-07-00; online 2021-07-28]

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

Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.

Bellenberg S, Turner S, Seidel L, ..., Leiviskä T, Dopson M

Front Microbiol 12 (-) 693615 [2021-06-30; online 2021-06-30]

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

DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.

Novotny A, Zamora-Terol S, Winder M

Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]

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

Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.

Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI

mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]

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

Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.

Bai X, Narayanan A, Nowak P, ..., Neogi U, Sönnerborg A

Front Microbiol 12 (-) 667718 [2021-06-25; online 2021-06-25]

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

Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.

Chen J, Bi H, Pettersson ME, ..., Scheerer P, Andersson L

Commun Biol 4 (1) 795 [2021-06-25; online 2021-06-25]

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

Toll-like receptor 4 methylation grade is linked to depressive symptom severity.

Rasmusson AJ, Gallwitz M, Soltanabadi B, ..., Schiöth HB, Cunningham JL

Transl Psychiatry 11 (1) 371 [2021-06-24; online 2021-06-24]

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

Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.

Singh A, Müller B, Schnürer A

Sci Rep 11 (1) 13298 [2021-06-24; online 2021-06-24]

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

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.

Simonetti M, Zhang N, Harbers L, ..., Ghisetti V, Crosetto N

Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]

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

Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.

Abu Hamdeh S, Ciuculete DM, Sarkisyan D, ..., Schiöth HB, Marklund N

J. Neurotrauma 38 (12) 1679-1688 [2021-06-15; online 2021-01-08]

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

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.

Chen ZQ, Zan Y, Milesi P, ..., Lascoux M, Wu HX

Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]

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

DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).

Krali O, Palle J, Bäcklin CL, ..., Zeller B, Nordlund J

Genes 12 (6) 895 [2021-06-10; online 2021-06-10]

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

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

Yaka R, Mapelli I, Kaptan D, ..., Özer F, Somel M

Curr. Biol. 31 (11) 2455-2468.e18 [2021-06-07; online 2021-04-14]

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

Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.

Karampelias C, Rezanejad H, Rosko M, ..., Korbutt GS, Andersson O

Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]

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

Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.

Friess L, Cheray M, Keane L, Grabert K, Joseph B

Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]

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

Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors.

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

Antiviral Res. 190 (-) 105074 [2021-06-00; online 2021-04-16]

Krzewińska M, Rodríguez-Varela R, Ahlström Arcini C, ..., Storå J, Götherström A

Journal of Archaeological Science: Reports 37 (-) 102939 [2021-06-00; online 2021-06-00]

Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.

Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Kular L

Mult. Scler. 27 (7) 1014-1026 [2021-06-00; online 2020-07-30]

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

Large-scale identification of protein histidine methylation in human cells.

Kapell S, Jakobsson ME

NAR Genom Bioinform 3 (2) lqab045 [2021-06-00; online 2021-05-22]

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

JAK/STAT inhibition augments soleus muscle function in a rat model of critical illness myopathy via regulation of complement C3/3R.

Addinsall AB, Cacciani N, Akkad H, ..., Kirkland JL, Larsson L

J Physiol 599 (11) 2869-2886 [2021-06-00; online 2021-05-02]

Genomic and fitness consequences of inbreeding in an endangered carnivore.

Hasselgren M, Dussex N, von Seth J, ..., Dalén L, Norén K

Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]

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

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.

Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A

Mar Biotechnol (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]

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

Deep immune profiling reveals targetable mechanisms of immune evasion in immune checkpoint inhibitor-refractory glioblastoma.

Simonds EF, Lu ED, Badillo O, ..., Weiss WA, Hellström M

J Immunother Cancer 9 (6) - [2021-06-00; online 2021-06-05]

Correction to: Deciphering the genetic and epidemiological landscape of mitochondrial DNA abundance.

Hägg S, Jylhävä J, Wang Y, Czene K, Grassmann F

Hum. Genet. 140 (6) 863 [2021-06-00; online 2021-02-07]

Combinations of dietary calcium intake and mediterranean-style diet on risk of hip fracture: A longitudinal cohort study of 82,000 women and men.

Warensjö Lemming E, Byberg L, Höijer J, ..., Wolk A, Michaëlsson K

Clin Nutr 40 (6) 4161-4170 [2021-06-00; online 2021-02-05]

Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.

Mold JE, Modolo L, Hård J, ..., Michaëlsson J, Frisén J

Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]

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

A combined approach for single-cell mRNA and intracellular protein expression analysis.

Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ

Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]

Affinity Proteomics Uppsala [Technology development] 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]

Stromal Heterogeneity in the Human Proliferative Endometrium-A Single-Cell RNA Sequencing Study.

Queckbörner S, von Grothusen C, Boggavarapu NR, ..., Davies LC, Gemzell-Danielsson K

J Pers Med 11 (6) - [2021-05-22; online 2021-05-22]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]

Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry.

de Miranda JR, Granberg F, Low M, ..., Jansson A, Berggren Å

Front Vet Sci 8 (-) 642085 [2021-05-20; online 2021-05-20]

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

Complement-Opsonized HIV Modulates Pathways Involved in Infection of Cervical Mucosal Tissues: A Transcriptomic and Proteomic Study.

Svanberg C, Ellegård R, Crisci E, ..., Shankar EM, Larsson M

Front Immunol 12 (-) 625649 [2021-05-20; online 2021-05-20]

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

Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.

Hartmann FE, Ament-Velásquez SL, Vogan AA, ..., Silar P, Giraud T

Mol. Biol. Evol. 38 (6) 2475-2492 [2021-05-19; online 2021-02-09]

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

X-chromosome variants are associated with aldosterone producing adenomas.

Dutta RK, Larsson M, Arnesen T, ..., Gimm O, Söderkvist P

Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18]

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

Phage Biocontrol of Pseudomonas aeruginosa in Water.

Kauppinen A, Siponen S, Pitkänen T, ..., Torvinen E, Miettinen IT

Viruses 13 (5) 928 [2021-05-17; online 2021-05-17]

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

Pulmonary fibrosis in relation to genetic loci in an inception cohort of patients with early rheumatoid arthritis from northern Sweden.

Jönsson E, Ljung L, Norrman E, ..., Dahlqvist J, Dahlqvist SR

Rheumatology (Oxford) - (-) - [2021-05-16; online 2021-05-16]

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

Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.

Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S

Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]

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

Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.

Salvà-Serra F, Donoso RA, Cho KH, ..., Moore ERB, Pérez-Pantoja D

Microbiol Resour Announc 10 (19) - [2021-05-13; online 2021-05-13]

Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.

Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S

mSystems 6 (3) - [2021-05-11; online 2021-05-11]

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

The Genomic Architecture and Evolutionary Fates of Supergenes.

Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-20]

The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.

Hollfelder N, Babiker H, Granehäll L, Schlebusch CM, Jakobsson M

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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

The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.

Boman J, Mugal CF, Backström N

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]

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]

Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).

Celorio-Mancera MP, Rastas P, Steward RA, Nylin S, Wheat CW

Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-23]

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

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent.

Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ

Mol. Biol. Evol. 38 (5) 1715-1730 [2021-05-04; online 2020-11-11]

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

Activation of endogenous retroviruses during brain development causes an inflammatory response.

Jönsson ME, Garza R, Sharma Y, ..., Jern P, Jakobsson J

EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]

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

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.

Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J

Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Enterprise, a massive transposon carrying Spok meiotic drive genes.

Vogan AA, Ament-Velásquez SL, Bastiaans E, ..., Suh A, Johannesson H

Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]

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

Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals.

Lihavainen J, Edlund E, Björkén L, ..., Robinson KM, Jansson S

Physiol Plantarum 172 (1) 201-217 [2021-05-00; online 2021-01-07]

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

Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.

Kameneva P, Artemov AV, Kastriti ME, ..., Kharchenko PV, Adameyko I

Nat. Genet. 53 (5) 694-706 [2021-05-00; online 2021-04-08]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.

Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S

J. Med. Genet. 58 (5) 351-356 [2021-05-00; online 2020-06-26]

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

In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.

Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O

Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.

Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A

Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]

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

Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes.

Granlund L, Hedin A, Wahlhütter M, ..., Skog O, Lundberg M

BMJ Open Diabetes Res Care 9 (1) - [2021-05-00; online 2021-05-26]

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

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.

Sandholt AKS, Xu F, Söderlund R, ..., Svärd SG, Wattrang E

Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]

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

Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.

Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C

Thromb. Haemost. 121 (5) 573-583 [2021-05-00; online 2020-11-17]

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

Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes.

Sahlén P, Spalinskas R, Asad S, ..., Bradley M, Tapia-Páez I

J. Allergy Clin. Immunol. 147 (5) 1742-1752 [2021-05-00; online 2020-10-16]

Complete Genome Sequence of an Antimicrobial-Producing Bacillus velezensis Sam8H1 Isolate from the Makgadikgadi Saltpans of Botswana.

Modikwe G, Manoharan L, Mabutho G, ..., Lebogang L, Zhou N

Microbiol Resour Announc 10 (17) - [2021-04-29; online 2021-04-29]

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

Genome-wide CRISPR screens reveal synthetic lethal interaction between CREBBP and EP300 in diffuse large B-cell lymphoma.

Nie M, Du L, Ren W, ..., Zhang F, Pan-Hammarström Q

Cell Death Dis 12 (5) 419 [2021-04-28; online 2021-04-28]

Cyanophage Diversity and Community Structure in Dead Zone Sediments.

Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA

mSphere 6 (2) - [2021-04-28; online 2021-04-28]

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

Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.

Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]

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

An introgressed gene causes meiotic drive in Neurospora sitophila.

Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H

Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]

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

Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.

von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L

Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]

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

No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy.

Seguin-Orlando A, Costedoat C, Der Sarkissian C, ..., Signoli M, Orlando L

iScience 24 (4) 102383 [2021-04-23; online 2021-03-31]

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Respir. Res. 22 (1) 118 [2021-04-23; online 2021-04-23]

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

Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.

Mattsson L, Sörenson E, Capo E, ..., Lindehoff E, Legrand C

Front Bioeng Biotechnol 9 (-) 651895 [2021-04-22; online 2021-04-22]

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

Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Pedersen NL

Clin Epigenetics 13 (1) 85 [2021-04-21; online 2021-04-21]

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

Phenological shifts in lake stratification under climate change.

Woolway RI, Sharma S, Weyhenmeyer GA, ..., Thiery W, Jennings E

Nat Commun 12 (1) 2318 [2021-04-19; online 2021-04-19]

Estimating divergence times from DNA sequences.

Sjödin P, McKenna J, Jakobsson M

Genetics 217 (4) - [2021-04-15; online 2021-03-27]

Active DNRA and denitrification in oxic hypereutrophic waters.

Broman E, Zilius M, Samuiloviene A, ..., Nascimento FJA, Bonaglia S

Water Res. 194 (-) 116954 [2021-04-15; online 2021-02-21]

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

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.

Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G

BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]

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

DNA methylation in cord blood in association with prenatal depressive symptoms.

Kallak TK, Bränn E, Fransson E, ..., Lyle R, Skalkidou A

Clin Epigenetics 13 (1) 78 [2021-04-12; online 2021-04-12]

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

A spinal organ of proprioception for integrated motor action feedback.

Picton LD, Bertuzzi M, Pallucchi I, ..., Shearing PR, El Manira A

Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Variants That Differentiate Wolf and Dog Populations Are Enriched in Regulatory Elements.

Sahlén P, Yanhu L, Xu J, ..., Wang GD, Savolainen P

Genome Biol Evol 13 (4) - [2021-04-05; online 2021-05-01]

Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds.

Ottenburghs J, Geng K, Suh A, Kutter C

Genome Biol Evol 13 (4) - [2021-04-05; online 2021-02-04]

Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.

Fatima A, Hoeber J, Schuster J, ..., Klar J, Dahl N

Am. J. Hum. Genet. 108 (4) 739-748 [2021-04-01; online 2021-03-11]

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

A draft transcriptome of a parasite Neocamacolaimus parasiticus (Camacolaimidae, Plectida).

Ahmed M, Adedidran F, Holovachov O

J Nematol 53 (-) - [2021-04-01; online 2021-04-01]

The heart microbiome of insectivorous bats from Central and South Eastern Europe.

Corduneanu A, Mihalca AD, Sándor AD, ..., Viso NP, Bongcam-Rudloff E

Comp Immunol Microbiol Infect Dis 75 (-) 101605 [2021-04-00; online 2021-01-07]

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

The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.

Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, ..., Laurila A, Höglund J

Heredity (Edinb) 126 (4) 656-667 [2021-04-00; online 2021-02-09]

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

Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.

Bruhn H, Samuelsson K, Schober FA, ..., Wedell A, Wredenberg A

Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.

Lind L, Sundström J, Ärnlöv J, ..., Lumbers RT, Lampa E

Circ Genom Precis Med 14 (2) e002963 [2021-04-00; online 2021-02-26]

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

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.

Dumanski JP, Halvardson J, Davies H, ..., Ryś J, Forsberg LA

Cell. Mol. Life Sci. 78 (8) 4019-4033 [2021-04-00; online 2021-04-10]

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

Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.

Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX

Mol Ecol Resour 21 (3) 880-896 [2021-04-00; online 2020-12-02]

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

Correction to: High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways.

Circ Genom Precis Med 14 (2) e000081 [2021-04-00; online 2021-03-02]

Burden of rare variants in synaptic genes in patients with severe tinnitus: An exome based extreme phenotype study.

Amanat S, Gallego-Martinez A, Sollini J, ..., Cederroth CR, Lopez-Escamez JA

EBioMedicine 66 (-) 103309 [2021-04-00; online 2021-04-01]

A modified protein marker panel to identify four consensus molecular subtypes in colorectal cancer using immunohistochemistry.

Li X, Larsson P, Ljuslinder I, ..., Edin S, Palmqvist R

Pathol Res Pract 220 (-) 153379 [2021-04-00; online 2021-03-05]

Bioinformatics Compute and Storage [Service] Clinical Genomics Umeå [Collaborative]

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.

Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F

Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]

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

Multiple migrations to the Philippines during the last 50,000 years.

Larena M, Sanchez-Quinto F, Sjödin P, ..., Endicott P, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]

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

Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.

Indukuri R, Hases L, Archer A, Williams C

Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]

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

High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.

Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y

Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]

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

A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids.

Strassert JFH, Irisarri I, Williams TA, Burki F

Nat Commun 12 (1) 1879 [2021-03-25; online 2021-03-25]

PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.

He L, Jones J, He W, ..., Wen J, Dai Q

Development 148 (6) - [2021-03-17; online 2021-03-17]

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

Effects of Lactobacillus reuteri supplementation on the gut microbiota in extremely preterm infants in a randomized placebo-controlled trial.

Martí M, Spreckels JE, Ranasinghe PD, ..., Jenmalm MC, Abrahamsson T

Cell Reports Medicine 2 (3) 100206 [2021-03-16; online 2021-02-22]

Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma.

Mitra S, Muralidharan SV, Di Marco M, ..., Mondal T, Kanduri C

Cancer Res. 81 (6) 1457-1471 [2021-03-15; online 2020-12-28]

Transcriptional analysis of islets of Langerhans from organ donors of different ages.

Seiron P, Stenwall A, Hedin A, ..., Lundberg M, Skog O

PLoS ONE 16 (3) e0247888 [2021-03-12; online 2021-03-12]

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

The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.

Holmfeldt K, Nilsson E, Simone D, ..., Bertilsson S, Dopson M

Commun Biol 4 (1) 307 [2021-03-08; online 2021-03-08]

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

Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.

Kupari J, Usoskin D, Parisien M, ..., Diatchenko L, Ernfors P

Nat Commun 12 (1) 1510 [2021-03-08; online 2021-03-08]

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

Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity.

Shakeri Yekta S, Liu T, Mendes Anacleto T, ..., Björn A, Schnürer A

Biotechnol Biofuels 14 (1) 56 [2021-03-04; online 2021-03-04]

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

Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.

Zhong X, Lundberg M, Råberg L

Genome Biol Evol 13 (3) - [2021-03-01; online 2021-02-11]

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

Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.

Smeds L, Aspi J, Berglund J, ..., Tirronen K, Ellegren H

Evol Appl 14 (3) 721-734 [2021-03-00; online 2020-11-09]

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

RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.

Barragán CE, Márquez MA, Dopson M, Montoya D

Extremophiles 25 (2) 143-158 [2021-03-00; online 2021-02-22]

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

Plasma metabolomics of presymptomatic PSEN1-H163Y mutation carriers: a pilot study.

Natarajan K, Ullgren A, Khoshnood B, ..., Blennow K, Graff C

Ann Clin Transl Neurol 8 (3) 579-591 [2021-03-00; online 2021-01-21]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Swedish Metabolomics Centre (SMC) [Service]

Million-year-old DNA sheds light on the genomic history of mammoths.

van der Valk T, Pečnerová P, Díez-Del-Molino D, ..., Götherström A, Dalén L

Nature 591 (7849) 265-269 [2021-03-00; online 2021-02-17]

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

Experimental evolution of adaptive divergence under varying degrees of gene flow.

Tusso S, Nieuwenhuis BPS, Weissensteiner B, Immler S, Wolf JBW

Nat Ecol Evol 5 (3) 338-349 [2021-03-00; online 2021-01-11]

Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.

Wäneskog M, Halvorsen T, Filek K, ..., Poole SJ, Koskiniemi S

Microb Genom 7 (3) - [2021-03-00; online 2021-03-01]

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

Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks.

Mihai IS, Das D, Maršalkaite G, Henriksson J

Genes 12 (2) - [2021-02-23; online 2021-02-23]

Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML.

Mareschal S, Palau A, Lindberg J, ..., Grönberg H, Lehmann S

Blood Adv 5 (4) 1003-1016 [2021-02-23; online 2021-02-17]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Single-Cell Analysis of Blood-Brain Barrier Response to Pericyte Loss.

Mäe MA, He L, Nordling S, ..., Keller A, Betsholtz C

Circ. Res. 128 (4) e46-e62 [2021-02-19; online 2020-12-30]

Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia.

Harzandi A, Lee S, Bidkhori G, ..., Shoaie S, Sharpe CC

iScience 24 (2) 102046 [2021-02-19; online 2021-01-09]

Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds.

Halvarsson P, Höglund J

Parasit Vectors 14 (1) 114 [2021-02-18; online 2021-02-18]

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

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.

Zaghlool A, Niazi A, Björklund ÅK, ..., Ameur A, Feuk L

Sci Rep 11 (1) 4076 [2021-02-18; online 2021-02-18]

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

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.

Schneider AN, Sundh J, Sundström G, ..., Hurry V, Street NR

mSystems 6 (1) - [2021-02-16; online 2021-02-16]

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

Time-Dependent Effects of Oral Contraceptive Use on Breast, Ovarian, and Endometrial Cancers.

Karlsson T, Johansson T, Höglund J, Ek WE, Johansson Å

Cancer Res. 81 (4) 1153-1162 [2021-02-15; online 2020-12-17]

Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.

Wu H, Petitpré C, Fontanet P, ..., Hadjab S, Lallemend F

Nat Commun 12 (1) 1026 [2021-02-15; online 2021-02-15]

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

Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.

Modrzyński JJ, Aamand J, Wittorf L, ..., Hallin S, Albers CN

Water Res. 190 (-) 116669 [2021-02-15; online 2020-11-25]

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

Asymmetric introgression reveals the genetic architecture of a plumage trait.

Semenov GA, Linck E, Enbody ED, ..., Andersson L, Taylor SA

Nat Commun 12 (1) 1019 [2021-02-15; online 2021-02-15]

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

Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass.

Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C

Front Microbiol 12 (-) 607601 [2021-02-11; online 2021-02-11]

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

GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility.

Eriksson D, Røyrvik EC, Aranda-Guillén M, ..., Kämpe O, Husebye ES

Nat Commun 12 (1) 959 [2021-02-11; online 2021-02-11]

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.

Wang C, Wallerman O, Arendt ML, ..., Meadows JRS, Lindblad-Toh K

Commun Biol 4 (1) 185 [2021-02-10; online 2021-02-10]

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

Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.

Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L

Blood Adv 5 (3) 900-912 [2021-02-09; online 2021-02-10]

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

Distinct developmental pathways from blood monocytes generate human lung macrophage diversity.

Evren E, Ringqvist E, Tripathi KP, ..., Villablanca EJ, Willinger T

Immunity 54 (2) 259-275.e7 [2021-02-09; online 2020-12-30]

Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients.

Wallander K, Eisfeldt J, Lindblad M, ..., Liedén A, Tham E

PLoS ONE 16 (2) e0245488 [2021-02-04; online 2021-02-04]

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

Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae.

Bendixsen DP, Gettle N, Gilchrist C, Zhang Z, Stelkens R

Genome Biol Evol 13 (2) - [2021-02-03; online 2021-01-13]

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

Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.

Stegmayr J, Alsafadi HN, Langwiński W, ..., Leigh ND, Wagner DE

Am J Physiol Lung Cell Mol Physiol 320 (2) L232-L240 [2021-02-01; online 2020-10-28]

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

The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.

Schober FA, Moore D, Atanassov I, ..., Freyer C, Wredenberg A

Sci Adv 7 (8) - [2021-02-00; online 2021-02-19]

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

Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians.

Sjöstrand AE, Sjödin P, Hegay T, ..., Heyer E, Jakobsson M

Eur. J. Hum. Genet. 29 (2) 325-337 [2021-02-00; online 2020-10-01]

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

Small-scale population divergence is driven by local larval environment in a temperate amphibian.

Rödin-Mörch P, Palejowski H, Cortazar-Chinarro M, ..., Höglund J, Laurila A

Heredity (Edinb) 126 (2) 279-292 [2021-02-00; online 2020-09-21]

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

Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.

Diamanti K, Inda Díaz JS, Raine A, ..., Wadelius C, Cavalli M

Hepatol Res 51 (2) 233-238 [2021-02-00; online 2020-11-28]

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

Sea‐ice microbial communities in the Central Arctic Ocean: Limited responses to short‐term <scp> pCO 2 </scp> perturbations

Torstensson A, Margolin AR, Showalter GM, ..., Bolinesi F, Deming JW

Limnol Oceanogr 66 (S1) - [2021-02-00; online 2021-01-20]

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.

Dziasek K, Simon L, Lafon-Placette C, ..., Slotte T, Köhler C

PLoS Genet. 17 (2) e1009370 [2021-02-00; online 2021-02-11]

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

Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.

Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D

Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]

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

Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales).

Broberg M, Dubey M, Iqbal M, ..., Brandström Durling M, Karlsson M

Evol Appl 14 (2) 476-497 [2021-02-00; online 2020-09-28]

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

A region of the sex chromosome associated with population differences in diapause induction contains highly divergent alleles at clock genes.

Pruisscher P, Nylin S, Wheat CW, Gotthard K

Evolution 75 (2) 490-500 [2021-02-00; online 2020-12-27]

A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.

Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U

Mol. Microbiol. 115 (2) 255-271 [2021-02-00; online 2020-10-12]

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

A novel heterozygous variant in FGF9 associated with previously unreported features of multiple synostosis syndrome 3.

Thuresson AC, Croft B, Hailer YD, ..., Harley VR, Stattin EL

Clin. Genet. 99 (2) 325-329 [2021-02-00; online 2020-11-12]

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

The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.

Hases L, Ibrahim A, Chen X, ..., Hartman J, Williams C

Int J Mol Sci 22 (3) 1354 [2021-01-29; online 2021-01-29]

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

Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes.

Rissanen AJ, Saarela T, Jäntti H, ..., Elvert M, Nykänen H

FEMS Microbiol. Ecol. 97 (2) - [2021-01-26; online 2020-12-15]

Ecological adaptation in European eels is based on phenotypic plasticity.

Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]

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

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.

Lindner M, Verhagen I, Viitaniemi HM, ..., Husby A, van Oers K

BMC Genomics 22 (1) 36 [2021-01-07; online 2021-01-07]

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

Regulation of Decay Accelerating Factor Primes Human Germinal Center B Cells for Phagocytosis.

Dernstedt A, Leidig J, Holm A, ..., Hultdin M, Forsell MNE

Front Immunol 11 (-) 599647 [2021-01-05; online 2021-01-05]

Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output.

Nordell E, Moestedt J, Österman J, ..., Sun L, Schnürer A

Waste Management 119 (-) 11-21 [2021-01-01; online 2020-10-05]

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

ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes.

Pettersson ME, Jern P

Virus Evol 7 (1) veaa083 [2021-01-00; online 2020-11-06]

Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications.

Rydzanicz M, Olszewski P, Kedra D, ..., Dumanski JP, Płoski R

Mol Genet Genomic Med 9 (1) e1526 [2021-01-00; online 2020-12-14]

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

Urbanization is associated with modifications in DNA methylation in a small passerine bird.

Watson H, Powell D, Salmón P, Jacobs A, Isaksson C

Evol Appl 14 (1) 85-98 [2021-01-00; online 2020-11-13]

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

Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.

Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B

Br. J. Haematol. 192 (1) 200-211 [2021-01-00; online 2020-11-18]

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

Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing.

Sandling JK, Pucholt P, Hultin Rosenberg L, ..., Lindblad-Toh K, Rönnblom L

Ann. Rheum. Dis. 80 (1) 109-117 [2021-01-00; online 2020-10-09]

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

Lake heatwaves under climate change.

Woolway RI, Jennings E, Shatwell T, ..., Pierson DC, Maberly SC

Nature 589 (7842) 402-407 [2021-01-00; online 2021-01-20]

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.

Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A

Mol Ecol Resour 21 (1) 263-286 [2021-01-00; online 2020-10-10]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Human population dynamics and Yersinia pestis in ancient northeast Asia.

Kılınç GM, Kashuba N, Koptekin D, ..., Storå J, Götherström A

Sci Adv 7 (2) - [2021-01-00; online 2021-01-06]

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

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.

Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N

Mol. Ecol. 30 (2) 499-516 [2021-01-00; online 2020-12-14]

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

Evaluating totipotency using criteria of increasing stringency.

Posfai E, Schell JP, Janiszewski A, ..., Lanner F, Rossant J

Nat Cell Biol 23 (1) 49-60 [2021-01-00; online 2021-01-08]

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

Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing.

Morarach K, Mikhailova A, Knoflach V, ..., Ernfors P, Marklund U

Nat. Neurosci. 24 (1) 34-46 [2021-01-00; online 2020-12-07]

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]

Crown‐fire severity is more important than ground‐fire severity in determining soil fungal community development in the boreal forest

Pérez‐Izquierdo L, Clemmensen KE, Strengbom J, ..., Nilsson M, Lindahl BD

J Ecol 109 (1) 504-518 [2021-01-00; online 2020-11-00]

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

BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features.

Tolomeo D, Agostini A, Macchia G, ..., Mertens F, Storlazzi CT

Hum Cell 34 (1) 238-245 [2021-01-00; online 2020-08-27]

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

A Tribute to Professor Per Artursson - Scientist, Explorer, Mentor, Innovator, and Giant in Pharmaceutical Research.

Matsson P, Baranczewski P, Giacomini KM, ..., Charman WN, Bergström CAS

J Pharm Sci 110 (1) 2-11 [2021-01-00; online 2020-10-21]

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

Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer.

Rendo V, Kundu S, Rameika N, ..., Stoimenov I, Sjöblom T

Sci Rep 10 (1) 22436 [2020-12-31; online 2020-12-31]

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

The Bactericidal Fatty Acid Mimetic 2CCA-1 Selectively Targets Pneumococcal Extracellular Polyunsaturated Fatty Acid Metabolism.

Reithuber E, Nannapaneni P, Rzhepishevska O, ..., Henriques-Normark B, Mellroth P

MBio 11 (6) e03027-20 [2020-12-15; online 2020-12-15]

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

Hodgkin Lymphoma Monozygotic Triplets Reveal Divergences in DNA Methylation Signatures.

Xia C, Olsen TK, Zirakzadeh AA, ..., Björkholm M, Strååt K

Front Oncol 10 (-) 598872 [2020-12-09; online 2020-12-09]

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

Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.

Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B

Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-12-08; online 2020-11-23]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

Ekman L, Bagge E, Nyman A, ..., Pringle M, Segerman B

PLoS ONE 15 (12) e0242880 [2020-12-02; online 2020-12-02]

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

Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity.

Höijer I, Johansson J, Gudmundsson S, ..., Gyllensten U, Ameur A

Genome Biol. 21 (1) 290 [2020-12-01; online 2020-12-01]

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

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids.

Mugal CF, Wang M, Backström N, ..., Qvarnström A, Ellegren H

Genome Res. 30 (12) 1727-1739 [2020-12-00; online 2020-11-03]

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

The methylation landscape and its role in domestication and gene regulation in the chicken.

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

Nat Ecol Evol 4 (12) 1713-1724 [2020-12-00; online 2020-09-21]

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

Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.

Nascimento Lemos L, Manoharan L, William Mendes L, ..., Satler Pylro V, Tsai SM

Environ Microbiol Rep 12 (6) 651-655 [2020-12-00; online 2020-09-07]

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

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. 20 (6) 770-783 [2020-12-00; online 2020-02-21]

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

Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.

Nilsson H, Lindgren D, Axelson H, ..., Lundgren J, Johansson ME

J. Pathol. 252 (4) 384-397 [2020-12-00; online 2020-09-24]

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

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.

Appelberg S, Gupta S, Svensson Akusjärvi S, ..., Mirazimi A, Neogi U

Emerg Microbes Infect 9 (1) 1748-1760 [2020-12-00; online 2020-07-22]

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

A metabolite roadmap of the wood-forming tissue in Populus tremula.

Abreu IN, Johansson AI, Sokołowska K, ..., Street NR, Moritz T

New Phytol. 228 (5) 1559-1572 [2020-12-00; online 2020-08-27]

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

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

Fatima N, Petri A, Gyllensten U, Feuk L, Ameur A

Genes 11 (12) 1444 [2020-11-30; online 2020-11-30]

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

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.

Feuerborn TR, Palkopoulou E, van der Valk T, ..., Dalén L, Díez-Del-Molino D

BMC Genomics 21 (1) 844 [2020-11-30; online 2020-11-30]

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

New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.

Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N

J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]

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

High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.

Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F

Sci Rep 10 (1) 20425 [2020-11-24; online 2020-11-24]

Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.

Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G

Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.

Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX

BMC Genomics 21 (1) 796 [2020-11-16; online 2020-11-16]

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

A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.

Martínez-Carranza M, Jonna VR, Lundin D, ..., Stenmark P, Hofer A

J. Biol. Chem. 295 (46) 15576-15587 [2020-11-13; online 2020-09-03]

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

The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.

Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P

Cell 183 (4) 968-981.e7 [2020-11-12; online 2020-09-06]

Affinity Proteomics Stockholm [Service] Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Identification of Pre-Diagnostic Metabolic Patterns for Glioma Using Subset Analysis of Matched Repeated Time Points.

Jonsson P, Antti H, Späth F, Melin B, Björkblom B

Cancers (Basel) 12 (11) 3349 [2020-11-12; online 2020-11-12]

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

Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.

Watanabe A, Miyake K, Nordlund J, ..., Sugita K, Inukai T

Blood 136 (20) 2319-2333 [2020-11-12; online 2020-06-24]

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

Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.

Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M

mSystems 5 (6) - [2020-11-10; online 2020-11-10]

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

Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.

Mathioudaki A, Ljungström V, Melin M, ..., Sjöblom T, Lindblad-Toh K

Sci Rep 10 (1) 19304 [2020-11-09; online 2020-11-09]

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

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.

Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K

Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]

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

Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.

Subramaniam A, Žemaitis K, Talkhoncheh MS, ..., Zubarev RA, Larsson J

Blood 136 (19) 2151-2161 [2020-11-05; online 2020-06-26]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.

Ozerov MY, Flajšhans M, Noreikiene K, Vasemägi A, Gross R

G3 (Bethesda) 10 (11) 3897-3906 [2020-11-05; online 2020-11-05]

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

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.

Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R

Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]

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

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.

Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M

Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]

Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.

Kalsoom Khan F, Kluting K, Tångrot J, ..., Ryberg M, Rosling A

IMA Fungus 11 (1) 23 [2020-11-03; online 2020-11-03]

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

From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.

Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F

Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]

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

Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis.

He Q, Li X, He L, ..., Betsholtz C, Welsh M

Int. J. Cancer 147 (9) 2634-2644 [2020-11-01; online 2020-05-30]

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

Sahelian pastoralism from the perspective of variants associated with lactase persistence.

Priehodová E, Austerlitz F, Čížková M, ..., Schlebusch CM, Černý V

Am. J. Phys. Anthropol. 173 (3) 423-436 [2020-11-00; online 2020-08-19]

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

Leaf shape in Populus tremula is a complex, omnigenic trait.

Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR

Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]

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

Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.

Ramos J, Proven M, Halvardson J, ..., Thuresson AC, Fu D

RNA 26 (11) 1654-1666 [2020-11-00; online 2020-08-06]

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

Cytogenetically visible inversions are formed by multiple molecular mechanisms.

Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A

Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]

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

Intra-Individual Behavioural Variability: A Trait under Genetic Control.

Henriksen R, Höglund A, Fogelholm J, ..., Dingemanse NJ, Wright D

Int J Mol Sci 21 (21) 8069 [2020-10-29; online 2020-10-29]

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

Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma.

Rossitti HM, Dutta RK, Larsson C, ..., Söderkvist P, Gimm O

Int J Mol Sci 21 (21) 8072 [2020-10-29; online 2020-10-29]

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

Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.

Tarbier M, Mackowiak SD, Frade J, ..., Gallant CJ, Friedländer MR

Nat Commun 11 (1) 5445 [2020-10-28; online 2020-10-28]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.

Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L

Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]

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

Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.

Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A

Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]

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

Automated identification of the mouse brain's spatial compartments from in situ sequencing data.

Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C

BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service]

The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder.

Li D, Choque-Olsson N, Jiao H, ..., Bölte S, Tammimies K

npj Genom. Med. 5 (1) 45 [2020-10-12; online 2020-10-12]

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

Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2.

Berggrund M, Gustavsson I, Aarnio R, ..., Olovsson M, Gyllensten U

Virol J 17 (1) 147 [2020-10-07; online 2020-10-07]

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

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.

Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D

BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]

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

Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.

Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M

BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]

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

Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L

Curr. Biol. 30 (19) 3871-3879.e7 [2020-10-05; online 2020-08-13]

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]

Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.

Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U

Exp. Cell Res. 395 (1) 112156 [2020-10-01; online 2020-07-22]

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

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.

Schlebusch CM, Sjödin P, Breton G, ..., Soodyall H, Jakobsson M

Mol. Biol. Evol. 37 (10) 2944-2954 [2020-10-01; online 2020-07-23]

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

Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.

Sato DX, Rafati N, Ring H, ..., Carneiro M, Andersson L

Genome Biol Evol 12 (10) 1918-1928 [2020-10-01; online 2020-08-25]

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

Unraveling the Immune Response in Severe COVID-19.

Rodriguez L, Brodin P

J Clin Immunol 40 (7) 958-959 [2020-10-00; online 2020-08-22]

Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.

Hong MG, Dodig-Crnković T, Chen X, ..., Magnusson PK, Schwenk JM

Life Sci. Alliance 3 (10) e202000817 [2020-10-00; online 2020-07-31]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service]

Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro.

Akaberi D, Krambrich J, Ling J, ..., Lennerstrand J, Lundkvist Å

Redox Biol 37 (-) 101734 [2020-10-00; online 2020-09-21]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

Metagenomic analysis of bacteria in stallion semen.

Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM

Animal Reproduction Science 221 (-) 106568 [2020-10-00; online 2020-08-01]

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

Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.

Lundtoft C, Pucholt P, Imgenberg-Kreuz J, ..., Rönnblom L, Hagberg N

PLoS Genet. 16 (10) e1009199 [2020-10-00; online 2020-10-26]

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

High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.

Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C

Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]

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

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.

Mondav R, Bertilsson S, Buck M, ..., Lindström ES, Garcia SL

mSystems 5 (5) - [2020-09-29; online 2020-09-29]

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

Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-29; online 2020-09-16]

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

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.

Pontiller B, Martínez-García S, Lundin D, Pinhassi J

Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]

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

Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.

Ignatov D, Vaitkevicius K, Johansson J

STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]

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

Presynaptic dysfunction in CASK-related neurodevelopmental disorders.

Becker M, Mastropasqua F, Reising JP, ..., Bölte S, Tammimies K

Transl Psychiatry 10 (1) 312 [2020-09-14; online 2020-09-14]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.

Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E

Microorganisms 8 (9) 1394 [2020-09-11; online 2020-09-11]

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

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S

Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]

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

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.

Svensson D, Rentoft M, Dahlin AM, ..., Trygg J, Johansson E

PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]

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

Integration of molecular profiles in a longitudinal wellness profiling cohort.

Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L

Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Cellular Immunomonitoring [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]

Genome sequence of segmented filamentous bacteria present in the human intestine.

Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF

Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]

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

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.

Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM

Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]

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

River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs.

Freixa A, Perujo N, Langenheder S, Romaní AM

FEMS Microbiol. Ecol. 96 (9) - [2020-09-01; online 2020-08-09]

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

Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.

Ericson PGP, Irestedt M, Nylander JAA, ..., Joseph L, Qu Y

Syst. Biol. 69 (5) 820-829 [2020-09-01; online 2020-05-18]

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

Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.

Mahajan M, Seeger C, Yee B, Andersson SGE

Genome Biol Evol 12 (9) 1528-1548 [2020-09-01; online 2020-08-08]

Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service]

Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.

Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ

Hum. Mutat. 41 (9) 1671-1679 [2020-09-00; online 2020-06-29]

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

Reconstructing marine plankton food web interactions using DNA metabarcoding.

Zamora-Terol S, Novotny A, Winder M

Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]

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

Linked-read sequencing enables haplotype-resolved resequencing at population scale.

Lutgen D, Ritter R, Olsen RA, ..., Suh A, Burri R

Mol Ecol Resour 20 (5) 1311-1322 [2020-09-00; online 2020-06-29]

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

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.

van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K

Mol Ecol Resour 20 (5) 1171-1181 [2020-09-00; online 2019-05-05]

Bioinformatics Compute and Storage [Service] 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 15 (9) 972-987 [2020-09-00; online 2020-03-31]

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

Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.

Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B

Front Microbiol 11 (-) 2066 [2020-08-27; online 2020-08-27]

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

Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.

Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B

Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]

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

Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19.

Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P

Cell Reports Medicine 1 (5) 100078 [2020-08-25; online 2020-08-05]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.

Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H

npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]

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

Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates.

Faure L, Wang Y, Kastriti ME, ..., Adameyko I, Hadjab S

Nat Commun 11 (1) 4175 [2020-08-21; online 2020-08-21]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Natural killer cell immunotypes related to COVID-19 disease severity.

Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group

Sci Immunol 5 (50) eabd6832 [2020-08-21; online 2020-08-23]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service]

Designing custom CRISPR libraries for hypothesis-driven drug target discovery.

Iyer VS, Jiang L, Shen Y, ..., Schmierer B, Wermeling F

Computational and Structural Biotechnology Journal 18 (-) 2237-2246 [2020-08-18; online 2020-08-18]

Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Collaborative]

Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.

Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F

Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]

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

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.

Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A

Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]

BioImage Informatics [Technology development] Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

The importance of the ZBED6-IGF2 axis for metabolic regulation in mouse myoblast cells.

Younis S, Naboulsi R, Wang X, ..., Welsh N, Andersson L

FASEB J. 34 (8) 10250-10266 [2020-08-00; online 2020-06-19]

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

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.

Coutinho A, Günther T, Munters AR, ..., Malmström H, Jakobsson M

Am. J. Phys. Anthropol. 172 (4) 638-649 [2020-08-00; online 2020-06-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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. 20 (4) 579-585 [2020-08-00; online 2020-01-17]

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

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.

Ottenburghs J, Honka J, Müskens GJDM, Ellegren H

Heredity (Edinb) 125 (1-2) 73-84 [2020-08-00; online 2020-05-26]

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

Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.

Petrus-Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F

Stem Cells Transl Med 9 (8) 936-953 [2020-08-00; online 2020-04-22]

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]

Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.

Trell K, Jörgensen J, Rasmussen M, Senneby E

J. Hosp. Infect. 105 (4) 752-756 [2020-08-00; online 2020-06-01]

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

Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.

Tomata Y, Li X, Karlsson IK, ..., Pedersen NL, Hägg S

J. Intern. Med. 288 (2) 234-247 [2020-08-00; online 2020-05-03]

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

Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.

Abrego N, Huotari T, Tack AJM, ..., Ovaskainen O, Roslin T

Ecol Evol 10 (16) 8989-9002 [2020-08-00; online 2020-08-06]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [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 82 (-) 104290 [2020-08-00; online 2020-03-20]

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

Determinants of genetic variation across eco-evolutionary scales in pinnipeds.

Peart CR, Tusso S, Pophaly SD, ..., Shafer ABA, Wolf JBW

Nat Ecol Evol 4 (8) 1095-1104 [2020-08-00; online 2020-06-08]

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

Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.

Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E

J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]

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

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.

Juottonen H, Fontaine L, Wurzbacher C, ..., Peura S, Eiler A

Environ. Microbiol. 22 (8) 3158-3171 [2020-08-00; online 2020-06-03]

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

A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.

Reynolds CA, Tan Q, Munoz E, ..., Hägg S, Pedersen NL

Aging Cell 19 (8) e13197 [2020-08-00; online 2020-07-24]

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

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.

Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R

BMC Genomics 21 (1) 518 [2020-07-29; online 2020-07-29]

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

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.

Chaudhary R, Lundén K, Dalman K, ..., Stenlid J, Elfstrand M

Sci Rep 10 (1) 12711 [2020-07-29; online 2020-07-29]

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

Prototypical pacemaker neurons interact with the resident microbiota.

Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG

Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]

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

Human Immune System Variation during 1 Year.

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

Cell Rep 32 (3) 107923 [2020-07-21; online 2020-07-23]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Descriptive Proteome Analysis to Investigate Context-Dependent Treatment Responses to OXPHOS Inhibition in Colon Carcinoma Cells Grown as Monolayer and Multicellular Tumor Spheroids.

Steinmetz J, Senkowski W, Lengqvist J, ..., Fryknäs M, Kultima K

ACS Omega 5 (28) 17242-17254 [2020-07-21; online 2020-07-06]

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

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.

von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M

Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]

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

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.

Bergenstråhle J, Larsson L, Lundeberg J

BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]

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

A Patient-Derived Cell Atlas Informs Precision Targeting of Glioblastoma.

Johansson P, Krona C, Kundu S, ..., Marino S, Nelander S

Cell Rep 32 (2) 107897 [2020-07-14; online 2020-07-16]

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

Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole.

Martin F, Dube F, Karlsson Lindsjö O, ..., Bergström TF, Tydén E

Parasit Vectors 13 (1) 342 [2020-07-09; online 2020-07-09]

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

Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.

Renes SE, Sjöstedt J, Fetzer I, Langenheder S

Sci Rep 10 (1) 11333 [2020-07-09; online 2020-07-09]

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

Systems biology of acidophile biofilms for efficient metal extraction.

Buetti-Dinh A, Herold M, Christel S, ..., Pivkin IV, Dopson M

Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]

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

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.

Broman E, Sun X, Stranne C, ..., Humborg C, Nascimento FJA

Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]

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

Discovery and population genomics of structural variation in a songbird genus.

Weissensteiner MH, Bunikis I, Catalán A, ..., Warmuth VM, Wolf JBW

Nat Commun 11 (1) 3403 [2020-07-07; online 2020-07-07]

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

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.

Wallén-Mackenzie Å, Dumas S, Papathanou M, ..., König N, Björklund ÅK

Commun Biol 3 (1) 338 [2020-07-03; online 2020-07-03]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.

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

Clin Epigenetics 12 (1) 99 [2020-07-02; online 2020-07-02]

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

Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.

Naidoo T, Xu J, Vicente M, ..., Jakobsson M, Schlebusch CM

Genome Biol Evol 12 (7) 1031-1039 [2020-07-01; online 2020-07-23]

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

Loqusdb: added value of an observations database of local genomic variation.

Magnusson M, Eisfeldt J, Nilsson D, ..., Wedell A, Stranneheim H

BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]

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

Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin.

Tengvall K, Bergvall K, Olsson M, ..., Lindblad-Toh K, Andersson G

Immunogenetics 72 (5) 315-323 [2020-07-00; online 2020-06-18]

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

Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.

Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J

Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Collaborative] Global Proteomics and Proteogenomics [Technology development]

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 31 (5) 544-553 [2020-07-00; online 2020-04-03]

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

Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.

Gonzalez F, Borrero-Echeverry F, Jósvai JK, ..., Bengtsson M, Walker WB

Ecol Evol 10 (14) 7334-7348 [2020-07-00; online 2020-06-30]

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

Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.

Bonaglia S, Hedberg J, Marzocchi U, ..., Glud RN, Nascimento FJA

Mar Environ Res 159 (-) 104968 [2020-07-00; online 2020-03-29]

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

Inflammatory markers in women with postpartum depressive symptoms.

Bränn E, Fransson E, White RA, ..., Sundström-Poromaa I, Skalkidou A

J Neuro Res 98 (7) 1309-1321 [2020-07-00; online 2018-09-05]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression.

Dalmo E, Johansson P, Niklasson M, ..., Nelander S, Westermark B

Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]

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

Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.

Ndegwa N, Ploner A, Andersson AF, ..., Agreus L, Ye W

Clin Transl Gastroenterol 11 (7) e00191 [2020-07-00; online 2020-08-09]

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

Female-biased gene flow between two species of Darwin's finches.

Lamichhaney S, Han F, Webster MT, ..., Grant PR, Andersson L

Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]

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

Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.

Zhong X, Lundberg M, Råberg L

Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]

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

Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.

Klar J, Engstrand-Lilja H, Maqbool K, ..., Feuk L, Dahl N

BMC Med Genomics 13 (1) 85 [2020-06-26; online 2020-06-26]

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

Evolutionary History of the Marchantia polymorpha Complex.

Linde AM, Sawangproh W, Cronberg N, Szövényi P, Lagercrantz U

Front Plant Sci 11 (-) 829 [2020-06-26; online 2020-06-26]

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

Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.

Zhong W, Gummesson A, Tebani A, ..., Fagerberg L, Uhlén M

Genome Med 12 (1) 53 [2020-06-23; online 2020-06-23]

Affinity Proteomics Stockholm [Collaborative] Bioinformatics Compute and Storage [Service]

Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.

Chapman MA, Arif M, Emanuelsson EB, ..., Mardinoglu A, Sundberg CJ

Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]

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

Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.

Remnestål J, Öijerstedt L, Ullgren A, ..., Graff C, Nilsson P

Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]

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

Illuminating Genetic Mysteries of the Dead Sea Scrolls.

Anava S, Neuhof M, Gingold H, ..., Jakobsson M, Rechavi O

Cell 181 (6) 1218-1231.e27 [2020-06-11; online 2020-06-02]

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

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes.

Sakthikumar S, Roy A, Haseeb L, ..., Lindblad-Toh K, Forsberg-Nilsson K

Genome Biol. 21 (1) 127 [2020-06-09; online 2020-06-09]

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

CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.

Hagey DW, Topcic D, Kee N, ..., Perlmann T, Muhr J

Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]

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

The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells.

Hjorton K, Hagberg N, Pucholt P, Eloranta ML, Rönnblom L

Arthritis Res. Ther. 22 (1) 130 [2020-06-05; online 2020-06-05]

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