NGI Uppsala (Uppsala Genome Center) (359 publications)

Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique

Cholleti H, Hayer J, ..., Berg M, Blomström AL

Virol J 15 (1) - [2018-12-00; online 2018-04-18]

Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing

Onuț-Brännström I, Benjamin M, ..., Lindström ES, Johannesson H

Sci Rep 8 (1) - [2018-12-00; online 2018-03-13]

Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants

Delgado-Vega AM, Martínez-Bueno M, ..., Kozyrev SV, Alarcón-Riquelme ME

Sci Rep 8 (1) - [2018-12-00; online 2018-06-08]

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest

Castaño C, Alday JG, ..., Pera J, Bonet JA

Forest Ecology and Management 424 (-) 420-427 [2018-09-00; online 2018-09-00]

Cárdenas CA, González-Aravena M, ..., Malmberg M, Bongcam-Rudloff E

PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]

Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Karlsson J, Valind A, ..., Bexell D, Gisselsson D

Nat Genet - (-) - [2018-06-04; online 2018-06-04]

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

Schmidt R, Durling MB, ..., Karlsson M, Garbeva P

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]

Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

Porseryd T, Reyhanian Caspillo N, ..., Olsson PE, Porsch-Hällström I

General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]

A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases

Stattin EL, Johansson J, ..., Bondeson ML, Wilbe M

Am J Med Genet 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Castaño C, Lindahl BD, ..., Pera J, Bonet JA

New Phytol - (-) - [2018-05-14; online 2018-05-14]

Molecular barcoding of viral vectors enables mapping and optimization of mRNAtrans-splicing

Davidsson M, Díaz-Fernández P, ..., Lundberg C, Björklund T

RNA 24 (5) 673-687 [2018-05-00; online 2018-01-31]

Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens

Zida PE, Néya BJ, ..., Sérémé P, Lund OS

Crop Protection 107 (-) 48-55 [2018-05-00; online 2018-05-00]

Introducing ribosomal tandem repeat barcoding for fungi

Wurzbacher C, Larsson E, ..., Kagami M, Nilsson RH

- - (-) - [2018-04-28; online 2018-04-28]

Repeated evolution of self-compatibility for reproductive assurance.

Nieuwenhuis BPS, Tusso S, ..., Wolf JBW, Immler S

Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Genes 9 (4) 225 [2018-04-23; online 2018-04-23]

Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Vanderpool D, Bracewell RR, McCutcheon JP

Mol Ecol 27 (8) 2077-2094 [2018-04-00; online 2017-11-23]

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Rasmussen PU, Hugerth LW, ..., Lindahl BD, Tack AJM

New Phytol - (-) - [2018-03-24; online 2018-03-24]

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res 46 (5) 2159-2168 [2018-03-16; online 2018-02-01]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Hagenbo A, Kyaschenko J, ..., Lindahl BD, Fransson P

J Ecol 106 (2) 490-501 [2018-03-00; online 2018-02-13]

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, ..., Steige KA, Slotte T

G3 (Bethesda) - (-) g3.300467.2017 [2018-02-23; online 2018-02-23]

RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding

Humble E, Dasmahapatra KK, ..., Wolf J, Hoffman J

- - (-) - [2018-02-22; online 2018-02-22]

Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity

Olivo G, Latini F, ..., Larsson EM, Schiöth HB

Front Hum Neurosci 12 (-) - [2018-02-22; online 2018-02-22]

De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

Ameur A, Che H, ..., Feuk L, Gyllensten U

- - (-) - [2018-02-18; online 2018-02-18]

The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Couturier M, Lindås AC

Front Microbiol 9 (-) - [2018-02-08; online 2018-02-08]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res - (-) - [2018-02-01; online 2018-02-01]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Undabarrena A, Salvà-Serra F, ..., Seeger M, Cámara B

Marine Genomics - (-) - [2018-02-00; online 2018-02-00]

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA

Klingstrom T, Bongcam-Rudloff E, Vinnere Pettersson O

- - (-) - [2018-01-27; online 2018-01-27]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, ..., Ennis DG, Kirsebom L

- - (-) - [2018-01-17; online 2018-01-17]

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone

Vowles T, Lindwall F, ..., Ryberg M, Björk RG

Ecol Evol 8 (2) 1019-1030 [2018-01-00; online 2017-12-14]

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Lodé L, Ameur A, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

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

Homozygosity for a missense variant in COMP gene associated with severe pseudoachondroplasia

Tariq M, Khan TN, ..., Dahl N, Klar J

Clin Genet 93 (1) 182-186 [2018-01-00; online 2017-11-21]

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

Year 2017

Amplicon sequencing of the 16S-ITS-23S rRNA operon with long-read technology for improved phylogenetic classification of uncultured prokaryotes

Martijn J, Lind AE, ..., Vinnere Pettersson O, Ettema TJG

- - (-) - [2017-12-15; online 2017-12-15]

Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells

Ma’ayeh SY, Liu J, ..., Bergquist J, Svärd SG

PLoS Negl Trop Dis 11 (12) e0006120 [2017-12-11; online 2017-12-11]

Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

Berlin A, Samils B, Andersson B

Fungal Biol Biotechnol 4 (1) - [2017-12-00; online 2017-05-03]

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

Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4

Kancherla RP, Durling MB, Stenlid J, Högberg N

Data Brief 15 (-) 496-500 [2017-12-00; online 2017-12-00]

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

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts

Stattin EL, Henning P, ..., Wikström J, Lerner UH

Sci Rep 7 (1) - [2017-12-00; online 2017-06-07]

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

Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma

Sun Y, Svedberg J, ..., Corcoran P, Johannesson H

Nat Commun 8 (1) - [2017-12-00; online 2017-10-26]

Identification of NCAN as a candidate gene for developmental dyslexia

Einarsdottir E, Peyrard-Janvid M, ..., Leinonen E, Kere J

Sci Rep 7 (1) - [2017-12-00; online 2017-08-24]

Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition

Amlinger L, Hoekzema M, ..., Koskiniemi S, Lundgren M

Sci Rep 7 (1) - [2017-12-00; online 2017-09-04]

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

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Christel S, Herold M, ..., Poetsch A, Dopson M

Appl Environ Microbiol 84 (3) e02091-17 [2017-11-17; online 2018-01-17]

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

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

Bondeson ML, Ericson K, ..., Frykholm C, Wilbe M

Clin. Genet. 92 (5) 510-516 [2017-11-00; online 2017-05-03]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] Tissue Profiling [Collaborative]

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

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

Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities

Kyaschenko J, Clemmensen KE, Karltun E, Lindahl BD

Ecol Lett - (-) - [2017-10-22; online 2017-10-22]

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

De novo design and synthesis of a 30-cistron translation-factor module

Shepherd TR, Du L, ..., Yomo T, Forster AC

Nucleic Acids Res 45 (18) 10895-10905 [2017-10-13; online 2017-09-04]

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

Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.

Zhao JJ, Halvardson J, ..., Thuresson AC, Feuk L

Am. J. Med. Genet. B Neuropsychiatr. Genet. - (-) - [2017-10-09; online 2017-10-09]

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

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Pértille F, Brantsæter M, ..., Jensen P, Guerrero-Bosagna C

J Exp Biol 220 (19) 3579-3587 [2017-10-01; online 2017-08-07]

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

Shaping the Tumor Stroma and Sparking Immune Activation by CD40 and 4-1BB Signaling Induced by an Armed Oncolytic Virus

Eriksson E, Milenova I, ..., Alemany R, Loskog A

Clin. Cancer Res. 23 (19) 5846-5857 [2017-10-01; online 2017-05-23]

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

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G

Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

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

Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function

Zhao JJ, Halvardson J, ..., Thuresson AC, Feuk L

Human Mutation 38 (10) 1394-1401 [2017-10-00; online 2017-06-12]

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

Quantitative interactions between the biocontrol fungus Phlebiopsis gigantea , the forest pathogen Heterobasidion annosum and the fungal community inhabiting Norway spruce stumps

Oliva J, Messal M, Wendt L, Elfstrand M

Forest Ecology and Management 402 (-) 253-264 [2017-10-00; online 2017-10-00]

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

The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.

Kaján GL, Kajon AE, ..., Bartha D, Arnberg N

Virus Res. 242 (-) 79-84 [2017-09-18; online 2017-09-18]

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

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders.

Wilbe M, Gudmundsson S, ..., Frykholm C, Bondeson M

Prenat. Diagn. - (-) - [2017-09-16; online 2017-09-16]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development]

Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.

Varenius K, Lindahl BD, Dahlberg A

FEMS Microbiol. Ecol. 93 (9) - [2017-09-01; online 2017-09-29]

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

Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.

Thammarongtham C, Nookaew I, ..., Jeennor S, Laoteng K

Curr. Microbiol. - (-) - [2017-09-01; online 2017-09-01]

A CRISPR-Cas9 Generated MDCK Cell Line Expressing Human MDR1 Without Endogenous Canine MDR1 (cABCB1): An Improved Tool for Drug Efflux Studies.

Karlgren M, Simoff I, ..., Oswald S, Artursson P

J Pharm Sci 106 (9) 2909-2913 [2017-09-00; online 2017-04-24]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development] Drug Discovery and Development (DDD) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service]

Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.

Azimi A, Tuominen R, ..., Hansson J, Egyhazi Brage S

Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]

Chemical Proteomics & Proteogenomics [Service] Clinical Proteomics Mass spectrometry [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service]

Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum.

Persson CU, von Stedingk K, ..., Påhlman S, Wigerup C

Sci Rep 7 (1) 10274 [2017-08-31; online 2017-08-31]

Identification of NCAN as a candidate gene for developmental dyslexia.

Einarsdottir E, Peyrard-Janvid M, ..., Leinonen E, Kere J

Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]

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

A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.

Dumanski JP, Rasi C, ..., Hellman P, Tiensuu Janson E

Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]

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

Regional genetic differentiation in the blue mussel from the Baltic Sea area

Larsson J, Lind EE, ..., Smolarz K, Lönn M

Estuarine, Coastal and Shelf Science 195 (-) 98-109 [2017-08-00; online 2017-08-00]

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

Rates of gene flow in a freshwater snail and the evolution of phenotypic plasticity

Hollander J, Ahlgren J, Brönmark C

- 121 (4) 764-770 [2017-08-00; online 2017-06-01]

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

Larsson C, Ali MA, ..., He L, Sjöblom T

BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]

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

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, ..., Hedfalk K, Blomberg A

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

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

Genomewide analysis of admixture and adaptation in the Africanized honeybee.

Nelson RM, Wallberg A, ..., Lawson DJ, Webster MT

Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]

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

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.

Töpel M, Pinder MIM, ..., Godhe A, Clarke AK

Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]

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

A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers

Klar J, Ali Z, ..., Baig SM, Dahl N

Eur J Hum Genet 25 (7) 848-853 [2017-06-00; online 2017-05-10]

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

Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden

Blomström AL, Oma V, ..., Berg M, Myrmel M

Genome Announc 5 (19) e00172-17 [2017-05-11; online 2017-05-11]

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

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Weissensteiner MH, Pang AWC, ..., Suh A, Wolf JBW

Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior

Porseryd T, Volkova K, ..., Dinnetz P, Porsh Hällström I

Front. Behav. Neurosci. 11 (-) - [2017-04-20; online 2017-04-20]

Bioinformatics Support and Infrastructure [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service]

Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.

Weber HS, Habicht KS, Thamdrup B

Front Microbiol 8 (-) 619 [2017-04-12; online 2017-04-12]

Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715

Moreno AD, Tellgren-Roth C, ..., Olsson L, Geijer C

Genome Announc 5 (14) e00138-17 [2017-04-06; online 2017-04-06]

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

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands

Kyaschenko J, Clemmensen KE, ..., Karltun E, Lindahl BD

ISME J 11 (4) 863-874 [2017-04-00; online 2017-01-13]

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

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology

Viļuma A, Mikko S, ..., Andersson G, Bergström TF

Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]

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

Atrophin controls developmental signaling pathways via interactions with Trithorax-like

Yeung K, Boija A, ..., Mannervik M, McNeill H

Elife 6 (-) - [2017-03-22; online 2017-03-22]

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

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, ..., Scheynius A, Lehtiö J

Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Chemical Proteomics & Proteogenomics [Technology development] Clinical Proteomics Mass spectrometry [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative]

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, ..., Gyllensten U, Wadelius C

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

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

Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus

Elbir H, Sitlani P, Bergström S, Barbour AG

Genome Announc 5 (11) e00018-17 [2017-03-16; online 2017-03-16]

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26

Gudmundsson S, Wilbe M, ..., Törmä H, Bondeson ML

- 26 (6) 1070-1077 [2017-03-15; online 2017-02-01]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] PLA Proteomics [Service]

Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.

Immonen E, Sayadi A, Bayram H, Arnqvist G

Genome Biol Evol 9 (3) 677-699 [2017-03-01; online 2017-04-10]

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

Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees

Barbosa RN, Leong SL, ..., Oliveira NT, Houbraken J

Studies in Mycology 86 (-) 29-51 [2017-03-00; online 2017-03-00]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.

Wahlestedt M, Erlandsson E, ..., Martin-Gonzalez J, Bryder D

Nat Commun 8 (-) 14533 [2017-02-22; online 2017-02-22]

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

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

Samad MS, Bertilsson S

Front Microbiol 8 (-) - [2017-02-03; online 2017-02-03]

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

Evolution of bird genomes-a transposon's-eye view.

Kapusta A, Suh A

Ann. N. Y. Acad. Sci. 1389 (1) 164-185 [2017-02-00; online 2016-12-20]

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

Activation of myeloid and endothelial cells by CD40L gene therapy supports T-cell expansion and migration into the tumor microenvironment

Eriksson E, Moreno R, ..., Alemany R, Loskog A

Gene Ther 24 (2) 92-103 [2017-02-00; online 2016-12-01]

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

Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.

Cimdins A, Lüthje P, ..., Brauner A, Römling U

Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]

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

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

Fletcher E, Feizi A, ..., Siewers V, Nielsen J

Metabolic Engineering 39 (-) 19-28 [2017-01-00; online 2017-01-00]

Year 2016

Novel SACS mutations associated with intellectual disability, epilepsy and widespread supratentorial abnormalities.

Ali Z, Klar J, ..., Baig S, Dahl N

J. Neurol. Sci. 371 (-) 105-111 [2016-12-15; online 2016-11-23]

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

Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.

Pandzic T, Larsson J, ..., Sjöblom T, Hellström M

Clin. Cancer Res. 22 (24) 6217-6227 [2016-12-15; online 2016-03-10]

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

Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica

Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J

npj Syst Biol Appl 2 (1) - [2016-12-00; online 2016-03-03]

Abnormal primary and permanent dentitions with ectodermal symptoms predict WNT10A deficiency.

Bergendal B, Norderyd J, ..., Klar J, Dahl N

BMC Med. Genet. 17 (1) 88 [2016-11-24; online 2016-11-24]

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

The great spruce bark beetle (Dendroctonus micans Kug.) (Coleoptera: Scolytidae) in Lithuania: occurrence, phenology, morphology and communities of associated fungi.

Menkis A, Lynikienė J, ..., Gedminas A, Povilaitienė A

Bull. Entomol. Res. - (-) 1-8 [2016-11-22; online 2016-11-22]

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

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.

Davidsson M, Diaz-Fernandez P, ..., Wang G, Björklund T

Sci Rep 6 (-) 37563 [2016-11-22; online 2016-11-22]

Complete Genome Sequence of an African Swine Fever Virus Isolate from Sardinia, Italy.

Granberg F, Torresi C, ..., De Mia GM, Belák S

Genome Announc 4 (6) - [2016-11-17; online 2016-11-17]

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

Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease.

Matsson H, Söderhäll C, ..., Lundbäck B, Klar J

BMC Pulm Med 16 (1) 146 [2016-11-11; online 2016-11-11]

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

Targeting SOX9 for degradation to inhibit chemoresistance, metastatic spread, and recurrence.

Suryo Rahmanto A, Swartling FJ, Sangfelt O

Mol Cell Oncol 4 (1) e1252871 [2016-11-08; online 2016-11-08]

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

A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda.

Blomström AL, Lalander C, ..., Vinnerås B, Boqvist S

Infect Ecol Epidemiol 6 (-) 32453 [2016-11-08; online 2016-11-08]

Long-term effects of tree harvesting on ectomycorrhizal fungal communities in boreal Scots pine forests

Varenius K, Kårén O, Lindahl B, Dahlberg A

Forest Ecology and Management 380 (-) 41-49 [2016-11-00; online 2016-11-00]

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

Introduction and persistence of tularemia in Bulgaria.

Myrtennäs K, Marinov K, ..., Byström M, Forsman M

Infect Ecol Epidemiol 6 (-) 32838 [2016-10-26; online 2016-10-26]

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

Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence.

Kreuger J, O'Callaghan P

PLoS ONE 11 (10) e0165012 [2016-10-21; online 2016-10-21]

Differential selection on pollen and pistil traits in relation to pollen competition in the context of a sexual conflict over timing of stigma receptivity.

Lankinen Å, Strandh M

AoB Plants 8 (-) - [2016-10-13; online 2016-08-27]

Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Stand Genomic Sci 11 (-) 80 [2016-10-12; online 2016-10-12]

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

Expression of Interferon-Stimulated Genes in Insulitic Pancreatic Islets of Patients Recently Diagnosed With Type 1 Diabetes.

Lundberg M, Krogvold L, ..., Dahl-Jørgensen K, Skog O

Diabetes 65 (10) 3104-3110 [2016-10-00; online 2016-07-17]

Mutations in HECW2 are associated with intellectual disability and epilepsy.

Halvardson J, Zhao JJ, ..., Thuresson AC, Feuk L

J. Med. Genet. 53 (10) 697-704 [2016-10-00; online 2016-06-24]

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

Genetic rescue in a severely inbred wolf population.

Åkesson M, Liberg O, ..., Bensch S, Flagstad Ø

Mol. Ecol. 25 (19) 4745-4756 [2016-10-00; online 2016-08-09]

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

Feralisation targets different genomic loci to domestication in the chicken.

Johnsson M, Gering E, ..., Friberg U, Wright D

Nat Commun 7 (-) 12950 [2016-09-30; online 2016-09-30]

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

Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique.

Cholleti H, Hayer J, ..., Berg M, Blomström AL

PLoS ONE 11 (9) e0162751 [2016-09-28; online 2016-09-28]

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

A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description.

Hannuksela M, Stattin EL, ..., Sörensen K, Carlberg B

BMC Med. Genet. 17 (1) 61 [2016-09-01; online 2016-09-01]

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

A Role for the Chromatin-Remodeling Factor BAZ1A in Neurodevelopment.

Zaghlool A, Halvardson J, ..., Thuresson AC, Feuk L

Hum. Mutat. 37 (9) 964-975 [2016-09-00; online 2016-06-23]

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

Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level.

Kristiansen TA, Jaensson Gyllenbäck E, ..., Bryder D, Yuan J

Immunity 45 (2) 346-357 [2016-08-16; online 2016-08-18]

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

Assessing the taxonomic status ofOsmoderma cristinae(Coleoptera: Scarabaeidae), endemic to Sicily, by genetic, morphological and pheromonal analyses

Zauli A, Carpaneto GM, ..., Bologna MA, Svensson GP

J Zool Syst Evol Res 54 (3) 206-214 [2016-08-00; online 2016-02-12]

A new class of fatty acid allene oxide formed by the DOX-P450 fusion proteins of human and plant pathogenic fungi, C. immitis and Z. tritici.

Oliw EH, Aragó M, Chen Y, Jernerén F

J. Lipid Res. 57 (8) 1518-1528 [2016-08-00; online 2016-06-11]

Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements.

Åsman AK, Fogelqvist J, Vetukuri RR, Dixelius C

New Phytol. 211 (3) 993-1007 [2016-08-00; online 2016-03-25]

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

DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.

Svennerholm K, Rodsand P, ..., Ronquist G, Haney M

PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]

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

Abstract 2688: A forward genetics screen of murine brain tumors identifies novel candidate genes involved in gliomagenesis

Cancer M, Weishaupt H, ..., Ameur A, Swartling FJ

Cancer Res 76 (14 Supplement) 2688-2688 [2016-07-15; online 2016-07-22]

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

Abstract 2473: Combined BET-bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Bolin S, Borgenvik A, ..., Weishaupt H, Swartling FJ

Cancer Res 76 (14 Supplement) 2473-2473 [2016-07-15; online 2016-07-22]

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

Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, ..., Andersson O, Stainier DY

Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service]

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Rafati N, Andersson LS, ..., Lindgren G, Rubin CJ

G3 (Bethesda) 6 (7) 2213-2223 [2016-07-07; online 2016-05-22]

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

Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus.

Chen D, Enroth S, ..., Xu S, Gyllensten U

Oncotarget 7 (27) 42216-42224 [2016-07-05; online 2016-06-11]

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

Scolytus multistriatus associated with Dutch elm disease on the island of Gotland: phenology and communities of vectored fungi

Menkis A, Östbrant IL, ..., Balalaikins M, Vasaitis R

Mycol Progress 15 (6) - [2016-06-00; online 2016-05-26]

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

mRNA GPR162 changes are associated with decreased food intake in rat, and its human genetic variants with impairments in glucose homeostasis in two Swedish cohorts.

Caruso V, Sreedharan S, ..., Fredriksson R, Schiöth HB

Gene 581 (2) 139-145 [2016-05-01; online 2016-02-02]

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

Displacement of US-1 clonal lineage by a new lineage of Phytophthora infestanson potato in Kenya and Uganda

Njoroge AW, Tusiime G, Forbes GA, Yuen JE

Plant Pathol 65 (4) 587-592 [2016-05-00; online 2015-09-16]

DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Urbina H, Scofield DG, Cafaro M, Rosling A

Mycoscience 57 (3) 217-227 [2016-05-00; online 2016-05-00]

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

An obesity-associated risk allele within the FTO gene affects human brain activity for areas important for emotion, impulse control and reward in response to food images.

Wiemerslage L, Nilsson EK, ..., Brooks SJ, Schiöth HB

Eur. J. Neurosci. 43 (9) 1173-1180 [2016-05-00; online 2016-01-23]

The Mycobacterium phlei Genome: Expectations and Surprises.

Das S, Pettersson BM, ..., Bhattacharya A, Kirsebom LA

Genome Biol Evol 8 (4) 975-985 [2016-04-08; online 2016-03-05]

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

Sex-dependent expression of anti-Müllerian hormone (amh) and amh receptor 2 during sex organ differentiation and characterization of the Müllerian duct development in Xenopus tropicalis.

Jansson E, Mattsson A, Goldstone J, Berg C

Gen. Comp. Endocrinol. 229 (-) 132-144 [2016-04-01; online 2016-03-19]

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

Granberg F, Bálint Á, Belák S

Rev. - Off. Int. Epizoot. 35 (1) 25-42 [2016-04-00; online 2016-05-25]

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

Hovmøller MS, Walter S, ..., Ali S, de Vallavieille-Pope C

Plant Pathol 65 (3) 402-411 [2016-04-00; online 2015-07-20]

Fatal acquisition of vanD gene during vancomycin treatment of septicaemia caused by Enterococcus faecium.

Starlander G, Tellgren-Roth C, Melhus Å

J. Hosp. Infect. 92 (4) 409-410 [2016-04-00; online 2016-02-16]

VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.

Li X, Padhan N, ..., Jansson L, Claesson-Welsh L

Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]

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

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.

Karlsson OE, Larsson J, ..., Berg M, Jacobson M

PLoS ONE 11 (3) e0151481 [2016-03-16; online 2016-03-16]

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

Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.

Müller B, Sun L, Westerholm M, Schnürer A

Biotechnol Biofuels 9 (-) 48 [2016-02-27; online 2016-02-27]

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

Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes.

Olivo G, Wiemerslage L, ..., Brooks SJ, Schiöth HB

Front Hum Neurosci 10 (-) 52 [2016-02-17; online 2016-02-17]

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

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target.

Agarwal P, Alzrigat M, ..., Kalushkova A, Jernberg-Wiklund H

Oncotarget 7 (6) 6809-6823 [2016-02-09; online 2016-01-13]

Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

Sooman L, Wennman A, ..., Hoffmann I, Oliw EH

Biochim. Biophys. Acta 1861 (2) 108-118 [2016-02-00; online 2015-11-26]

Complete Knockout of Endogenous Mdr1 ( Abcb1 ) in MDCK Cells by CRISPR-Cas9

Simoff I, Karlgren M, ..., Matsson P, Artursson P

Journal of Pharmaceutical Sciences 105 (2) 1017-1021 [2016-02-00; online 2016-02-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service]

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing.

Bergfors A, Leenheer D, ..., Ameur A, Lennerstrand J

Antiviral Res. 126 (-) 81-89 [2016-02-00; online 2015-12-29]

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

Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past.

Thach T, Ali S, ..., Justesen AF, Hovmøller MS

Fungal Genet. Biol. 87 (-) 1-8 [2016-02-00; online 2016-01-03]

Analyses of the ash dieback pathogen,Hymenoscyphus fraxineus, suggest role of tree species diversity on colonization and population structure differentiation

Nguyen DT, Cleary MR, ..., Berlin A, Stenlid J

For. Path. 46 (1) 82-84 [2016-02-00; online 2015-10-28]

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

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development.

Johansson MM, Lundin E, ..., Nilsson M, Jazin E

Biol Sex Differ 7 (-) 5 [2016-01-12; online 2016-01-12]

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

Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis.

Sayyab S, Viluma A, ..., Andersson G, Bergström TF

G3 (Bethesda) 6 (3) 521-527 [2016-01-08; online 2016-01-08]

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

Development of single-tube nested real-time PCR assays with long internally quenched probes for detection of norovirus genogroup II.

Xia H, Gravelsina S, ..., Ottoson J, Blomberg J

BioTechniques 60 (1) 28-34 [2016-01-00; online 2016-01-01]

Year 2015

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

Klar J, Raykova D, ..., Wanders A, Dahl N

Eur. J. Hum. Genet. 23 (12) 1679-1683 [2015-12-00; online 2015-03-19]

Freshwater protists do not go with the flow: population structure in Gonyostomum semen independent of connectivity among lakes.

Sassenhagen I, Sefbom J, ..., Godhe A, Rengefors K

Environ. Microbiol. 17 (12) 5063-5072 [2015-12-00; online 2015-07-18]

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, ..., Käller M, Vezzi F

Gigascience 4 (-) 56 [2015-11-26; online 2015-11-26]

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

Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.

Manzoor S, Müller B, ..., Schnürer A, Bongcam-Rudloff E

Stand Genomic Sci 10 (-) 99 [2015-11-11; online 2015-11-11]

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae).

Menkis A, Marčiulynas A, ..., Lynikienė J, Povilaitienė A

Microb. Ecol. 70 (4) 904-911 [2015-11-00; online 2015-06-10]

Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family.

Einarsdottir E, Svensson I, ..., Kere J, Matsson H

Hum. Genet. 134 (11-12) 1239-1248 [2015-11-00; online 2015-09-25]

Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.

Mushtaq M, Zubair S, ..., Bongcam-Rudloff E, Jansson DS

BMC Microbiol. 15 (-) 208 [2015-10-12; online 2015-10-12]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system.

Viluma A, Sayyab S, ..., Andersson G, Bergström TF

Canine Genet Epidemiol 2 (-) 16 [2015-10-08; online 2015-10-08]

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling.

Schuster J, Halvardson J, ..., Feuk L, Dahl N

Cell Reprogram 17 (5) 327-337 [2015-10-00; online 2015-09-09]

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Norling M, Bishop RP, ..., Daubenberger CA, Silva JC

BMC Genomics 16 (-) 729 [2015-09-24; online 2015-09-24]

Genetic and morphological evidence for introgression between three species of willows.

Fogelqvist J, Verkhozina AV, ..., Lascoux M, Berlin S

BMC Evol. Biol. 15 (-) 193 [2015-09-16; online 2015-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

Rask-Andersen M, Sällman Almén M, ..., Fredriksson R, Schiöth HB

Genet Res (Camb) 97 (-) e16 [2015-09-14; online 2015-09-14]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

An Exopolysaccharide-Deficient Mutant of Lactobacillus rhamnosus GG Efficiently Displays a Protective Llama Antibody Fragment against Rotavirus on Its Surface.

Álvarez B, Krogh-Andersen K, ..., Hammarström L, Marcotte H

Appl. Environ. Microbiol. 81 (17) 5784-5793 [2015-09-01; online 2015-06-21]

Whole exome sequencing identifies LRP1 as a pathogenic gene in autosomal recessive keratosis pilaris atrophicans.

Klar J, Schuster J, ..., Baig SM, Dahl N

J. Med. Genet. 52 (9) 599-606 [2015-09-00; online 2015-07-05]

Manganese lipoxygenase of F. oxysporum and the structural basis for biosynthesis of distinct 11-hydroperoxy stereoisomers.

Wennman A, Magnuson A, Hamberg M, Oliw EH

J. Lipid Res. 56 (8) 1606-1615 [2015-08-00; online 2015-06-27]

Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden.

Lindström I, Kjellin M, ..., Lannergard A, Lennerstrand J

Infect Dis (Lond) 47 (8) 555-562 [2015-08-00; online 2015-04-09]

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Osman A, Hitzler WE, Ameur A, Provost P

PLoS ONE 10 (7) e0133070 [2015-07-14; online 2015-07-14]

Identification of large variation in pfcrt, pfmdr-1 and pfubp-1 markers in Plasmodium falciparum isolates from Ethiopia and Tanzania.

Golassa L, Kamugisha E, ..., Choy A, Swedberg G

Malar. J. 14 (-) 264 [2015-07-08; online 2015-07-08]

Scaffolding of a bacterial genome using MinION nanopore sequencing.

Karlsson E, Lärkeryd A, ..., Forsman M, Stenberg P

Sci Rep 5 (-) 11996 [2015-07-07; online 2015-07-07]

Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor.

de Miranda JR, Cornman RS, ..., Neumann P, Gauthier L

Viruses 7 (7) 3586-3602 [2015-07-06; online 2015-07-06]

Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Krogvold L, Skog O, ..., Korsgren O, Dahl-Jørgensen K

Diabetes 64 (7) 2506-2512 [2015-07-00; online 2015-02-14]

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Schwelm A, Fogelqvist J, ..., Ludwig-Müller J, Dixelius C

Sci Rep 5 (-) 11153 [2015-06-18; online 2015-06-18]

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

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

Agarwal P, Collier P, ..., Westermark B, Singh U

BMC Genomics 16 (-) 390 [2015-05-16; online 2015-05-16]

Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.

Gering E, Johnsson M, ..., Getty T, Wright D

Mol. Ecol. 24 (9) 2112-2124 [2015-05-00; online 2015-02-07]

Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents.

Voisin S, Almén MS, ..., Manios Y, Schiöth HB

Eur. J. Hum. Genet. 23 (5) 654-662 [2015-05-00; online 2014-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Polymorphisms in chloroquine resistance-associated genes in Plasmodium vivax in Ethiopia.

Golassa L, Erko B, ..., Aseffa A, Swedberg G

Malar. J. 14 (-) 164 [2015-04-16; online 2015-04-16]

Inter-relationships between the metrics of instrumental meat color and microbial growth during aerobic storage of beef at 4°C

Li S, Zamaratskaia G, ..., Borch E, Johansson M

Acta Agriculturae Scandinavica, Section A - Animal Science 65 (2) 97-106 [2015-04-03; online 2015-09-00]

Mixture effects of levonorgestrel and ethinylestradiol: estrogenic biomarkers and hormone receptor mRNA expression during sexual programming.

Säfholm M, Jansson E, Fick J, Berg C

Aquat. Toxicol. 161 (-) 146-153 [2015-04-00; online 2015-02-24]

Fluctuating expression of microRNAs in adenovirus infected cells.

Zhao H, Chen M, Tellgren-Roth C, Pettersson U

Virology 478 (-) 99-111 [2015-04-00; online 2015-03-07]

Functional anti-CD94/NKG2A and anti-CD94/NKG2C autoantibodies in patients with systemic lupus erythematosus.

Hagberg N, Theorell J, ..., Bryceson YT, Rönnblom L

Arthritis & rheumatology (Hoboken, N.J.) 67 (4) 1000-1011 [2015-04-00; online 2014-12-17]

Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards.

Gillman A, Muradrasoli S, ..., Olsen B, Järhult JD

Appl. Environ. Microbiol. 81 (7) 2378-2383 [2015-04-00; online 2015-01-27]

Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity.

Zheleznyakova GY, Nilsson EK, ..., Baranov VS, Schiöth HB

PLoS ONE 10 (3) e0121964 [2015-03-30; online 2015-03-30]

Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis.

Schüler W, Bunikis I, ..., Bergström S, Lundberg U

PLoS ONE 10 (3) e0120548 [2015-03-23; online 2015-03-23]

Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.

Svensson D, Öhrman C, ..., Forsman M, Sjödin A

Genome Announc 3 (2) - [2015-03-19; online 2015-03-19]

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

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

Wilbe M, Ekvall S, ..., Annerén G, Bondeson ML

J. Med. Genet. 52 (3) 195-202 [2015-03-00; online 2015-01-24]

Clinical Genomics Uppsala [] NGI Uppsala (Uppsala Genome Center) []

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

Forth M, Liljebladh B, ..., Hall PO, Treusch AH

ISME J 9 (3) 656-669 [2015-03-00; online 2014-09-23]

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing.

Cavelier L, Ameur A, ..., Olsson-Strömberg U, Hermanson M

BMC Cancer 15 (-) 45 [2015-02-12; online 2015-02-12]

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

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Leong SL, Lantz H, ..., Tellgren-Roth C, Schnürer J

Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]

Bioinformatics Support and Infrastructure [] NGI Stockholm (Genomics Applications) [] NGI Stockholm (Genomics Production) [] NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer.

Mengelbier LH, Karlsson J, ..., Mayrhofer M, Gisselsson D

Nat Commun 6 (-) 6125 [2015-01-27; online 2015-01-27]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.

Skog O, Korsgren S, ..., Korsgren O, Dahl-Jørgensen K

Am. J. Pathol. 185 (1) 129-138 [2015-01-00; online 2014-12-20]

Phenotypic plasticity and differentiation in an invasive freshwater microalga

Sassenhagen I, Wilken S, Godhe A, Rengefors K

Harmful Algae 41 (-) 38-45 [2015-01-00; online 2015-01-00]

Anti-Obesity Effects and Metabolism in DIO Mice of a Novel Hybrid Lipid with Lauric and Lipoic Acid

Madawala SR, Manubolu M, ..., Malmlöf K, Dutta PC

J Obes Weight Loss Ther 05 (02) - [2015-00-00; online 2015-00-00]

Year 2014

Serotonin receptor gene (5HT-2A) polymorphism is associated with provoked vestibulodynia and comorbid symptoms of pain.

Heddini U, Bohm-Starke N, ..., Nilsson KW, Johannesson U

J Sex Med 11 (12) 3064-3071 [2014-12-00; online 2014-09-02]

Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.

Sjödin A, Ohrman C, ..., Stenberg P, Thelaus J

Genome Announc 2 (6) - [2014-11-26; online 2014-11-26]

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

Metagenomic approaches to disclose disease-associated pathogens: detection of viral pathogens in honeybees.

Granberg F, Karlsson OE, Belák S

Methods Mol. Biol. 1247 (-) 491-511 [2014-11-17; online 2014-11-17]

Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells.

Kruczyk M, Przanowski P, ..., Kaminska B, Komorowski J

Biochim. Biophys. Acta 1839 (11) 1341-1350 [2014-11-00; online 2014-08-12]

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice.

Klar J, Hisatsune C, ..., Mikoshiba K, Dahl N

J. Clin. Invest. 124 (11) 4773-4780 [2014-11-00; online 2014-10-21]

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.

Ameur A, Bunikis I, Enroth S, Gyllensten U

Database (Oxford) 2014 (-) - [2014-10-03; online 2014-10-03]

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

Wallberg A, Han F, ..., Pirk CW, Webster MT

Nat. Genet. 46 (10) 1081-1088 [2014-10-00; online 2014-08-26]

Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation.

Khan TN, Klar J, ..., Baig SM, Dahl N

Eur. J. Hum. Genet. 22 (10) 1180-1184 [2014-10-00; online 2014-01-30]

Epoxy alcohol synthase of the rice blast fungus represents a novel subfamily of dioxygenase-cytochrome P450 fusion enzymes.

Hoffmann I, Jernerén F, Oliw EH

J. Lipid Res. 55 (10) 2113-2123 [2014-10-00; online 2014-08-15]

Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris.

Rodriguez-Algaba J, Walter S, ..., Hovmøller MS, Justesen AF

Fungal Genet. Biol. 70 (-) 77-85 [2014-09-00; online 2014-07-22]

Splicing in the human brain.

Zaghlool A, Ameur A, Cavelier L, Feuk L

Int. Rev. Neurobiol. 116 (-) 95-125 [2014-08-31; online 2014-08-31]

The Arthonialean challenge: Restructuring Arthoniaceae

Frisch A, Thor G, Ertz D, Grube M

Taxon 63 (4) 727-744 [2014-08-28; online 2014-08-28]

Small RNA sequence analysis of adenovirus VA RNA-derived miRNAs reveals an unexpected serotype-specific difference in structure and abundance.

Kamel W, Segerman B, Punga T, Akusjärvi G

PLoS ONE 9 (8) e105746 [2014-08-21; online 2014-08-21]

Cluster of infections caused by methicillin-resistant Staphylococcus pseudintermedius in humans in a tertiary hospital.

Starlander G, Börjesson S, ..., Tellgren-Roth C, Melhus A

J. Clin. Microbiol. 52 (8) 3118-3120 [2014-08-00; online 2014-05-30]

Distinct roles of Candida albicans-specific genes in host-pathogen interactions.

Wilson D, Mayer FL, ..., Jacobsen ID, Hube B

Eukaryotic Cell 13 (8) 977-989 [2014-08-00; online 2014-03-13]

Management intensity at field and landscape levels affects the structure of generalist predator communities.

Rusch A, Birkhofer K, ..., Smith HG, Ekbom B

Oecologia 175 (3) 971-983 [2014-07-00; online 2014-05-09]

Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy.

Schuster J, Khan TN, ..., Baig SM, Klar J

BMC Med. Genet. 15 (-) 71 [2014-06-24; online 2014-06-24]

Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.

Niazi A, Manzoor S, ..., Meijer J, Bongcam-Rudloff E

Stand Genomic Sci 9 (3) 718-725 [2014-06-15; online 2014-02-15]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, ..., Komorowski J, Wadelius C

Nucleic Acids Res. 42 (11) 6921-6934 [2014-06-00; online 2014-04-29]

Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.

Bäckdahl L, Ekman D, ..., Olsson T, Holmdahl R

BMC Genomics 15 (-) 391 [2014-05-21; online 2014-05-21]

The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings.

Xu D, Lin F, ..., Holm M, Deng XW

Plant Cell 26 (5) 1981-1991 [2014-05-00; online 2014-05-16]

Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.

Wahlestedt M, Ameur A, ..., Woods NB, Bryder D

Stem Cells 32 (5) 1173-1182 [2014-05-00; online 2014-01-22]

Impact of soil transfer between test fields on fungal diversity and wood durability

Råberg U, Terziev N, Daniel G

International Wood Products Journal 5 (2) 83-91 [2014-05-00; online 2013-12-19]

Seasonal pattern of lesion development in diseased Fraxinus excelsior infected by Hymenoscyphus pseudoalbidus.

Bengtsson SB, Barklund P, von Brömssen C, Stenlid J

PLoS ONE 9 (4) e76429 [2014-04-23; online 2014-04-23]

Erysipelothrix rhusiopathiae contamination in the poultry house environment during erysipelas outbreaks in organic laying hen flocks.

Eriksson H, Bagge E, ..., Fellström C, Jansson DS

Avian Pathol. 43 (3) 231-237 [2014-04-22; online 2014-03-26]

Autosomal recessive transmission of a rare KRT74 variant causes hair and nail ectodermal dysplasia: allelism with dominant woolly hair/hypotrichosis.

Raykova D, Klar J, ..., Baig SM, Dahl N

PLoS ONE 9 (4) e93607 [2014-04-08; online 2014-04-08]

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, ..., Andersson G, Andersson L

PLoS ONE 9 (4) e94187 [2014-04-08; online 2014-04-08]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Rask-Andersen M, Philippot G, ..., Fredriksson R, Schiöth HB

PLoS ONE 9 (4) e93193 [2014-04-02; online 2014-04-02]

High prevalence of pfcrt-CVIET haplotype in isolates from asymptomatic and symptomatic patients in south-central Oromia, Ethiopia.

Golassa L, Enweji N, ..., Aseffa A, Swedberg G

Malar. J. 13 (-) 120 [2014-03-27; online 2014-03-27]

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.

Ameur A, Meiring TL, ..., Williamson A, Gyllensten U

Sci Rep 4 (-) 4398 [2014-03-18; online 2014-03-18]

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution.

Wang B, Ekblom R, ..., Siitari H, Höglund J

BMC Genomics 15 (-) 180 [2014-03-06; online 2014-03-06]

Increased alpha-9 human papillomavirus species viral load in human immunodeficiency virus positive women.

Mbulawa ZZ, Johnson LF, ..., Gyllensten U, Williamson AL

BMC Infect. Dis. 14 (-) 51 [2014-01-31; online 2014-01-31]

Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden.

Danielsson A, Palanisamy N, ..., Sylvan S, Lennerstrand J

Infect Ecol Epidemiol 4 (-) - [2014-01-15; online 2014-01-15]

The maintenance of mitochondrial genetic variation by negative frequency-dependent selection.

Kazancıoğlu E, Arnqvist G

Ecol. Lett. 17 (1) 22-27 [2014-01-00; online 2013-10-19]

Year 2013

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

Zaghlool A, Ameur A, ..., Cavelier L, Feuk L

BMC Biotechnol. 13 (-) 99 [2013-11-13; online 2013-11-13]

Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data.

Ahsan M, Li X, ..., Carlborg O, Marklund S

Front Genet 4 (-) 226 [2013-11-05; online 2013-11-05]

In vitro and in vivo evaluation of osteoporosis therapeutic peptide PTH 1-34 loaded pegylated chitosan nanoparticles.

Narayanan D, Anitha A, Jayakumar R, Chennazhi KP

Mol. Pharm. 10 (11) 4159-4167 [2013-11-04; online 2013-09-07]

7,8- and 5,8-Linoleate diol synthases support the heterolytic scission of oxygen-oxygen bonds by different amide residues.

Hoffmann I, Oliw EH

Arch. Biochem. Biophys. 539 (1) 87-91 [2013-11-01; online 2013-09-26]

Discovery and refinement of loci associated with lipid levels.

Global Lipids Genetics Consortium N, Willer CJ, ..., Ingelsson E, Abecasis GR

Nat. Genet. 45 (11) 1274-1283 [2013-11-00; online 2013-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.

Wang X, Jiang L, ..., Andersson L, Welsh N

Proc. Natl. Acad. Sci. U.S.A. 110 (40) 15997-16002 [2013-10-01; online 2013-09-18]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity.

Zheleznyakova GY, Voisin S, ..., Baranov VS, Schiöth HB

Eur. J. Hum. Genet. 21 (9) 988-993 [2013-09-00; online 2013-01-10]

Automated serial extraction of DNA and RNA from biobanked tissue specimens.

Mathot L, Wallin M, Sjöblom T

BMC Biotechnol. 13 (-) 66 [2013-08-19; online 2013-08-19]

The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.

Rask-Andersen M, Moschonis G, ..., Fredriksson R, Schiöth HB

PLoS ONE 8 (8) e71353 [2013-08-15; online 2013-08-15]

Identification of adenovirus-encoded small RNAs by deep RNA sequencing.

Zhao H, Chen M, Pettersson U

Virology 442 (2) 148-155 [2013-08-01; online 2013-05-11]

Molecular identification and phylogenic analysis by sequencing the rDNA of copper-tolerant soft-rot Phialophora spp.

Karunasekera H, Daniel G

International Biodeterioration & Biodegradation 82 (-) 45-52 [2013-08-00; online 2013-08-00]

New viruses in veterinary medicine, detected by metagenomic approaches.

Belák S, Karlsson OE, ..., Berg M, Granberg F

Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]

Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.

Palanisamy N, Danielsson A, ..., Duberg AS, Lennerstrand J

Antiviral Res. 99 (1) 12-17 [2013-07-00; online 2013-05-08]

Parallel visualization of multiple protein complexes in individual cells in tumor tissue.

Leuchowius KJ, Clausson CM, ..., Landegren U, Söderberg O

Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]

NGI Uppsala (Uppsala Genome Center) [] PLA Proteomics []

Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.

Cassel-Lundhagen A, Ronnås C, ..., Wallén J, Larsson S

Mol. Ecol. 22 (12) 3362-3375 [2013-06-00; online 2013-05-31]

Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in healthy Swedish preschool children.

Kaarme J, Molin Y, Olsen B, Melhus A

Acta Paediatr. 102 (6) 655-660 [2013-06-00; online 2013-02-20]

Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.

Vandieken V, Thamdrup B

FEMS Microbiol. Ecol. 84 (2) 373-386 [2013-05-00; online 2013-01-08]

Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.

Hoffmann I, Jernerén F, Oliw EH

J. Biol. Chem. 288 (16) 11459-11469 [2013-04-19; online 2013-03-13]

Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B

EMBnet j. 19 (A) 60 [2013-04-08; online 2013-04-08]

Metagenomics sample preparation and sequencing.

Karlsson OE, Norling M, Bongcam-Rudloff E

EMBnet j. 19 (A) 55 [2013-04-08; online 2013-04-08]

Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings

Karlsson OE, Norling M, ..., Belák S, Bongcam-Rudloff E

EMBnet j. 19 (A) 21 [2013-04-08; online 2013-04-08]

RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.

Radomska KJ, Halvardson J, ..., Feuk L, Jazin E

Hum. Mol. Genet. 22 (7) 1373-1382 [2013-04-01; online 2013-01-17]

Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives

Råberg U, Terziev N, Daniel G

International Biodeterioration & Biodegradation 79 (-) 20-27 [2013-04-00; online 2013-04-00]

Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms.

Woodcock S, Besemer K, ..., Curtis TP, Sloan WT

Environ. Microbiol. 15 (4) 1216-1225 [2013-04-00; online 2012-12-18]

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

Klar J, Sobol M, ..., Casar-Borota O, Dahl N

Hum. Mutat. 34 (4) 572-577 [2013-04-00; online 2013-01-26]

The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

Axelsson E, Ratnakumar A, ..., Hedhammar A, Lindblad-Toh K

Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]

Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.

Tiukova IA, Petterson ME, ..., Pettersson OV, Passoth V

PLoS ONE 8 (3) e58455 [2013-03-13; online 2013-03-13]

Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.

Jiao X, Hooper SD, ..., Botling J, Sjöblom T

BMC Genomics 14 (-) 165 [2013-03-12; online 2013-03-12]

Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii.

Wennman A, Oliw EH

J. Lipid Res. 54 (3) 762-775 [2013-03-00; online 2012-12-13]

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.

Sällman Almén M, Rask-Andersen M, ..., Fredriksson R, Schiöth HB

Int J Obes (Lond) 37 (3) 424-431 [2013-03-00; online 2012-04-26]

The effect of substrate and operational parameters on the abundance of sulphate-reducing bacteria in industrial anaerobic biogas digesters.

Moestedt J, Nilsson Påledal S, Schnürer A

Bioresour. Technol. 132 (-) 327-332 [2013-03-00; online 2013-02-19]

Oral rehydration solution with glycerol to dairy calves: Effects on fluid balance, metabolism, and intestinal microbiota

Omazic AW, Tråvén M, ..., Mellgren E, Holtenius K

Acta Agriculturae Scandinavica, Section A - Animal Science 63 (1) 47-56 [2013-03-00; online 2013-03-00]

Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.

Pichler I, Schwienbacher C, ..., Hicks AA, Pramstaller PP

J. Mol. Neurosci. 49 (3) 600-605 [2013-03-00; online 2012-10-12]

The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).

Svensson J, Fick J, Brandt I, Brunström B

Environ. Sci. Technol. 47 (4) 2043-2051 [2013-02-19; online 2013-02-01]

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

Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas.

Cui T, Tsolakis AV, ..., Öberg K, Giandomenico V

Eur. J. Endocrinol. 168 (2) 253-261 [2013-02-00; online 2012-11-28]

Sequence variation in mitochondrial ATP synthase subunit 6 & 8 and nuclear genes ITS1 and ITS2 in 17 cyprinid species

Demandt MH

J. Appl. Ichthyol. 29 (1) 278-280 [2013-02-00; online 2012-06-22]

First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.

Müller B, Sun L, Schnürer A

Microbiologyopen 2 (1) 35-53 [2013-02-00; online 2012-12-15]

Exome RNA sequencing reveals rare and novel alternative transcripts.

Halvardson J, Zaghlool A, Feuk L

Nucleic Acids Res. 41 (1) e6 [2013-01-07; online 2012-09-04]

The genetic structure of the Lithuanian wolf population

Baltrūnaitė L, Balčiauskas L, Åkesson M

Open Life Sci 8 (5) - [2013-01-01; online 2013-01-01]

Proceedings of the 15th International Congress on Circumpolar Health

International Journal of Circumpolar Health 72 (1) 22447 [2013-01-00; online 2013-08-05]

First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B

Genome Announc 1 (1) - [2013-01-00; online 2013-02-21]

Year 2012

Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder.

Hooper SD, Johansson ACV, ..., Cavelier L, Feuk L

BMC Med. Genet. 13 (-) 123 [2012-12-19; online 2012-12-19]

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

Chasman DI, Fuchsberger C, ..., Fox CS, Köttgen A

Hum. Mol. Genet. 21 (24) 5329-5343 [2012-12-15; online 2012-09-11]

Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans.

Vetukuri RR, Åsman AKM, ..., Whisson SC, Dixelius C

PLoS ONE 7 (12) e51399 [2012-12-14; online 2012-12-14]

Strong signatures of selection in the domestic pig genome.

Rubin C, Megens H, ..., Groenen MAM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 109 (48) 19529-19536 [2012-11-27; online 2012-11-16]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements.

Hooper SD, Jiao X, ..., Sjöblom T, Cavelier L

BMC Res Notes 5 (-) 648 [2012-11-22; online 2012-11-22]

Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.

Cendejas-Bueno E, Kolecka A, ..., Gómez-López A, Boekhout T

J. Clin. Microbiol. 50 (11) 3641-3651 [2012-11-00; online 2012-09-07]

Human cord blood derived immature basophils show dual characteristics, expressing both basophil and eosinophil associated proteins.

Grundström J, Reimer JM, ..., Wernersson S, Hellman L

PLoS ONE 7 (10) e48308 [2012-10-31; online 2012-10-31]

Multiply-primed rolling circle amplification of human papillomavirus using sequence-specific primers.

Marincevic-Zuniga Y, Gustavsson I, Gyllensten U

Virology 432 (1) 57-62 [2012-10-10; online 2012-06-29]

Genetic variation in Puccinia graminis collected from oats, rye, and barberry.

Berlin A, Djurle A, Samils B, Yuen J

Phytopathology 102 (10) 1006-1012 [2012-10-00; online 2012-06-28]

MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.

Avesson L, Reimegård J, Wagner EGH, Söderbom F

RNA 18 (10) 1771-1782 [2012-10-00; online 2012-08-10]

Catalytic convergence of manganese and iron lipoxygenases by replacement of a single amino acid.

Wennman A, Jernerén F, Hamberg M, Oliw EH

J. Biol. Chem. 287 (38) 31757-31765 [2012-09-14; online 2012-07-24]

GCH1-polymorphism and pain sensitivity among women with provoked vestibulodynia.

Heddini U, Bohm-Starke N, ..., Nilsson KW, Johannesson U

Mol Pain 8 (-) 68 [2012-09-12; online 2012-09-12]

A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication.

Johnsson M, Gustafson I, ..., Jensen P, Wright D

PLoS Genet. 8 (8) e1002914 [2012-08-30; online 2012-08-30]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Intractable epilepsy of infancy due to homozygous mutation in the EFHC1 gene.

Berger I, Dor T, ..., Feuk L, Elpeleg O

Epilepsia 53 (8) 1436-1440 [2012-08-00; online 2012-06-14]

Unraveling assembly of stream biofilm communities.

Besemer K, Peter H, ..., Tranvik LJ, Battin TJ

ISME J 6 (8) 1459-1468 [2012-08-00; online 2012-01-13]

Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing.

Mohammad F, Pandey GK, ..., Gyllensten U, Kanduri C

Development 139 (15) 2792-2803 [2012-08-00; online 2012-06-23]

A-to-I editing of microRNAs in the mammalian brain increases during development.

Ekdahl Y, Farahani HS, ..., Lagergren J, Öhman M

Genome Res. 22 (8) 1477-1487 [2012-08-00; online 2012-05-31]

Polymorphisms in sh2b1 and spns1 loci are associated with triglyceride levels in a healthy population in northern Sweden.

PubMed

Västermark Å, Jacobsson JA, ..., Gyllensten U, Schiöth HB

J. Genet. 91 (2) 237-240 [2012-08-00; online 2012-09-04]

Polymorphisms and variants in the prion protein sequence of European moose (Alces alces), reindeer (Rangifer tarandus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Scandinavia.

Wik L, Mikko S, ..., Simonsson M, Linné T

Prion 6 (3) 256-260 [2012-07-01; online 2012-03-24]

Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia.

Mansouri L, Gunnarsson R, ..., Gyllensten U, Rosenquist R

Am. J. Hematol. 87 (7) 737-740 [2012-07-00; online 2012-06-08]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos.

Holmqvist P, Boija A, ..., Stenberg P, Mannervik M

PLoS Genet. 8 (6) e1002769 [2012-06-21; online 2012-06-21]

Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod.

Bach L, Dahllöf I

Aquat. Toxicol. 114-115 (-) 58-66 [2012-06-15; online 2012-03-17]

Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors.

Edlund K, Larsson O, ..., Botling J, Soussi T

Proc. Natl. Acad. Sci. U.S.A. 109 (24) 9551-9556 [2012-06-12; online 2012-05-26]

The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility.

Imsland F, Feng C, ..., Li N, Andersson L

PLoS Genet. 8 (6) e1002775 [2012-06-00; online 2012-06-28]

Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene.

Melkersson K, Persson B

Neuro Endocrinol. Lett. 33 (3) 321-330 [2012-05-29; online 2012-05-29]

The MAP2K5-linked SNP rs2241423 is associated with BMI and obesity in two cohorts of Swedish and Greek children.

Rask-Andersen M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

BMC Med. Genet. 13 (-) 36 [2012-05-17; online 2012-05-17]

Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids.

Ameur A, Enroth S, ..., Campbell H, Gyllensten U

Am. J. Hum. Genet. 90 (5) 809-820 [2012-05-04; online 2012-04-17]

Can weed hosts increase aggressiveness of Phytophthora infestans on potato?

Grönberg L, Andersson B, Yuen J

Phytopathology 102 (4) 429-433 [2012-04-00; online 2011-12-22]

The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus.

Kindgren P, Kremnev D, ..., Small I, Strand A

Plant J. 70 (2) 279-291 [2012-04-00; online 2012-01-04]

Proteinase production in Pseudomonas fluorescens ON2 is affected by carbon sources and allows surface-attached but not planktonic cells to utilize protein for growth in lake water.

Nicolaisen MH, Worm J, ..., Middelboe M, Nybroe O

FEMS Microbiol. Ecol. 80 (1) 168-178 [2012-04-00; online 2012-01-10]

Prevalence of Rickettsia spp., Anaplasma phagocytophilum, and Coxiella burnetii in adult Ixodes ricinus ticks from 29 study areas in central and southern Sweden.

Wallménius K, Pettersson JH, Jaenson TGT, Nilsson K

Ticks Tick Borne Dis 3 (2) 100-106 [2012-04-00; online 2012-01-09]

Mutational analysis of human glutathione transferase A2-2 identifies structural elements supporting high activity with the prodrug azathioprine.

Modén O, Zhang W, Mannervik B

Protein Eng. Des. Sel. 25 (4) 189-197 [2012-04-00; online 2012-02-16]

Genome-wide association and functional follow-up reveals new loci for kidney function.

Pattaro C, Köttgen A, ..., Kao WH, Fox CS

PLoS Genet. 8 (3) e1002584 [2012-03-29; online 2012-03-29]

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

Dastani Z, Hivert MF, ..., Rader DJ, Kathiresan S

PLoS Genet. 8 (3) e1002607 [2012-03-29; online 2012-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans.

Olszewski PK, Rozman J, ..., Schiöth HB, Kilimann MW

PLoS Genet. 8 (3) e1002568 [2012-03-15; online 2012-03-15]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes.

Edlund A, Ek K, Breitholtz M, Gorokhova E

PLoS ONE 7 (3) e33107 [2012-03-12; online 2012-03-12]

Infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aconitase, ACO2.

Spiegel R, Pines O, ..., Feuk L, Elpeleg O

Am. J. Hum. Genet. 90 (3) 518-523 [2012-03-09; online 2012-03-13]

Ecosystem effects of materials proposed for thin‑layer capping of contaminated sediments

Näslund J, Samuelsson G, ..., Cornelissen G, Schaanning M

Mar. Ecol. Prog. Ser. 449 (-) 27-40 [2012-03-08; online 2012-03-08]

Phenotypic variation within a clonal lineage of Phytophthora infestans infecting both tomato and potato in Nicaragua.

Blandón-Díaz JU, Widmark A, ..., Högberg N, Yuen JE

Phytopathology 102 (3) 323-330 [2012-03-00; online 2011-11-17]

Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.

Demirkan A, van Duijn CM, ..., Schmitz G, EUROSPAN consortium

PLoS Genet. 8 (2) e1002490 [2012-02-16; online 2012-02-16]

Association of TMEM18 variants with BMI and waist circumference in children and correlation of mRNA expression in the PFC with body weight in rats.

Rask-Andersen M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Eur. J. Hum. Genet. 20 (2) 192-197 [2012-02-00; online 2011-09-29]

Mutations in CTC1, encoding conserved telomere maintenance component 1, cause Coats plus.

Anderson BH, Kasher PR, ..., Rice GI, Crow YJ

Nat. Genet. 44 (3) 338-342 [2012-01-22; online 2012-01-22]

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.

Enroth S, Andersson CR, ..., Gustafsson MG, Komorowski J

Algorithms Mol Biol 7 (1) 2 [2012-01-16; online 2012-01-16]

Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility.

Castro FA, Ivansson EL, ..., Gyllensten UB, Pawlita M

Int. J. Cancer 130 (2) 349-355 [2012-01-15; online 2011-03-10]

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.

Bizuayehu TT, Lanes CFC, ..., Johansen SD, Babiak I

BMC Genomics 13 (-) 11 [2012-01-10; online 2012-01-10]

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.

Zaboli G, Ameur A, ..., Gyllensten U, EUROSPAN Consortium N

Eur. J. Hum. Genet. 20 (1) 77-83 [2012-01-00; online 2011-08-04]

Genetic variants near the MGAT1 gene are associated with body weight, BMI and fatty acid metabolism among adults and children.

Jacobsson JA, Rask-Andersen M, ..., Schiöth HB, Fredriksson R

Int J Obes (Lond) 36 (1) 119-129 [2012-01-00; online 2011-02-10]

NGI Uppsala (SNP&SEQ Technology Platform) [] NGI Uppsala (Uppsala Genome Center) []

Year 2011

PubMed

Association between body mass index and insulin receptor substrate-4 (IRS-4) gene polymorphisms in patients with schizophrenia.

Melkersson K, Persson B

Neuro Endocrinol. Lett. 32 (5) 634-640 [2011-12-15; online 2011-12-15]

Identification of immunogenic proteins in Treponema phagedenis-like strain V1 from digital dermatitis lesions by phage display.

Rosander A, Guss B, ..., Näslund K, Pringle M

Vet. Microbiol. 153 (3-4) 315-322 [2011-12-15; online 2011-07-19]

Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults.

Huffman JE, Knezevic A, ..., Wright AF, Lauc G

Hum. Mol. Genet. 20 (24) 5000-5011 [2011-12-15; online 2011-09-13]

Pathway-based analysis of genetic susceptibility to cervical cancer in situ: HLA-DPB1 affects risk in Swedish women.

Ivansson EL, Juko-Pecirep I, Erlich HA, Gyllensten UB

Genes Immun. 12 (8) 605-614 [2011-12-00; online 2011-07-01]

A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken.

Dorshorst B, Molin A, ..., Ashwell C, Andersson L

PLoS Genet. 7 (12) e1002412 [2011-12-00; online 2011-12-22]

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.

Ameur A, Zaghlool A, ..., Cavelier L, Feuk L

Nat. Struct. Mol. Biol. 18 (12) 1435-1440 [2011-11-06; online 2011-11-06]

Abundant class of non-coding RNA regulates development in the social amoeba Dictyostelium discoideum.

Avesson L, Schumacher HT, ..., Hellman U, Söderbom F

RNA Biol 8 (6) 1094-1104 [2011-11-01; online 2011-09-24]

Tracking Phytophthora infestans with SSR markers within and between seasons - a field study in Sweden

Widmark AK, Andersson B, Sandström M, Yuen JE

Plant Pathol 60 (5) 938-945 [2011-10-00; online 2011-03-16]

Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.

Norrgård MA, Mannervik B

J. Mol. Biol. 412 (1) 111-120 [2011-09-09; online 2011-08-09]

Genomic and clinical characteristics of six patients with partially overlapping interstitial deletions at 10p12p11.

Wentzel C, Rajcan-Separovic E, ..., Giurgea I, Thuresson AC

Eur. J. Hum. Genet. 19 (9) 959-964 [2011-09-00; online 2011-04-28]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

Variants in STAT5B associate with serum TC and LDL-C levels.

Kornfeld JW, Isaacs A, ..., Pramstaller PP, Hicks AA

J. Clin. Endocrinol. Metab. 96 (9) E1496-E1501 [2011-09-00; online 2011-07-15]

Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration.

Westerholm M, Müller B, Arthurson V, Schnürer A

Microbes Environ. 26 (4) 347-353 [2011-08-24; online 2011-08-24]

Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype.

Palomares M, Delicado A, ..., Hennekam RC, Lapunzina P

Am. J. Hum. Genet. 89 (2) 295-301 [2011-08-12; online 2011-08-02]

Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.

Cuong ND, Nicolaisen MH, Sørensen J, Olsson S

Microb. Ecol. 62 (2) 425-434 [2011-08-00; online 2011-03-03]

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.

Franzén O, Arner E, ..., Andersson B, Daub CO

PLoS Negl Trop Dis 5 (8) e1283 [2011-08-00; online 2011-08-30]

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

Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).

Jansson DS, Pringle M

Avian Pathol. 40 (4) 387-393 [2011-08-00; online 2011-08-05]

Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.

Jiao X, Rosenlund M, ..., Mangion J, Sjöblom T

PLoS ONE 6 (7) e22250 [2011-07-22; online 2011-07-22]

(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

Paulin MM, Nicolaisen MH, Sørensen J

Environ. Microbiol. 13 (6) 1513-1523 [2011-06-00; online 2011-03-23]

Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer.

Gao K, Brandt I, Goldstone JV, Jönsson ME

Comp. Biochem. Physiol. C Toxicol. Pharmacol. 154 (1) 42-55 [2011-06-00; online 2011-03-01]

Co-occurring SHOC2 and PTPN11 mutations in a patient with severe/complex Noonan syndrome-like phenotype.

Ekvall S, Hagenäs L, ..., Annerén G, Bondeson ML

Am. J. Med. Genet. A 155A (6) 1217-1224 [2011-06-00; online 2011-05-07]

Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.

Westerholm M, Roos S, Schnürer A

Syst. Appl. Microbiol. 34 (4) 260-266 [2011-06-00; online 2011-04-19]

Cardio-facio-cutaneous syndrome: does genotype predict phenotype?

Allanson JE, Annerén G, ..., Verloes A, Zenker M

Am J Med Genet C Semin Med Genet 157C (2) 129-135 [2011-05-15; online 2011-04-16]

Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.

Norrgård MA, Hellman U, Mannervik B

J. Biol. Chem. 286 (19) 16871-16878 [2011-05-13; online 2011-04-02]

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

Lind EE, Grahn M

Ecotoxicology 20 (3) 503-512 [2011-05-00; online 2011-04-02]

The 12q14 microdeletion syndrome: six new cases confirming the role of HMGA2 in growth.

Lynch SA, Foulds N, ..., Ennis S, Sharkey F

Eur. J. Hum. Genet. 19 (5) 534-539 [2011-05-00; online 2011-01-27]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

FATP4 missense and nonsense mutations cause similar features in Ichthyosis Prematurity Syndrome.

Sobol M, Dahl N, Klar J

BMC Res Notes 4 (-) 90 [2011-03-30; online 2011-03-30]

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.

Ameur A, Stewart JB, ..., Larsson N, Gyllensten U

PLoS Genet. 7 (3) e1002028 [2011-03-00; online 2011-03-24]

Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase.

Hoffmann I, Jernerén F, Garscha U, Oliw EH

Arch. Biochem. Biophys. 506 (2) 216-222 [2011-02-15; online 2010-12-07]

New CYP1 genes in the frog Xenopus (Silurana) tropicalis: induction patterns and effects of AHR agonists during development.

Jönsson ME, Berg C, Goldstone JV, Stegeman JJ

Toxicol. Appl. Pharmacol. 250 (2) 170-183 [2011-01-15; online 2010-10-23]

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.

Street NR, Jansson S, Hvidsten TR

BMC Plant Biol. 11 (-) 13 [2011-01-13; online 2011-01-13]

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

Targeted resequencing of candidate genes using selector probes.

Johansson H, Isaksson M, ..., Ericsson O, Nilsson M

Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-10]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

Year 2010

Unbalanced translocation 9;16 in two children with dysmorphic features, and severe developmental delay: Evidence of cross-over within derivative chromosome 9 in patient #1.

Zambrano RM, Wohler E, ..., Cutting GR, Batista DA

Eur J Med Genet 54 (2) 189-193 [2010-12-07; online 2010-12-07]

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

Cell Profiling [] NGI Uppsala (Uppsala Genome Center) []

Distinct gene expression profiles in subsets of chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors.

Marincevic M, Mansouri M, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (12) 2072-2079 [2010-12-00; online 2010-08-31]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.

Marklund S, Carlborg O

BMC Genomics 11 (-) 665 [2010-11-25; online 2010-11-25]

Meiofauna reduces bacterial mineralization of naphthalene in marine sediment.

Näslund J, Nascimento FJ, Gunnarsson JS

ISME J 4 (11) 1421-1430 [2010-11-00; online 2010-05-14]

Brain gene expression in relation to fearfulness in female red junglefowl (Gallus gallus).

Jöngren M, Westander J, Nätt D, Jensen P

Genes Brain Behav. 9 (7) 751-758 [2010-10-00; online 2010-07-06]

Lycosid spiders and alternative food: Feeding behavior and implications for biological control

Kuusk AK, Ekbom B

Biological Control 55 (1) 20-26 [2010-10-00; online 2010-10-00]

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.

Wetterbom A, Ameur A, ..., Gyllensten U, Cavelier L

Genome Biol. 11 (7) R78 [2010-07-23; online 2010-07-23]

Induction patterns of new CYP1 genes in environmentally exposed rainbow trout.

Jönsson ME, Gao K, ..., Goldstone JV, Brandt I

Aquat. Toxicol. 98 (4) 311-321 [2010-07-15; online 2010-04-08]

Different SNP combinations in the GCH1 gene and use of labor analgesia.

Dabo F, Grönbladh A, ..., Sundström-Poromaa I, Akerud H

Mol Pain 6 (-) 41 [2010-07-15; online 2010-07-15]

Interstitial Deletions at 6q14.1-q15 Associated with Obesity, Developmental Delay and a Distinct Clinical Phenotype.

Wentzel C, Lynch SA, ..., Annerén G, Thuresson AC

Mol Syndromol 1 (2) 75-81 [2010-06-09; online 2010-06-09]

Array and Analysis Facility [] NGI Uppsala (Uppsala Genome Center) []

Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.

Paulin MM, Nicolaisen MH, Sørensen J

Appl. Environ. Microbiol. 76 (9) 2873-2883 [2010-05-00; online 2010-03-23]

Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus.

Jernerén F, Garscha U, ..., Hamberg M, Oliw EH

Biochim. Biophys. Acta 1801 (4) 503-507 [2010-04-00; online 2010-01-05]

Whole-genome resequencing reveals loci under selection during chicken domestication.

Rubin C, Zody MC, ..., Lindblad-Toh K, Andersson L

Nature 464 (7288) 587-591 [2010-03-25; online 2010-03-12]

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J

PLoS ONE 5 (3) e9762 [2010-03-25; online 2010-03-25]

Investigation of gene dosage imbalances in patients with Noonan syndrome using multiplex ligation-dependent probe amplification analysis.

Nyström AM, Ekvall S, ..., Annerén G, Bondeson ML

Eur J Med Genet 53 (3) 117-121 [2010-03-17; online 2010-03-17]

Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U

Genome Biol. 11 (3) R34 [2010-03-17; online 2010-03-17]