BMC Genomics

ISSN	1471-2164
ISSN-L	1471-2164
IUID	195595009e0546a29b69d3586c38783f
Modified	2020-11-27T13:14:03.639Z
Created	2017-05-09T09:12:44.789Z

Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.

de Haas EN, Pértille F, Kjaer JB, Jensen P, Guerrero-Bosagna C

BMC Genomics 25 (1) 1219 [2024-12-19; online 2024-12-19]

Bioinformatics Support for Computational Resources [Service]

Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting.

Frisk C, Ekström M, Eriksson MJ, ..., Linde C, Persson B

BMC Genomics 25 (1) 938 [2024-10-07; online 2024-10-07]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S

BMC Genomics 25 (1) 772 [2024-08-08; online 2024-08-08]

Bioinformatics (NBIS) [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.

Biswas T, Vogel H, Biedermann PHW, ..., Yuvaraj JK, Andersson MN

BMC Genomics 25 (1) 764 [2024-08-06; online 2024-08-06]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis.

Rosling A, Eshghi Sahraei S, Kalsoom Khan F, ..., Bonito G, Sánchez-García M

BMC Genomics 25 (1) 529 [2024-05-29; online 2024-05-29]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.

Mohamadnejad Sangdehi F, Jamsandekar MS, Enbody ED, Pettersson ME, Andersson L

BMC Genomics 25 (1) 459 [2024-05-10; online 2024-05-10]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Loss of chromosome Y in regulatory T cells.

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

BMC Genomics 25 (1) 243 [2024-03-05; online 2024-03-05]

Bioinformatics Support for Computational Resources [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Single-cell RNA-seq mapping of chicken peripheral blood leukocytes.

Maxwell M, Söderlund R, Härtle S, Wattrang E

BMC Genomics 25 (1) 124 [2024-01-29; online 2024-01-29]

Bioinformatics Support for Computational Resources [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.

Harish A, Lopes Pinto FA, Eriksson S, Johansson AM

BMC Genomics 25 (1) 89 [2024-01-22; online 2024-01-22]

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

PubMed DOI Crossref

Functional annotation of a divergent genome using sequence and structure-based similarity.

Svedberg D, Winiger RR, Berg A, ..., Vossbrinck CR, Barandun J

BMC Genomics 25 (1) 6 [2024-01-02; online 2024-01-02]

Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.

Hafstað V, Häkkinen J, Larsson M, ..., Vallon-Christersson J, Persson H

BMC Genomics 24 (1) 783 [2023-12-18; online 2023-12-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

RecView: an interactive R application for locating recombination positions using pedigree data.

Zhang H, Hansson B

BMC Genomics 24 (1) 712 [2023-11-25; online 2023-11-25]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).

Kurta K, Jeuthe H, Naboulsi R, de Koning DJ, Palaiokostas C

BMC Genomics 24 (1) 519 [2023-09-04; online 2023-09-04]

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

PubMed DOI Crossref

T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.

Gustafsson C, Hauenstein J, Frengen N, ..., Luc S, Månsson R

BMC Genomics 24 (1) 205 [2023-04-17; online 2023-04-17]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

The genetic basis of wing spots in Pieris canidia butterflies.

Wee JLQ, Murugesan SN, Wheat CW, Monteiro A

BMC Genomics 24 (1) 169 [2023-04-04; online 2023-04-04]

NGI Long read [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce.

Chen ZQ, Klingberg A, Hallingbäck HR, Wu HX

BMC Genomics 24 (1) 147 [2023-03-27; online 2023-03-27]

Bioinformatics (NBIS) [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis.

van Creij J, Auxier B, An J, ..., Pan Z, Limpens E

BMC Genomics 24 (1) 53 [2023-01-28; online 2023-01-28]

Microbial Single Cell Genomics [Service]

PubMed DOI Crossref

Early changes in gene expression profiles in AML patients during induction chemotherapy.

Jakobsen I, Sundkvist M, Björn N, Gréen H, Lotfi K

BMC Genomics 23 (1) 752 [2022-11-14; online 2022-11-14]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genomic trajectories of a near-extinction event in the Chatham Island black robin.

von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N

BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.

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

BMC Genomics 23 (1) 704 [2022-10-15; online 2022-10-15]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.

Sigeman H, Sinclair B, Hansson B

BMC Genomics 23 (1) 328 [2022-04-27; online 2022-04-27]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.

Lewerentz J, Johansson A, Larsson J, Stenberg P

BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

Börjesson V, Martinez-Monleon A, Fransson S, ..., Milosevic J, López MD

BMC Genomics 23 (1) 149 [2022-02-20; online 2022-02-20]

Clinical Genomics [Technology development] Clinical Genomics Gothenburg [Technology development]

PubMed DOI Crossref

Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia.

Pagnon de la Vega M, Näslund C, Brundin R, ..., Ingelsson M, Giedraitis V

BMC Genomics 23 (1) 99 [2022-02-04; online 2022-02-04]

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

PubMed DOI Crossref

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes.

Anderson BM, Krause K, Petersen G

BMC Genomics 22 (1) 816 [2021-11-12; online 2021-11-12]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

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

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

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

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

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

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

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

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires.

Elfstrand M, Chen J, Cleary M, ..., Stadler M, Durling MB

BMC Genomics 22 (1) 503 [2021-07-04; online 2021-07-04]

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

PubMed DOI Crossref

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

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

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

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.

Lindner M, Verhagen I, Viitaniemi HM, ..., Husby A, van Oers K

BMC Genomics 22 (1) 36 [2021-01-07; online 2021-01-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Moose genomes reveal past glacial demography and the origin of modern lineages.

Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D

BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]

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

PubMed DOI Crossref

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.

Feuerborn TR, Palkopoulou E, van der Valk T, ..., Dalén L, Díez-Del-Molino D

BMC Genomics 21 (1) 844 [2020-11-30; online 2020-11-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.

Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX

BMC Genomics 21 (1) 796 [2020-11-16; online 2020-11-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity.

Lytrivi M, Ghaddar K, Lopes M, ..., Eizirik DL, Cnop M

BMC Genomics 21 (1) 590 [2020-08-26; online 2020-08-26]

Global Proteomics and Proteogenomics [Collaborative]

PubMed DOI Crossref

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.

Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R

BMC Genomics 21 (1) 518 [2020-07-29; online 2020-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.

Bergenstråhle J, Larsson L, Lundeberg J

BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.

Onsbring H, Tice AK, Barton BT, Brown MW, Ettema TJG

BMC Genomics 21 (1) 448 [2020-06-29; online 2020-06-29]

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

PubMed DOI Crossref

LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

Jhamat N, Niazi A, Guo Y, ..., Andersson G, Humblot P

BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.

Bianchi M, Rafati N, Karlsson Å, ..., Lindblad-Toh K, Rosengren Pielberg G

BMC Genomics 21 (1) 307 [2020-04-16; online 2020-04-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

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

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

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

Rugiu L, Panova M, Pereyra RT, Jormalainen V

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

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

Nakamura M, Köhler C, Hennig L

BMC Genomics 20 (1) 997 [2019-12-19; online 2019-12-19]

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

PubMed DOI Crossref

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

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

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

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

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

BMC Genomics 20 (1) 106 [2019-12-00; online 2019-02-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

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

Baião GC, Schneider DI, Miller WJ, Klasson L

BMC Genomics 20 (1) 465 [2019-06-07; online 2019-06-07]

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

PubMed DOI Crossref

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.

Wallberg A, Bunikis I, Pettersson OV, ..., Robinson GE, Webster MT

BMC Genomics 20 (1) 275 [2019-04-08; online 2019-04-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

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

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

BMC Genomics 20 (1) 104 [2019-02-04; online 2019-02-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

De Wit P, Durland E, Ventura A, Langdon CJ

BMC Genomics 19 (1) - [2018-12-00; online 2018-02-22]

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

PubMed DOI Crossref

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Bornelöv S, Seroussi E, Yosefi S, ..., Andersson L, Friedman-Einat M

BMC Genomics 19 (1) - [2018-12-00; online 2018-04-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Reimer C, Rubin CJ, Sharifi AR, ..., Schlather M, Simianer H

BMC Genomics 19 (1) - [2018-12-00; online 2018-09-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N

BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

BMC Genomics 19 (1) 72 [2018-01-23; online 2018-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees.

Obudulu O, Mähler N, Skotare T, ..., Trygg J, Tuominen H

BMC Genomics 19 (1) 11 [2018-01-03; online 2018-01-03]

Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C

BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

Lillie M, Sheng Z, Honaker CF, ..., Siegel PB, Carlborg Ö

BMC Genomics 18 (1) - [2017-12-00; online 2017-01-18]

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

PubMed DOI Crossref

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.

Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, ..., Dalén L, Gilbert MTP

BMC Genomics 18 (1) 495 [2017-06-29; online 2017-06-29]

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

PubMed DOI Crossref

The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.

Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P

BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.

Liu H, Wang K, Lindås AC, Peeters E

BMC Genomics 17 (-) 569 [2016-08-08; online 2016-08-08]

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

PubMed DOI Crossref

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Troell K, Hallström B, Divne AM, ..., Beser J, Bertilsson S

BMC Genomics 17 (-) 471 [2016-06-23; online 2016-06-23]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

Obudulu O, Bygdell J, Sundberg B, ..., Trygg J, Wingsle G

BMC Genomics 17 (-) 119 [2016-02-18; online 2016-02-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

PubMed DOI Crossref

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, Pelle R, ..., Daubenberger CA, Silva JC

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.

Gkarmiri K, Finlay RD, Alström S, ..., Cubeta MA, Högberg N

BMC Genomics 16 (-) 630 [2015-08-22; online 2015-08-22]

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

PubMed DOI Crossref

Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.

Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF

BMC Genomics 16 (-) 514 [2015-07-09; online 2015-07-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M

BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]

PubMed DOI Crossref

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

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

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

Vigil-Stenman T, Larsson J, Nylander JA, Bergman B

BMC Genomics 16 (-) 193 [2015-03-17; online 2015-03-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

PubMed DOI Crossref

High opsin diversity in a non-visual infaunal brittle star.

Delroisse J, Ullrich-Lüter E, Ortega-Martinez O, ..., Mallefet J, Flammang P

BMC Genomics 15 (-) 1035 [2014-11-28; online 2014-11-28]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

PubMed DOI Crossref

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.

Kutsenko A, Svensson T, Nystedt B, ..., Visa N, Wieslander L

BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.

Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A

BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

PubMed DOI Crossref

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.

Panova M, Johansson T, Canbäck B, ..., Tunlid A, André C

BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

Analysis of stranded information using an automated procedure for strand specific RNA sequencing.

Sigurgeirsson B, Emanuelsson O, Lundeberg J

BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.

Ekblom R, Smeds L, Ellegren H

BMC Genomics 15 (-) 467 [2014-06-12; online 2014-06-12]

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

PubMed DOI Crossref

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.

Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J

BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

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

Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

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

Wang B, Ekblom R, Bunikis I, Siitari H, Höglund J

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.

Berglund EC, Lindqvist CM, Hayat S, ..., Lönnerholm G, Syvänen AC

BMC Genomics 14 (-) 856 [2013-12-05; online 2013-12-05]

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

PubMed DOI Crossref

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

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

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

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms.

Chen J, Uebbing S, Gyllenstrand N, ..., Lascoux M, Källman T

BMC Genomics 13 (-) 589 [2012-11-02; online 2012-11-02]

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

PubMed DOI Crossref

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.

Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P

BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

PubMed DOI Crossref

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.

Nätt D, Rubin CJ, Wright D, ..., Andersson L, Jensen P

BMC Genomics 13 (-) 59 [2012-02-04; online 2012-02-04]

Array and Analysis Facility

PubMed DOI Crossref

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.

Bizuayehu TT, Lanes CFC, Furmanek T, ..., Johansen SD, Babiak I

BMC Genomics 13 (-) 11 [2012-01-10; online 2012-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.

Llano-Diez M, Gustafson AM, Olsson C, Goransson H, Larsson L

BMC Genomics 12 (-) 602 [2011-12-13; online 2011-12-13]

Array and Analysis Facility

PubMed DOI Crossref

Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.

Håfström T, Jansson DS, Segerman B

BMC Genomics 12 (-) 395 [2011-08-04; online 2011-08-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.

Skarin H, Håfström T, Westerberg J, Segerman B

BMC Genomics 12 (-) 185 [2011-04-12; online 2011-04-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics

PubMed DOI Crossref

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]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.

Xue-Franzén Y, Johnsson A, Brodin D, ..., Bürglin TR, Wright AP

BMC Genomics 11 (-) 200 [2010-03-25; online 2010-03-25]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.

Sandberg J, Neiman M, Ahmadian A, Lundeberg J

BMC Genomics 11 (-) 140 [2010-02-26; online 2010-02-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed DOI Crossref

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.

Berlin S, Lagercrantz U, von Arnold S, Ost T, Rönnberg-Wästljung AC

BMC Genomics 11 (-) 129 [2010-02-23; online 2010-02-23]

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

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