BMC Genomics

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]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

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

BioProject

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

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

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

Dryad SRA SRA SRA SRA SRA BioProject

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

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

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

BioProject Dryad

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

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

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) - [2018-12-00; online 2018-01-03]

Swedish Metabolomics Centre (SMC) [Service]

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

pmc GEO

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

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

Genetical genomics of growth in a chicken model.

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

pmc

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

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

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

pmc

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

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

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

SRA SRA SRA SRA SRA

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

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

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

pmc

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

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

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

pmc

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

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

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

pmc

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

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

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

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

pmc

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

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service]

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

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

pmc

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

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

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

pmc

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

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

pmc

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

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

pmc

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

Bioinformatics Support and Infrastructure [Collaborative]

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

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

pmc GEO GEO

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

Bioinformatics Long-term Support WABI [Collaborative] Tissue Profiling [Collaborative]

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

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

pmc

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

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

pmc

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

Bioinformatics Support and Infrastructure

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

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

pmc

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

Bioinformatics Support and Infrastructure [Service]

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

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

pmc

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

Bioinformatics Support and Infrastructure

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

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

pmc GEO

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

Bioinformatics Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Sigurgeirsson B, Emanuelsson O, Lundeberg J

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Ekblom R, Smeds L, Ellegren H

pmc

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

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

pmc

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

Bioinformatics Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

pmc SRA

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

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

pmc SRA

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

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 A

pmc

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

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

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

pmc

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

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

pmc

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

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

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

pmc

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

Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

pmc

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

Array and Analysis Facility

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

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

pmc

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

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

pmc

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

Array and Analysis Facility

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Skarin H, Håfström T, Westerberg J, Segerman B

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

pmc BioProject SRA

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

Cell Profiling NGI Uppsala (Uppsala Genome Center)

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.

Marklund S, Carlborg O

pmc

BMC Genomics 11 (-) 665 [2010-11-25; online 2010-11-25]

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

pmc

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

Bioinformatics and Expression Analysis (BEA)

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

Sandberg J, Neiman M, Ahmadian A, Lundeberg J

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)