BMC Genomics

Genetical genomics of growth in a chicken model.

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

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

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

Year 2017

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

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

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, ..., 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]

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, ..., Blomberg A, Burkhardt-Holm P

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]

Year 2016

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]

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

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

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, ..., Trygg J, Wingsle G

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

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

Year 2015

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]

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, ..., Cubeta MA, Högberg N

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

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, ..., Pontén F, Uhlén M

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, ..., Westermark B, Singh U

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

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

Bioinformatics Support and Infrastructure

Year 2014

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

Delroisse J, Ullrich-Lüter E, ..., Mallefet J, Flammang P

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, ..., Visa N, Wieslander L

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

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, ..., Tunlid A, André C

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

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

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, ..., Wu CC, Lundeberg J

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, ..., Olsson T, Holmdahl R

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, ..., Siitari H, Höglund J

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

Year 2013

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

Berglund EC, Lindqvist CM, ..., Lönnerholm G, Syvänen A

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, ..., Botling J, Sjöblom T

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

Year 2012

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, ..., Lascoux M, Källman T

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, ..., Lundeberg J, Akan P

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, ..., Andersson L, Jensen P

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, ..., Johansen SD, Babiak I

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

Year 2011

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

Llano-Diez M, Gustafson AM, ..., Goransson H, Larsson L

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

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

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

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

Year 2010

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)

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]

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, ..., Bürglin TR, Wright AP

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

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

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