BMC Genomics

ISSN	1471-2164
IUID	195595009e0546a29b69d3586c38783f
Modified	2017-05-09T09:12:44.789Z
Created	2017-05-09T09:12:44.789Z

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) - [2020-12-00; online 2020-06-29]

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

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

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

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

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]

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

pmc

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

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

pmc

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

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

pmc

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

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

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) - [2019-12-00; online 2019-02-06]

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

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) - [2019-12-00; online 2019-02-04]

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

DOI Crossref

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

Nakamura M, Köhler C, Hennig L

BMC Genomics 20 (1) - [2019-12-00; online 2019-12-19]

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

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) - [2019-12-00; 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 Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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

BioProject Dryad

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

BioProject

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

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

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

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] 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

pmc GEO

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

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

PubMed DOI Crossref

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] National Genomics Infrastructure [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

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] 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

SRA SRA SRA SRA SRA

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

pmc

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

pmc

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

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

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

pmc

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

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] 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

pmc

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

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

pmc

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

pmc

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

pmc

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

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

pmc GEO GEO

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

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

pmc

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

pmc

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

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

pmc

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

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

pmc

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

pmc

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

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

pmc GEO

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

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

pmc

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

pmc

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

pmc

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

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

pmc SRA

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

pmc SRA

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 A

pmc

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

pmc

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

pmc

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

pmc

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

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

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

pmc

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

pmc

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

pmc

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

pmc

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

pmc

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

pmc BioProject SRA

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

Cell Profiling NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed DOI Crossref

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]

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

pmc

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

pmc

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

pmc

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

BMC Genomics

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