BMC Genomics

Metagenomic assemblies tend to break around antibiotic resistance genes.

Abramova A, Karkman A, Bengtsson-Palme J

BMC Genomics 25 (1) 959 [2024-10-14; online 2024-10-14]

Year 2022

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]

DDLS Fellow Tom van der Valk

Year 2019

ProTstab - predictor for cellular protein stability.

Yang Y, Ding X, Zhu G, ..., Lv Q, Vihinen M

BMC Genomics 20 (1) 804 [2019-11-04; online 2019-11-04]

Abhishek Niroula DDLS Fellow

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies.

Rangavittal S, Stopa N, Tomaszkiewicz M, ..., Makova KD, Medvedev P

BMC Genomics 20 (1) 641 [2019-08-09; online 2019-08-09]

Kristoffer Sahlin SciLifeLab Fellow

Year 2018

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) 295 [2018-04-26; online 2018-04-26]

Characterization of the human RFX transcription factor family by regulatory and target gene analysis.

Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, ..., Kere J, Swoboda P

BMC Genomics 19 (1) 181 [2018-03-06; online 2018-03-06]

Patterns of variation in cis-regulatory regions: examining evidence of purifying selection.

Naidoo T, Sjödin P, Schlebusch C, Jakobsson M

BMC Genomics 19 (1) 95 [2018-01-26; online 2018-01-26]

A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence.

Komseli ES, Pateras IS, Krejsgaard T, ..., Bartek J, Gorgoulis VG

BMC Genomics 19 (1) 37 [2018-01-10; online 2018-01-10]

Year 2017

Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets.

Boulund F, Berglund F, Flach CF, ..., Larsson DGJ, Kristiansson E

BMC Genomics 18 (1) 682 [2017-09-02; online 2017-09-02]

The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.

Kumar A, Kankainen M, Parsons A, ..., Mattila P, Heckman CA

BMC Genomics 18 (1) 629 [2017-08-17; online 2017-08-17]

Year 2016

Genome-wide association and replication study of anti-tuberculosis drugs-induced liver toxicity.

Petros Z, Lee MM, Takahashi A, ..., Kubo M, Aklillu E

BMC Genomics 17 (1) 755 [2016-09-26; online 2016-09-26]

Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes.

Khaliq Z, Leijon M, Belák S, Komorowski J

BMC Genomics 17 (-) 529 [2016-07-29; online 2016-07-29]

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]

Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease.

Olsson M, Kierczak M, Karlsson Å, ..., Lindblad-Toh K, Meadows JR

BMC Genomics 17 (-) 299 [2016-04-23; online 2016-04-23]

Year 2015

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG

BMC Genomics 16 (-) 964 [2015-11-17; online 2015-11-17]

Gene-pseudogene evolution: a probabilistic approach.

Mahmudi O, Sennblad B, Arvestad L, Nowick K, Lagergren J

BMC Genomics 16 Suppl 10 (-) S12 [2015-10-02; online 2015-10-02]

Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates.

Ankarklev J, Franzén O, Peirasmaki D, ..., Andersson B, Svärd SG

BMC Genomics 16 (-) 697 [2015-09-15; online 2015-09-15]

Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains.

Reis-Cunha JL, Rodrigues-Luiz GF, Valdivia HO, ..., Vasconcelos AT, Bartholomeu DC

BMC Genomics 16 (-) 499 [2015-07-04; online 2015-07-04]

Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.

Katayama S, Skoog T, Jouhilahti EM, ..., Kankuri E, Kere J

BMC Genomics 16 (-) 476 [2015-06-25; online 2015-06-25]

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 (1) 475 [2015-06-25; online 2015-06-25]

Adil Mardinoglu Affiliated researcher SciLifeLab Fellow

Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds.

Webster MT, Kamgari N, Perloski M, ..., Pielberg G, Lindblad-Toh K

BMC Genomics 16 (-) 474 [2015-06-23; online 2015-06-23]

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]

Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription.

Bornelöv S, Komorowski J, Wadelius C

BMC Genomics 16 (-) 300 [2015-04-15; online 2015-04-15]

Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut.

Ellegaard KM, Tamarit D, Javelind E, ..., Andersson SG, Vásquez A

BMC Genomics 16 (-) 284 [2015-04-11; online 2015-04-11]

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]

Year 2014

Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism.

Stranneheim H, Engvall M, Naess K, ..., von Döbeln U, Wedell A

BMC Genomics 15 (-) 1090 [2014-12-11; online 2014-12-11]

Analysis of the early heterocyst Cys-proteome in the multicellular cyanobacterium Nostoc punctiforme reveals novel insights into the division of labor within diazotrophic filaments.

Sandh G, Ramström M, Stensjö K

BMC Genomics 15 (-) 1064 [2014-12-04; online 2014-12-04]

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]

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]

Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing.

Cowled C, Stewart CR, Likic VA, ..., Bean AG, Wang LF

BMC Genomics 15 (1) 682 [2014-08-15; online 2014-08-15]

Marc Friedländer SciLifeLab Fellow

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]

Analysis of structural diversity in wolf-like canids reveals post-domestication variants.

Ramirez O, Olalde I, Berglund J, ..., Vilà C, Marques-Bonet T

BMC Genomics 15 (-) 465 [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

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

Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array.

Molin AM, Berglund J, Webster MT, Lindblad-Toh K

BMC Genomics 15 (-) 210 [2014-03-19; online 2014-03-19]

Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae

Magraner-Pardo L, Pelechano V, Coloma M, Tordera V

BMC Genomics 15 (1) 247 [2014-00-00; online 2014-00-00]

SciLifeLab Fellow Vicent Pelechano

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, Hayat S, ..., Lönnerholm G, Syvänen AC

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

Unsupervised genome-wide recognition of local relationship patterns.

Zamani N, Russell P, Lantz H, ..., Jern P, Grabherr MG

BMC Genomics 14 (-) 347 [2013-05-24; online 2013-05-24]

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

Rands CM, Darling A, Fujita M, ..., Abzhanov A, Ponting CP

BMC Genomics 14 (-) 95 [2013-02-12; online 2013-02-12]

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes.

Eckalbar WL, Hutchins ED, Markov GJ, ..., Huentelman MJ, Kusumi K

BMC Genomics 14 (-) 49 [2013-01-23; online 2013-01-23]

Year 2012

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]

Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses.

Sundström E, Imsland F, Mikko S, ..., Lindblad-Toh K, Andersson L

BMC Genomics 13 (-) 365 [2012-08-02; online 2012-08-02]

Year 2010

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]

Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.

Jerlström-Hultqvist J, Franzén O, Ankarklev J, ..., Svärd SG, Andersson B

BMC Genomics 11 (-) 543 [2010-10-07; online 2010-10-07]

Replication-biased genome organisation in the crenarchaeon Sulfolobus.

Andersson AF, Pelve EA, Lindeberg S, ..., Nilsson P, Bernander R

BMC Genomics 11 (-) 454 [2010-07-28; online 2010-07-28]