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Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.
Huber W, et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115-121; doi:10.1038/nmeth.3252 (full-text free with registration). PMC4509590
Kannan L, et al. (2015). Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. doi:10.1093/bib/bbv080
Love M, Huber W, and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550; doi:10.1186/s13059-014-0550-8
Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi: 10.1371/journal.pcbi.1003118


20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2015-11-30T16:40:07-05:00.

George P, Jensen S, Pogorelcnik R, Lee J, Xing Y, Brasset E, Vaury C, Sharakhov IV. Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophilamelanogaster Epigenetics Chromatin, 8, pp. 50. doi:10.1186/s13072-015-0041-5 (27 November 2015)
Graham DB, Root DE. Resources for the design of CRISPR gene editing experiments Genome Biol, 16, pp. 260. doi:10.1186/s13059-015-0823-x (27 November 2015)
Rise ML, Hall JR, Nash GW, Xue X, Booman M, Katan T, Gamperl AK. Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis BMC Genomics, 16, pp. 1016. doi:10.1186/s12864-015-2120-1 (26 November 2015)
Rittirsch D, Schoenborn V, Lindig S, Wanner E, Sprengel K, Günkel S, Schaarschmidt B, Märsmann S, Simmen HP, Cinelli P, Bauer M, Claus RA, Wanner GA. Improvement of prognostic performance in severely injured patients by integrated clinico-transcriptomics: a translational approach Crit Care, 19, pp. 414. doi:10.1186/s13054-015-1127-y (26 November 2015)
Trumbić Ž, Bekaert M, Taggart JB, Bron JE, Gharbi K, Mladineo I. Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758) BMC Genomics, 16, pp. 1007. doi:10.1186/s12864-015-2208-7 (25 November 2015)
Peng J, Wei P, Zhang B, Zhao Y, Zeng D, Chen X, Li M, Chen X. Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei) BMC Genomics, 16, pp. 1006. doi:10.1186/s12864-015-2219-4 (25 November 2015)
Daca-Roszak P, Pfeifer A, Żebracka-Gala J, Rusinek D, Szybińska A, Jarząb B, Witt M, Ziętkiewicz E. Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies BMC Genomics, 16, pp. 1003. doi:10.1186/s12864-015-2202-0 (25 November 2015)
Hamzić E, Buitenhuis B, Hérault F, Hawken R, Abrahamsen MS, Servin B, Elsen JM, Pinard - van der Laan MH, Bed’Hom B. Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers Genet Sel Evol, 47, pp. 91. doi:10.1186/s12711-015-0170-0 (25 November 2015)
de la Torre A, Metivier A, Chu F, Laurens LM, Beck DA, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1) Microb Cell Fact, 14, pp. 188. doi:10.1186/s12934-015-0377-3 (25 November 2015)
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B. Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinformatics. doi:10.1093/bioinformatics/btv693 (24 November 2015)
Coit P, Ognenovski M, Gensterblum E, Maksimowicz-McKinnon K, Wren JD, Sawalha AH. Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity Epigenetics Chromatin, 8, pp. 49. doi:10.1186/s13072-015-0037-1 (24 November 2015)
Herbert F, Tchitchek N, Bansal D, Jacques J, Pathak S, Bécavin C, Fesel C, Dalko E, Cazenave PA, Preda C, Ravindran B, Sharma S, Das B, Pied S. Evidence of IL-17, IP-10, and IL-10 involvement in multiple-organ dysfunction and IL-17 pathway in acute renal failure associated to Plasmodium falciparum malaria J Transl Med, 13, pp. 369. doi:10.1186/s12967-015-0731-6 (24 November 2015)
Chamberlain AJ, Vander Jagt CJ, Hayes BJ, Khansefid M, Marett LC, Millen CA, Nguyen TT, Goddard ME. Extensive variation between tissues in allele specific expression in an outbred mammal BMC Genomics, 16, pp. 993. doi:10.1186/s12864-015-2174-0 (23 November 2015)
Webb A, Papp AC, Curtis A, Newman LC, Pietrzak M, Seweryn M, Handelman SK, Rempala GA, Wang D, Graziosa E, Tyndale RF, Lerman C, Kelsoe JR, Mash DC, Sadee W. RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles BMC Genomics, 16, pp. 990. doi:10.1186/s12864-015-2207-8 (23 November 2015)
Lu Y, Li J, Cheng J, Lubahn DB. Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β BMC Mol Biol, 16, pp. 19. doi:10.1186/s12867-015-0047-3 (23 November 2015)
Mesak F, Tatarenkov A, Avise JC. Transcriptomics of diapause in an isogenic self-fertilizing vertebrate BMC Genomics, 16, pp. 989. doi:10.1186/s12864-015-2210-0 (23 November 2015)
Liang H, Zeng E. RNA-Seq Experiment and Data Analysis. Methods Mol Biol, 1366, pp. 99-114. doi:10.1007/978-1-4939-3127-9_9 (21 November 2015)
Gurevich M, Miron G, Falb RZ, Magalashvili D, Dolev M, Stern Y, Achiron A. Transcriptional response to interferon beta-1a treatment in patients with secondary progressive multiple sclerosis BMC Neurol, 15, pp. 240. doi:10.1186/s12883-015-0495-x (21 November 2015)
Marino RB, Kingsley LA, Hussain SK, Bream JH, Penogonda S, Duggal P, Martinson JJ. Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes BMC Res Notes, 8, pp. 697. doi:10.1186/s13104-015-1665-z (21 November 2015)
Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2 BMC Genomics, 16, pp. 982. doi:10.1186/s12864-015-2137-5 (21 November 2015)


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