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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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2017-04-29T03:40:10-04:00.

Pérez-Riesgo E, Gutiérrez LG, Ubierna D, Acedo A, Moyer MP, Núñez L, Villalobos C. Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer. Int J Mol Sci, 18(5). doi:10.3390/ijms18050922 (27 April 2017)
Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes Genome Med, 9, pp. 40. doi:10.1186/s13073-017-0429-x (26 April 2017)
Guérin F, Arnaiz O, Boggetto N, Denby Wilkes C, Meyer E, Sperling L, Duharcourt S. Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements BMC Genomics, 18, pp. 327. doi:10.1186/s12864-017-3713-7 (26 April 2017)
Ibarra-Soria X, Nakahara TS, Lilue J, Jiang Y, Trimmer C, Souza MA, Netto PH, Ikegami K, Murphy NR, Kusma M, Kirton A, Saraiva LR, Keane TM, Matsunami H, Mainland J, Papes F, Logan DW. Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated eLife, 6, pp. e21476. doi:10.7554/eLife.21476 (25 April 2017)
Larhammar M, Huntwork-Rodriguez S, Jiang Z, Solanoy H, Sengupta Ghosh A, Wang B, Kaminker JS, Huang K, Eastham-Anderson J, Siu M, Modrusan Z, Farley MM, Tessier-Lavigne M, Lewcock JW, Watkins TA. Dual leucine zipper kinase-dependent PERK activation contributes to neuronal degeneration following insult eLife, 6, pp. e20725. doi:10.7554/eLife.20725 (25 April 2017)
Suh HC, Benoukraf T, Shyamsunder P, Yin T, Cao Q, Said J, Lee S, Lim R, Yang H, Salotti J, Johnson PF, Madan V, Koeffler HP. LPS independent activation of the pro-inflammatory receptor Trem1 by C/EBPε in granulocytes Sci Rep, 7, pp. 46440. doi:10.1038/srep46440 (25 April 2017)
Obeidat M, Nie Y, Chen V, Shannon CP, Andiappan AK, Lee B, Rotzschke O, Castaldi PJ, Hersh CP, Fishbane N, Ng RT, McManus B, Miller BE, Rennard S, Paré PD, Sin DD. Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease Respir Res, 18, pp. 72. doi:10.1186/s12931-017-0558-1 (24 April 2017)
Broz AK, Guerrero RF, Randle AM, Baek YS, Hahn MW, Bedinger PA. Transcriptomic analysis links gene expression to unilateral pollen-pistil reproductive barriers BMC Plant Biol, 17, pp. 81. doi:10.1186/s12870-017-1032-4 (24 April 2017)
Bauernfeind AL, Babbitt CC. The predictive nature of transcript expression levels on protein expression in adult human brain BMC Genomics, 18, pp. 322. doi:10.1186/s12864-017-3674-x (24 April 2017)
Khan F, Chai HH, Ajmera I, Hodgman C, Mayes S, Lu C. A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress Genes (Basel), 8(4), pp. 121. doi:10.3390/genes8040121 (18 April 2017)
Bennett BD, Bushel PR. goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med, 12, pp. 6. doi:10.1186/s13029-017-0066-1 (13 April 2017)
Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F. Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput Biol, 13(4), pp. e1005496. doi:10.1371/journal.pcbi.1005496 (13 April 2017)
Li Y, Wan L, Bi S, Wan X, Li Z, Cao J, Tong Z, Xu H, He F, Li X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing Genes (Basel), 8(4), pp. 119. doi:10.3390/genes8040119 (13 April 2017)
Grimbs A, Shrestha A, Rezk AS, Grimbs S, Hakeem Said I, Schepker H, Hütt MT, Albach DC, Brix K, Kuhnert N, Ullrich MS. Bioactivity in Rhododendron: A Systemic Analysis of Antimicrobial and Cytotoxic Activities and Their Phylogenetic and Phytochemical Origins Front Plant Sci, 8, pp. 551. doi:10.3389/fpls.2017.00551 (13 April 2017)
Naake T, Gaquerel E. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data. Bioinformatics. doi:10.1093/bioinformatics/btx159 (11 April 2017)
Parodi AC, Sangalli LM, Vantini S, Amati B, Secchi P, Morelli MJ. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. Bioinformatics. doi:10.1093/bioinformatics/btx201 (7 April 2017)
Zhou X, Meng G, Nardini C, Mei H. Systemic Evaluation of Cellular Reprogramming Processes exploiting a novel R-tool: eegc. Bioinformatics. doi:10.1093/bioinformatics/btx205 (7 April 2017)
del Valle I, Buonocore F, Duncan AJ, Lin L, Barenco M, Parnaik R, Shah S, Hubank M, Gerrelli D, Achermann JC. A genomic atlas of human adrenal and gonad development Wellcome Open Res, 2, pp. 25. doi:10.12688/wellcomeopenres.11253.1 (7 April 2017)
Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe NM. GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. PLoS One, 12(4), pp. e0174744. doi:10.1371/journal.pone.0174744 (5 April 2017)
Aleksandr I, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. doi:10.1093/bioinformatics/btx162 (4 April 2017)

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