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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
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).
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
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2017-12-14T17:20:07-05:00.

Yang H, Zhao L, Zhao S, Wang J, Shi H. Biochemical and transcriptomic analyses of drought stress responses of LY1306 tobacco strain Sci Rep, 7, pp. 17442. doi:10.1038/s41598-017-17045-2 (12 December 2017)
Yamazaki S, Tanaka Y, Araki H, Kohda A, Sanematsu F, Arasaki T, Duan X, Miura F, Katagiri T, Shindo R, Nakano H, Ito T, Fukui Y, Endo S, Sumimoto H. The AP-1 transcription factor JunB is required for Th17 cell differentiation Sci Rep, 7, pp. 17402. doi:10.1038/s41598-017-17597-3 (12 December 2017)
Wenric S, ElGuendi S, Caberg JH, Bezzaou W, Fasquelle C, Charloteaux B, Karim L, Hennuy B, Frères P, Collignon J, Boukerroucha M, Schroeder H, Olivier F, Jossa V, Jerusalem G, Josse C, Bours V. Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer Sci Rep, 7, pp. 17452. doi:10.1038/s41598-017-17811-2 (12 December 2017)
Chiesa M, Colombo GI, Piacentini L. DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification. Bioinformatics. doi:10.1093/bioinformatics/btx795 (11 December 2017)
Hassan MA, Vasquez JJ, Guo-Liang C, Meissner M, Nicolai Siegel T. Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii BMC Genomics, 18, pp. 961. doi:10.1186/s12864-017-4362-6 (11 December 2017)
Metri R, Mohan A, Nsengimana J, Pozniak J, Molina-Paris C, Newton-Bishop J, Bishop D, Chandra N. Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach Sci Rep, 7, pp. 17314. doi:10.1038/s41598-017-17330-0 (11 December 2017)
Pegolo S, Dadousis C, Mach N, Ramayo-Caldas Y, Mele M, Conte G, Schiavon S, Bittante G, Cecchinato A. SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile Sci Rep, 7, pp. 17317. doi:10.1038/s41598-017-17434-7 (11 December 2017)
Capobianco E, Valdes C, Sarti S, Jiang Z, Poliseno L, Tsinoremas NF. Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes Sci Rep, 7, pp. 17344. doi:10.1038/s41598-017-17337-7 (11 December 2017)
Suzuki T, Maeda S, Furuhata E, Shimizu Y, Nishimura H, Kishima M, Suzuki H. A screening system to identify transcription factors that induce binding site-directed DNA demethylation Epigenetics Chromatin, 10, pp. 60. doi:10.1186/s13072-017-0169-6 (8 December 2017)
Ceeraz S, Eszterhas SK, Sergent PA, Armstrong DA, Ashare A, Broughton T, Wang L, Pechenick D, Burns CM, Noelle RJ, Vincenti MP, Fava RA. VISTA deficiency attenuates antibody-induced arthritis and alters macrophage gene expression in response to simulated immune complexes Arthritis Res Ther, 19, pp. 270. doi:10.1186/s13075-017-1474-y (8 December 2017)
Chicco D. Ten quick tips for machine learning in computational biology BioData Min, 10, pp. 35. doi:10.1186/s13040-017-0155-3 (8 December 2017)
Ferrari N, Granata I, Capaia M, Piccirillo M, Guarracino MR, Venè R, Brizzolara A, Petretto A, Inglese E, Morini M, Astigiano S, Amaro AA, Boccardo F, Balbi C, Barboro P. Adaptive phenotype drives resistance to androgen deprivation therapy in prostate cancer Cell Commun Signal, 15, pp. 51. doi:10.1186/s12964-017-0206-x (8 December 2017)
Zhang J, Wallace SJ, Shiu MY, Smith I, Rhind SG, Langlois VS. Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low‐volume, high‐intensity interval training Physiol Rep, 5(23), pp. e13534. doi:10.14814/phy2.13534 (7 December 2017)
Wang D, Haley JD, Thompson P. Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages BMC Cancer, 17, pp. 830. doi:10.1186/s12885-017-3832-1 (6 December 2017)
Janostiak R, Rauniyar N, Lam TT, Ou J, Zhu LJ, Green MR, Wajapeyee N. MELK promotes melanoma growth by stimulating the NF-κB pathway Cell Rep, 21(10), pp. 2829-2841. doi:10.1016/j.celrep.2017.11.033 (5 December 2017)
Delabrière A, Hohenester UM, Colsch B, Junot C, Fenaille F, Thévenot EA. proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry. Bioinformatics, 33(23), pp. 3767-3775. doi:10.1093/bioinformatics/btx458 (1 December 2017)
Esquinas C, Janciauskiene S, Gonzalo R, Mas de Xaxars G, Olejnicka B, Belmonte I, Barrecheguren M, Rodriguez E, Nuñez A, Rodriguez-Frias F, Miravitlles M. Gene and miRNA expression profiles in PBMCs from patients with severe and mild emphysema and PiZZ alpha1-antitrypsin deficiency Int J Chron Obstruct Pulmon Dis, 12, pp. 3381-3390. doi:10.2147/COPD.S145445 (29 November 2017)
Heyneke E, Watanabe M, Erban A, Duan G, Buchner P, Walther D, Kopka J, Hawkesford MJ, Hoefgen R. Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply Front Plant Sci, 8, pp. 2048. doi:10.3389/fpls.2017.02048 (29 November 2017)
Li J, Sagendorf JM, Chiu TP, Pasi M, Perez A, Rohs R. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Res. doi:10.1093/nar/gkx1145 (20 November 2017)
Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. doi:10.1093/nar/gkx1126 (13 November 2017)

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