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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 2017-12-13T17:00:11-05:00.

Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC, Khaled WT. Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing Nat Commun, 8, pp. 2128. doi:10.1038/s41467-017-02001-5 (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)
Swenson NG, Iida Y, Howe R, Wolf A, Umaña MN, Petprakob K, Turner BL, Ma K. Tree co-occurrence and transcriptomic response to drought Nat Commun, 8, pp. 1996. doi:10.1038/s41467-017-02034-w (8 December 2017)
Chamorro-Garcia R, Diaz-Castillo C, Shoucri BM, Käch H, Leavitt R, Shioda T, Blumberg B. Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice Nat Commun, 8, pp. 2012. doi:10.1038/s41467-017-01944-z (8 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)
Walder F, Schlaeppi K, Wittwer R, Held AY, Vogelgsang S, van der Heijden MG. Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing Front Plant Sci, 8, pp. 2019. doi:10.3389/fpls.2017.02019 (28 November 2017)
Guo D, Song X, Yuan M, Wang Z, Ge W, Wang L, Wang J, Wang X. RNA-Seq Profiling Shows Divergent Gene Expression Patterns in Arabidopsis Grown under Different Densities Front Plant Sci, 8, pp. 2001. doi:10.3389/fpls.2017.02001 (28 November 2017)
Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA. Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities Front Microbiol, 8, pp. 2321. doi:10.3389/fmicb.2017.02321 (28 November 2017)
Saavedra C, Milan M, Leite RB, Cordero D, Patarnello T, Cancela ML, Bargelloni L. A Microarray Study of Carpet-Shell Clam (Ruditapes decussatus) Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland Front Physiol, 8, pp. 943. doi:10.3389/fphys.2017.00943 (28 November 2017)
Kandhaya-Pillai R, Miro-Mur F, Alijotas-Reig J, Tchkonia T, Kirkland JL, Schwartz S Jr. TNFα-senescence initiates a STAT-dependent positive feedback loop, leading to a sustained interferon signature, DNA damage, and cytokine secretion Aging (Albany NY), 9(11), pp. 2411-2435. doi:10.18632/aging.101328 (22 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)
Peng Z, Wang J, Shan B, Yuan F, Li B, Dong Y, Peng W, Shi W, Cheng Y, Gao Y, Zhang C, Duan C. Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma. Sci Rep, 7(1), pp. 15331. doi:10.1038/s41598-017-15712-y (10 November 2017)
Ruzicka WB, Subburaju S, Coyle JT, Benes FM. Location Matters: Distinct DNA Methylation Patterns in GABAergic Interneuronal Populations from Separate Microcircuits within the Human Hippocampus. Hum Mol Genet. doi:10.1093/hmg/ddx395 (2 November 2017)
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res, 77(21), pp. e39-e42. doi:10.1158/0008-5472.CAN-17-0344 (1 November 2017)

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