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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 2017-05-23T09:40:10-04:00.

Lågstad S, Zhao S, Hoff AM, Johannessen B, Christian Lingjærde O, Skotheim RI. chimeraviz: A tool for visualizing chimeric RNA. Bioinformatics. doi:10.1093/bioinformatics/btx329 (19 May 2017)
García K, Yáñez C, Plaza N, Peña F, Sepúlveda P, Pérez-Reytor D, Espejo RT. Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment BMC Microbiol, 17, pp. 118. doi:10.1186/s12866-017-1030-6 (19 May 2017)
Bocuk D, Wolff A, Krause P, Salinas G, Bleckmann A, Hackl C, Beissbarth T, Koenig S. The adaptation of colorectal cancer cells when forming metastases in the liver: expression of associated genes and pathways in a mouse model BMC Cancer, 17, pp. 342. doi:10.1186/s12885-017-3342-1 (19 May 2017)
Xu W, Cao Y, Xie Z, He H, He S, Hong H, Bo X, Li F. NFPscanner: a webtool for knowledge-based deciphering of biomedical networks BMC Bioinformatics, 18, pp. 262. doi:10.1186/s12859-017-1673-1 (18 May 2017)
Sharma M, Zhang X, Zhang S, Niu L, Ho SM, Chen A, Huang S. Inhibition of endocytic lipid antigen presentation by common lipophilic environmental pollutants Sci Rep, 7, pp. 2085. doi:10.1038/s41598-017-02229-7 (18 May 2017)
Alhakami H, Mirebrahim H, Lonardi S. A comparative evaluation of genome assembly reconciliation tools Genome Biol, 18, pp. 93. doi:10.1186/s13059-017-1213-3 (18 May 2017)
Prada-Medina CA, Fukutani KF, Pavan Kumar N, Gil-Santana L, Babu S, Lichtenstein F, West K, Sivakumar S, Menon PA, Viswanathan V, Andrade BB, Nakaya HI, Kornfeld H. Systems Immunology of Diabetes-Tuberculosis Comorbidity Reveals Signatures of Disease Complications Sci Rep, 7, pp. 1999. doi:10.1038/s41598-017-01767-4 (17 May 2017)
Goldental-Cohen S, Burstein C, Biton I, Ben Sasson S, Sadeh A, Many Y, Doron-Faigenboim A, Zemach H, Mugira Y, Schneider D, Birger R, Meir S, Philosoph-Hadas S, Irihomovitch V, Lavee S, Avidan B, Ben-Ari G. Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound BMC Plant Biol, 17, pp. 87. doi:10.1186/s12870-017-1035-1 (16 May 2017)
Pastenes L, Valdivieso C, Di Genova A, Travisany D, Hart A, Montecino M, Orellana A, Gonzalez M, Gutiérrez RA, Allende ML, Maass A, Méndez MA. Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa Sci Rep, 7, pp. 1966. doi:10.1038/s41598-017-01982-z (16 May 2017)
Zhu LJ, Lawrence M, Gupta A, Pagès H, Kucukural A, Garber M, Wolfe SA. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases. BMC Genomics, 18(1), pp. 379. doi:10.1186/s12864-017-3746-y (15 May 2017)
Lun ATL, Richard AC, Marioni JC. Testing for differential abundance in mass cytometry data. Nat Methods. doi:10.1038/nmeth.4295 (15 May 2017)
Wang Y, Skibbe JR, Hu C, Dong L, Ferchen K, Su R, Li C, Huang H, Weng H, Huang H, Qin X, Jin J, Chen J, Jiang X. ALOX5 exhibits anti-tumor and drug-sensitizing effects in MLL-rearranged leukemia Sci Rep, 7, pp. 1853. doi:10.1038/s41598-017-01913-y (12 May 2017)
Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF, Chung IF. Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood Sci Rep, 7, pp. 1820. doi:10.1038/s41598-017-02067-7 (12 May 2017)
van Hagen M, Piebes DG, de Leeuw WC, Vuist IM, van Roon-Mom WM, Moerland PD, Verschure PJ. The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model BMC Genomics, 18, pp. 373. doi:10.1186/s12864-017-3745-z (12 May 2017)
Saleem MA, Mendoza-Parra MA, Cholley PE, Blum M, Gronemeyer H. Epimetheus - a multi-profile normalizer for epigenomic sequencing data BMC Bioinformatics, 18, pp. 259. doi:10.1186/s12859-017-1655-3 (12 May 2017)
Li J, Yao W, Zhang L, Bao L, Chen H, Wang D, Yue Z, Li Y, Zhang M, Hao C. Genome-wide DNA methylation analysis in lung fibroblasts co-cultured with silica-exposed alveolar macrophages Respir Res, 18, pp. 91. doi:10.1186/s12931-017-0576-z (12 May 2017)
Zyla J, Marczyk M, Weiner J, Polanska J. Ranking metrics in gene set enrichment analysis: do they matter? BMC Bioinformatics, 18, pp. 256. doi:10.1186/s12859-017-1674-0 (12 May 2017)
He H, Sun D, Zeng Y, Wang R, Zhu W, Cao S, Bray GA, Chen W, Shen H, Sacks FM, Qi L, Deng HW. A Systems Genetics Approach Identified GPD1L and its Molecular Mechanism for Obesity in Human Adipose Tissue Sci Rep, 7, pp. 1799. doi:10.1038/s41598-017-01517-6 (11 May 2017)

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