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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 2016-08-26T11:00:14-04:00.

Akulenko R, Merl M, Helms V. BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data. PLoS One, 11(8), pp. e0159921. doi:10.1371/journal.pone.0159921 (25 August 2016)
Teschendorff AE, Zheng SC, Feber A, Yang Z, Beck S, Widschwendter M. The multi-omic landscape of transcription factor inactivation in cancer Genome Med, 8(1), pp. 89. doi:10.1186/s13073-016-0342-8 (25 August 2016)
Fakhry CT, Choudhary P, Gutteridge A, Sidders B, Chen P, Ziemek D, Zarringhalam K. Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinformatics, 17(1), pp. 318. doi:10.1186/s12859-016-1181-8 (24 August 2016)
Goetz F, Smith SE, Goetz G, Murphy CA. Sea lampreys elicit strong transcriptomic responses in the lake trout liver during parasitism BMC Genomics, 17(1), pp. 675. doi:10.1186/s12864-016-2959-9 (24 August 2016)
Humburg P, Maugeri N, Lee W, Mohr B, Knight JC. Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation Genome Med, 8(1), pp. 87. doi:10.1186/s13073-016-0345-5 (24 August 2016)
Hilinski WC, Bostrom JR, England SJ, Juárez-Morales JL, de Jager S, Armant O, Legradi J, Strähle U, Link BA, Lewis KE. Lmx1b is required for the glutamatergic fates of a subset of spinal cord neurons Neural Dev, 11(1), pp. 16. doi:10.1186/s13064-016-0070-1 (23 August 2016)
Majewska A, Gajewska M, Dembele K, Maciejewski H, Prostek A, Jank M. Lymphocytic, cytokine and transcriptomic profiles in peripheral blood of dogs with atopic dermatitis BMC Vet Res, 12(1), pp. 174. doi:10.1186/s12917-016-0805-6 (23 August 2016)
Vrahatis AG, Balomenos P, Tsakalidis AK, Bezerianos A. DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments. Bioinformatics. doi:10.1093/bioinformatics/btw544 (19 August 2016)
Manimaran S, Marie Selby H, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Corrada Bravo H, Evan Johnson W. BatchQC: Interactive software for evaluating sample and batch effects in genomic data. Bioinformatics. doi:10.1093/bioinformatics/btw538 (18 August 2016)
Joly Beauparlant C, Lamaze FC, Deschênes A, Samb R, Lemaçon A, Belleau P, Bilodeau S, Droit A. metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PLoS Comput Biol, 12(8), pp. e1004751. doi:10.1371/journal.pcbi.1004751 (18 August 2016)
Seno A, Kasai T, Ikeda M, Vaidyanath A, Masuda J, Mizutani A, Murakami H, Ishikawa T, Seno M. Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map Cancer Inform, 15, pp. 163-178. doi:10.4137/CIN.S39839 (16 August 2016)
Xu Z, Taylor JA, Leung YK, Ho SM, Niu L. oxBS-MLE: An efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics. doi:10.1093/bioinformatics/btw527 (13 August 2016)
Michna A, Braselmann H, Selmansberger M, Dietz A, Hess J, Gomolka M, Hornhardt S, Blüthgen N, Zitzelsberger H, Unger K. Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data. PLoS One, 11(8), pp. e0160791. doi:10.1371/journal.pone.0160791 (9 August 2016)
Westermark PO. Linking Core Promoter Classes to Circadian Transcription PLoS Genet, 12(8), pp. e1006231. doi:10.1371/journal.pgen.1006231 (9 August 2016)
Nunez JC, Oleksiak MF. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes PLoS One, 11(8), pp. e0160958. doi:10.1371/journal.pone.0160958 (9 August 2016)
Houston-Ludlam GA, Belew AT, El-Sayed NM. Comparative Transcriptome Profiling of Human Foreskin Fibroblasts Infected with the Sylvio and Y Strains of Trypanosoma cruzi PLoS One, 11(8), pp. e0159197. doi:10.1371/journal.pone.0159197 (9 August 2016)
Li F, Wang R, Qu C, Fu N, Luo C, Xu Y. Sequencing and Characterization of the Invasive Sycamore Lace Bug Corythucha ciliata (Hemiptera: Tingidae) Transcriptome PLoS One, 11(8), pp. e0160609. doi:10.1371/journal.pone.0160609 (5 August 2016)
Han B, Li W, Chen Z, Xu Q, Luo J, Shi Y, Li X, Yan X, Zhang J. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure PLoS One, 11(8), pp. e0160358. doi:10.1371/journal.pone.0160358 (5 August 2016)
Chow M, Lai K, Ahn R, Gupta R, Arron S, Liao W. Effect of Adalimumab on Gene Expression Profiles of Psoriatic Skin and Blood. J Drugs Dermatol, 15(8), pp. 988-94. doi: (1 August 2016)


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