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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 2015-11-28T16:00:09-05:00.

Rittirsch D, Schoenborn V, Lindig S, Wanner E, Sprengel K, Günkel S, Schaarschmidt B, Märsmann S, Simmen HP, Cinelli P, Bauer M, Claus RA, Wanner GA. Improvement of prognostic performance in severely injured patients by integrated clinico-transcriptomics: a translational approach Crit Care, 19, pp. 414. doi:10.1186/s13054-015-1127-y (26 November 2015)
Peng J, Wei P, Zhang B, Zhao Y, Zeng D, Chen X, Li M, Chen X. Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei) BMC Genomics, 16, pp. 1006. doi:10.1186/s12864-015-2219-4 (25 November 2015)
Daca-Roszak P, Pfeifer A, Żebracka-Gala J, Rusinek D, Szybińska A, Jarząb B, Witt M, Ziętkiewicz E. Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies BMC Genomics, 16, pp. 1003. doi:10.1186/s12864-015-2202-0 (25 November 2015)
de la Torre A, Metivier A, Chu F, Laurens LM, Beck DA, Pienkos PT, Lidstrom ME, Kalyuzhnaya MG. Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1) Microb Cell Fact, 14, pp. 188. doi:10.1186/s12934-015-0377-3 (25 November 2015)
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B. Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinformatics. doi:10.1093/bioinformatics/btv693 (24 November 2015)
Herbert F, Tchitchek N, Bansal D, Jacques J, Pathak S, Bécavin C, Fesel C, Dalko E, Cazenave PA, Preda C, Ravindran B, Sharma S, Das B, Pied S. Evidence of IL-17, IP-10, and IL-10 involvement in multiple-organ dysfunction and IL-17 pathway in acute renal failure associated to Plasmodium falciparum malaria J Transl Med, 13, pp. 369. doi:10.1186/s12967-015-0731-6 (24 November 2015)
Liang H, Zeng E. RNA-Seq Experiment and Data Analysis. Methods Mol Biol, 1366, pp. 99-114. doi:10.1007/978-1-4939-3127-9_9 (21 November 2015)
Fischer M, Renard BY. iPQF: A new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Bioinformatics. doi:10.1093/bioinformatics/btv675 (20 November 2015)
Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets PLoS Biol, 13(11), pp. e1002307. doi:10.1371/journal.pbio.1002307 (20 November 2015)
Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K. Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica PLoS One, 10(11), pp. e0143525. doi:10.1371/journal.pone.0143525 (20 November 2015)
Chao MC, Zhu S, Kimura S, Davis BM, Schadt EE, Fang G, Waldor MK. A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen PLoS Genet, 11(11), pp. e1005666. doi:10.1371/journal.pgen.1005666 (20 November 2015)
Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals PLoS Genet, 11(11), pp. e1005652. doi:10.1371/journal.pgen.1005652 (20 November 2015)
Meziane O, Piquet S, Bossé GD, Gagné D, Paquet E, Robert C, Tones MA, Simard MJ. The human decapping scavenger enzyme DcpS modulates microRNA turnover Sci Rep, 5, pp. 16688. doi:10.1038/srep16688 (20 November 2015)
Blischak JD, Tailleux L, Mitrano A, Barreiro LB, Gilad Y. Mycobacterial infection induces a specific human innate immune response Sci Rep, 5, pp. 16882. doi:10.1038/srep16882 (20 November 2015)
Meunchan M, Michely S, Devillers H, Nicaud JM, Marty A, Neuvéglise C. Comprehensive Analysis of a Yeast Lipase Family in the Yarrowia Clade PLoS One, 10(11), pp. e0143096. doi:10.1371/journal.pone.0143096 (18 November 2015)
Zhu W, Kuziora M, Creasy T, Lai Z, Morehouse C, Guo X, Sebastian Y, Shen D, Huang J, Dry JR, Xue F, Jiang L, Yao Y, Higgs BW. BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data. Nucleic Acids Res. doi:10.1093/nar/gkv1102 (17 November 2015)
Lun AT, Smyth GK. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. doi:10.1093/nar/gkv1191 (17 November 2015)
Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B. GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data. BMC Genomics, 16(1), pp. 963. doi:10.1186/s12864-015-2140-x (17 November 2015)
Wockner LF, Morris CP, Noble EP, Lawford BR, Whitehall VL, Young RM, Voisey J. Brain-specific epigenetic markers of schizophrenia. Transl Psychiatry, 5, pp. e680. doi:10.1038/tp.2015.177 (17 November 2015)
Li P, Nie Y, Yu J. An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases PLoS One, 10(11), pp. e0143045. doi:10.1371/journal.pone.0143045 (17 November 2015)


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