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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 2016-05-04T04:00:12-04:00.

Wright ML, Dozmorov MG, Wolen AR, Jackson-Cook C, Starkweather AR, Lyon DE, York TP. Establishing an analytic pipeline for genome-wide DNA methylation Clin Epigenetics, 8, pp. 45. doi:10.1186/s13148-016-0212-7 (27 April 2016)
Milicchio F, Rose R, Bian J, Min J, Prosperi M. Visual programming for next-generation sequencing data analytics BioData Min, 9, pp. 16. doi:10.1186/s13040-016-0095-3 (27 April 2016)
L. Lun AT, Bach K, Marioni JC. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts Genome Biol, 17, pp. 75. doi:10.1186/s13059-016-0947-7 (27 April 2016)
Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF. The transcriptomics of an experimentally evolved plant-virus interaction Sci Rep, 6, pp. 24901. doi:10.1038/srep24901 (26 April 2016)
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biol, 17(1), pp. 74. doi:10.1186/s13059-016-0940-1 (23 April 2016)
Stuchbery R, Macintyre G, Cmero M, Harewood LM, Peters JS, Costello AJ, Hovens CM, Corcoran NM. Reduction in expression of the benign AR transcriptome is a hallmark of localised prostate cancer progression. Oncotarget. doi:10.18632/oncotarget.8915 (22 April 2016)
Ericsson M, Henriksen R, Bélteky J, Sundman AS, Shionoya K, Jensen P. Long-Term and Transgenerational Effects of Stress Experienced during Different Life Phases in Chickens (Gallus gallus) PLoS One, 11(4), pp. e0153879. doi:10.1371/journal.pone.0153879 (22 April 2016)
Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools PLoS One, 11(4), pp. e0153782. doi:10.1371/journal.pone.0153782 (21 April 2016)
Gerl MJ, Bittl V, Kirchner S, Sachsenheimer T, Brunner HL, Lüchtenborg C, Özbalci C, Wiedemann H, Wegehingel S, Nickel W, Haberkant P, Schultz C, Krüger M, Brügger B. Sphingosine-1-Phosphate Lyase Deficient Cells as a Tool to Study Protein Lipid Interactions PLoS One, 11(4), pp. e0153009. doi:10.1371/journal.pone.0153009 (21 April 2016)
Riba M, Garcia Manteiga JM, Bošnjak B, Cittaro D, Mikolka P, Le C, Epstein MM, Stupka E. Revealing the acute asthma ignorome: characterization and validation of uninvestigated gene networks Sci Rep, 6, pp. 24647. doi:10.1038/srep24647 (21 April 2016)
Gilroy KL, Terry A, Naseer A, de Ridder J, Allahyar A, Wang W, Carpenter E, Mason A, Wong GK, Cameron ER, Kilbey A, Neil JC. Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics PLoS One, 11(4), pp. e0154070. doi:10.1371/journal.pone.0154070 (20 April 2016)
Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A. Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment Sci Rep, 6, pp. 24724. doi:10.1038/srep24724 (20 April 2016)
Huang F, Dang Z, Suzuki Y, Horiuchi T, Yagi K, Kouguchi H, Irie T, Kim K, Oku Y. Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis PLoS Negl Trop Dis, 10(4), pp. e0004634. doi:10.1371/journal.pntd.0004634 (19 April 2016)
Wilkinson JM, Ladinig A, Bao H, Kommadath A, Stothard P, Lunney JK, Harding JC, Plastow GS. Differences in Whole Blood Gene Expression Associated with Infection Time-Course and Extent of Fetal Mortality in a Reproductive Model of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Infection PLoS One, 11(4), pp. e0153615. doi:10.1371/journal.pone.0153615 (19 April 2016)
Ding XL, Yang X, Liang G, Wang K. Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2′-deoxycytidine Sci Rep, 6, pp. 24545. doi:10.1038/srep24545 (19 April 2016)
Bian C, Hu Y, Ravi V, Kuznetsova IS, Shen X, Mu X, Sun Y, You X, Li J, Li X, Qiu Y, Tay BH, Thevasagayam NM, Komissarov AS, Trifonov V, Kabilov M, Tupikin A, Luo J, Liu Y, Song H, Liu C, Wang X, Gu D, Yang Y, Li W, Polgar G, Fan G, Zeng P, Zhang H, Xiong Z, Tang Z, Peng C, Ruan Z, Yu H, Chen J, Fan M, Huang Y, Wang M, Zhao X, Hu G, Yang H, Wang J, Wang J, Xu X, Song L, Xu G, Xu P, Xu J, O’Brien SJ, Orbán L, Venkatesh B, Shi Q. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts Sci Rep, 6, pp. 24501. doi:10.1038/srep24501 (19 April 2016)
Gu Z, Eils R, Schlesner M. gtrellis: an R/Bioconductor package for making genome-level Trellis graphics. BMC Bioinformatics, 17, pp. 169. doi:10.1186/s12859-016-1051-4 (18 April 2016)
Smalheiser NR, Bonifield G. Two Similarity Metrics for Medical Subject Headings (MeSH):: An Aid to Biomedical Text Mining and Author Name Disambiguation J Biomed Discov Collab, 7, pp. e1. doi:10.5210/disco.v7i0.6654 (15 April 2016)
Busby B, Lesko M, Federer L. Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping. F1000Res, 5, pp. 672. doi:10.12688/f1000research.8382.1 (13 April 2016)
Castellano E, Molina-Arcas M, Krygowska AA, East P, Warne P, Nicol A, Downward J. RAS signalling through PI3-Kinase controls cell migration via modulation of Reelin expression Nat Commun, 7, pp. 11245. doi:10.1038/ncomms11245 (13 April 2016)

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