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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 2017-05-29T11:20:07-04:00.

Mock A, Murphy S, Morris J, Marass F, Rosenfeld N, Massie C. CVE: an R package for interactive variant prioritisation in precision oncology. BMC Med Genomics, 10(1), pp. 37. doi:10.1186/s12920-017-0261-6 (25 May 2017)
Suomi T, Seyednasrollah F, Jaakkola MK, Faux T, Elo LL. ROTS: An R package for reproducibility-optimized statistical testing. PLoS Comput Biol, 13(5), pp. e1005562. doi:10.1371/journal.pcbi.1005562 (25 May 2017)
Väremo L, Henriksen TI, Scheele C, Broholm C, Pedersen M, Uhlén M, Pedersen BK, Nielsen J. Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes Genome Med, 9, pp. 47. doi:10.1186/s13073-017-0432-2 (25 May 2017)
Qi Y, Li X, Chang C, Xu F, He Q, Zhao Y, Wu L. Ribosomal protein L23 negatively regulates cellular apoptosis via the RPL23/Miz-1/c-Myc circuit in higher-risk myelodysplastic syndrome Sci Rep, 7, pp. 2323. doi:10.1038/s41598-017-02403-x (24 May 2017)
Bouvier-Muller J, Allain C, Tabouret G, Enjalbert F, Portes D, Noirot C, Rupp R, Foucras G. Whole blood transcriptome analysis reveals potential competition in metabolic pathways between negative energy balance and response to inflammatory challenge Sci Rep, 7, pp. 2379. doi:10.1038/s41598-017-02391-y (24 May 2017)
Städler N, Dondelinger F, Hill SM, Akbani R, Lu Y, Mills GB, Mukherjee S. Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. Bioinformatics. doi:10.1093/bioinformatics/btx322 (23 May 2017)
Otto R, Sers C, Leser U. Robust in-silico identification of cancer cell lines based on next generation sequencing. Oncotarget, 8(21), pp. 34310-34320. doi:10.18632/oncotarget.16110 (23 May 2017)
Wang Z, Jin S, Liu G, Zhang X, Wang N, Wu D, Hu Y, Zhang C, Jiang Q, Xu L, Wang Y. DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data BMC Bioinformatics, 18, pp. 270. doi:10.1186/s12859-017-1647-3 (23 May 2017)
Corley SM, MacKenzie KL, Beverdam A, Roddam LF, Wilkins MR. Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols BMC Genomics, 18, pp. 399. doi:10.1186/s12864-017-3797-0 (23 May 2017)
Qian Y, Wang C, Wang J, Zhang X, Zhou Z, Zhao M, Lu C. Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation Sci Rep, 7, pp. 2284. doi:10.1038/s41598-017-02255-5 (23 May 2017)
Cimino PJ, Zager M, McFerrin L, Wirsching HG, Bolouri H, Hentschel B, von Deimling A, Jones D, Reifenberger G, Weller M, Holland EC. Multidimensional scaling of diffuse gliomas: application to the 2016 World Health Organization classification system with prognostically relevant molecular subtype discovery Acta Neuropathol Commun, 5, pp. 39. doi:10.1186/s40478-017-0443-7 (22 May 2017)
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)
Guo C, McDowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, Reddy TE. Transversions have larger regulatory effects than transitions BMC Genomics, 18, pp. 394. doi:10.1186/s12864-017-3785-4 (19 May 2017)
Campanini EB, Congrains C, Torres FR, de Brito RA. Odorant-binding proteins expression patterns in recently diverged species of Anastrepha fruit flies Sci Rep, 7, pp. 2194. doi:10.1038/s41598-017-02371-2 (19 May 2017)
Cao F, Fang Y, Tan HK, Goh Y, Choy JY, Koh BT, Hao Tan J, Bertin N, Ramadass A, Hunter E, Green J, Salter M, Akoulitchev A, Wang W, Chng WJ, Tenen DG, Fullwood MJ. Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions Sci Rep, 7, pp. 2186. doi:10.1038/s41598-017-02257-3 (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)
Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T. Transcriptomics technologies PLoS Comput Biol, 13(5), pp. e1005457. doi:10.1371/journal.pcbi.1005457 (18 May 2017)

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