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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 2017-07-26T01:40:13-04:00.

Kim G, Clarke CR, Larose H, Tran HT, Haak DC, Zhang L, Askew S, Barney J, Westwood JH. Herbicide injury induces DNA methylome alterations in Arabidopsis PeerJ, 5, pp. e3560. doi:10.7717/peerj.3560 (20 July 2017)
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity Sci Rep, 7, pp. 5894. doi:10.1038/s41598-017-05927-4 (19 July 2017)
Hernandez-Vargas H, Gruffat H, Cros MP, Diederichs A, Sirand C, Vargas-Ayala RC, Jay A, Durand G, Le Calvez-Kelm F, Herceg Z, Manet E, Wild CP, Tommasino M, Accardi R. Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines Sci Rep, 7, pp. 5852. doi:10.1038/s41598-017-05713-2 (19 July 2017)
Suomi T, Elo LL. Enhanced differential expression statistics for data-independent acquisition proteomics Sci Rep, 7, pp. 5869. doi:10.1038/s41598-017-05949-y (19 July 2017)
Maltby VE, Lea RA, Sanders KA, White N, Benton MC, Scott RJ, Lechner-Scott J. Differential methylation at MHC in CD4+ T cells is associated with multiple sclerosis independently of HLA-DRB1 Clin Epigenetics, 9, pp. 71. doi:10.1186/s13148-017-0371-1 (18 July 2017)
Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann JL, Brosch R, Barreiro LB, Gilad Y. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells Sci Rep, 7, pp. 5702. doi:10.1038/s41598-017-05878-w (18 July 2017)
Yadav RK, Jablonowski CM, Fernandez AG, Lowe BR, Henry RA, Finkelstein D, Barnum KJ, Pidoux AL, Kuo YM, Huang J, O’Connell MJ, Andrews AJ, Onar-Thomas A, Allshire RC, Partridge JF. Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe eLife, 6, pp. e27406. doi:10.7554/eLife.27406 (18 July 2017)
Alfaro JA, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC, Kislinger T. Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines Genome Med, 9, pp. 62. doi:10.1186/s13073-017-0454-9 (18 July 2017)
Zhao W, Mo Y, Wang S, Midorikawa K, Ma N, Hiraku Y, Oikawa S, Huang G, Zhang Z, Murata M, Takeuchi K. Quantitation of DNA methylation in Epstein-Barr virus–associated nasopharyngeal carcinoma by bisulfite amplicon sequencing BMC Cancer, 17, pp. 489. doi:10.1186/s12885-017-3482-3 (17 July 2017)
Ma S, Snyder M, Dinesh-Kumar SP. Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis Sci Rep, 7, pp. 5557. doi:10.1038/s41598-017-05705-2 (17 July 2017)
Bjørklund SS, Panda A, Kumar S, Seiler M, Robinson D, Gheeya J, Yao M, Alnæs GI, Toppmeyer D, Riis M, Naume B, Børresen-Dale AL, Kristensen VN, Ganesan S, Bhanot G. Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma Sci Rep, 7, pp. 5568. doi:10.1038/s41598-017-05537-0 (17 July 2017)
Toivanen PI, Nieminen T, Laakkonen JP, Heikura T, Kaikkonen MU, Ylä-Herttuala S. Snake venom VEGF Vammin induces a highly efficient angiogenic response in skeletal muscle via VEGFR-2/NRP specific signaling Sci Rep, 7, pp. 5525. doi:10.1038/s41598-017-05876-y (17 July 2017)
Johnston WL, Krizus A, Ramani AK, Dunham W, Youn JY, Fraser AG, Gingras AC, Dennis JW. C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility BMC Biol, 15, pp. 61. doi:10.1186/s12915-017-0398-y (17 July 2017)
Larsson C, Ali MA, Pandzic T, Lindroth AM, He L, Sjöblom T. Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition BMC Cancer, 17, pp. 487. doi:10.1186/s12885-017-3472-5 (17 July 2017)
Gonzalez LE, Keller K, Chan KX, Gessel MM, Thines BC. Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression BMC Genomics, 18, pp. 533. doi:10.1186/s12864-017-3864-6 (17 July 2017)
Rodríguez-García A, Sola-Landa A, Barreiro C. RNA-Seq-Based Comparative Transcriptomics: RNA Preparation and Bioinformatics. Methods Mol Biol, 1645, pp. 59-72. doi:10.1007/978-1-4939-7183-1_5 (16 July 2017)
Smith JR, Todd S, Ashander LM, Charitou T, Ma Y, Yeh S, Crozier I, Michael MZ, Appukuttan B, Williams KA, Lynn DJ, Marsh GA. Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye Transl Vis Sci Technol, 6(4), pp. 12. doi:10.1167/tvst.6.4.12 (14 July 2017)
Saxena A, Sachin K, Bhatia AK. System Level Meta-analysis of Microarray Datasets for Elucidation of Diabetes Mellitus Pathobiology. Curr Genomics, 18(3), pp. 298-304. doi:10.2174/1389202918666170105093339 (1 July 2017)
Bradley G, Barrett SJ. CausalR - extracting mechanistic sense from genome scale data. Bioinformatics. doi:10.1093/bioinformatics/btx425 (29 June 2017)
Bemis KA, Vitek O. matter: an R package for rapid prototyping with larger-than-memory datasets on disk. Bioinformatics. doi:10.1093/bioinformatics/btx392 (15 June 2017)


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