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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 2017-07-22T00:20:10-04:00.

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)
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)
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)
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)
Celen C, Chuang JC, Luo X, Nijem N, Walker AK, Chen F, Zhang S, Chung AS, Nguyen LH, Nassour I, Budhipramono A, Sun X, Bok LA, McEntagart M, Gevers EF, Birnbaum SG, Eisch AJ, Powell CM, Ge WP, Santen GW, Chahrour M, Zhu H. Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment eLife, 6, pp. e25730. doi:10.7554/eLife.25730 (11 July 2017)
Hörmanseder E, Simeone A, Allen GE, Bradshaw CR, Figlmüller M, Gurdon J, Jullien J. H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos Cell Stem Cell, 21(1), pp. 135-143.e6. doi:10.1016/j.stem.2017.03.003 (6 July 2017)
Zhao C, Hu S, Huo X, Zhang Y. Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data PLoS One, 12(7), pp. e0180583. doi:10.1371/journal.pone.0180583 (3 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)
Ghazanfar S, Vuocolo T, Morrison JL, Nicholas LM, McMillen IC, Yang JY, Buckley MJ, Tellam RL. Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis PLoS One, 12(6), pp. e0180378. doi:10.1371/journal.pone.0180378 (30 June 2017)
Bradley G, Barrett SJ. CausalR - extracting mechanistic sense from genome scale data. Bioinformatics. doi:10.1093/bioinformatics/btx425 (29 June 2017)
Gutiérrez-Sacristán A, Bravo À, Portero-Tresserra M, Valverde O, Armario A, Blanco-Gandía MC, Farré A, Fernández-Ibarrondo L, Fonseca F, Giraldo J, Leis A, Mané A, Mayer MA, Montagud-Romero S, Nadal R, Ortiz J, Pavon FJ, Perez EJ, Rodríguez-Arias M, Serrano A, Torrens M, Warnault V, Sanz F, Furlong LI. Text mining and expert curation to develop a database on psychiatric diseases and their genes Database (Oxford), 2017, pp. bax043. doi:10.1093/database/bax043 (26 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)
Patil SU, Calatroni A, Schneider M, Steinbrecher J, Smith N, Washburn C, Ma A, Shreffler WG. Data-driven programmatic approach to analysis of basophil activation tests. Cytometry B Clin Cytom. doi:10.1002/cyto.b.21537 (15 June 2017)
Drummond MJ, Reidy PT, Baird LM, Dalley BK, Howard MT. Leucine Differentially Regulates Gene-Specific Translation in Mouse Skeletal Muscle. J Nutr. doi:10.3945/jn.117.251181 (14 June 2017)
Xu T, Duy Le T, Liu L, Su N, Wang R, Sun B, Colaprico A, Bontempi G, Li J. CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation, and visualization. Bioinformatics. doi:10.1093/bioinformatics/btx378 (12 June 2017)
Landolt L, Eikrem Ø, Strauss P, Scherer A, Lovett DH, Beisland C, Finne K, Osman T, Ibrahim MM, Gausdal G, Ahmed L, Lorens JB, Thiery JP, Tan TZ, Sekulic M, Marti HP. Clear Cell Renal Cell Carcinoma is linked to Epithelial-to-Mesenchymal Transition and to Fibrosis. Physiol Rep, 5(11). doi:10.14814/phy2.13305 (10 June 2017)
Gel B, Serra E. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics. doi:10.1093/bioinformatics/btx346 (29 May 2017)


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