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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 2017-06-24T17:20:10-04:00.

Liang Y, Kelemen A. Computational dynamic approaches for temporal omics data with applications to systems medicine BioData Min, 10, pp. 20. doi:10.1186/s13040-017-0140-x (17 June 2017)
Siebenkäs C, Chiappinelli KB, Guzzetta AA, Sharma A, Jeschke J, Vatapalli R, Baylin SB, Ahuja N. Inhibiting DNA methylation activates cancer testis antigens and expression of the antigen processing and presentation machinery in colon and ovarian cancer cells PLoS One, 12(6), pp. e0179501. doi:10.1371/journal.pone.0179501 (16 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)
Liu H, Ma L, Yang X, Zhang L, Zeng X, Xie S, Peng H, Gao S, Lin H, Pan G, Wu Y, Shen Y. Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation BMC Plant Biol, 17, pp. 105. doi:10.1186/s12870-017-1055-x (15 June 2017)
Schiavinato JL, Haddad R, Saldanha-Araujo F, Baiochi J, Araujo AG, Santos Scheucher P, Covas DT, Zago MA, Panepucci RA. TGF-beta/atRA-induced Tregs express a selected set of microRNAs involved in the repression of transcripts related to Th17 differentiation Sci Rep, 7, pp. 3627. doi:10.1038/s41598-017-03456-8 (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)
Yip SS, Liu Y, Parmar C, Li Q, Liu S, Qu F, Ye Z, Gillies RJ, Aerts HJ. Associations between radiologist-defined semantic and automatically computed radiomic features in non-small cell lung cancer Sci Rep, 7, pp. 3519. doi:10.1038/s41598-017-02425-5 (14 June 2017)
Alloza I, Goikuria H, Idro JL, Triviño JC, Fernández Velasco JM, Elizagaray E, García-Barcina M, Montoya-Murillo G, Sarasola E, Vega Manrique R, Freijo MD, Vandenbroeck K. RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability Sci Rep, 7, pp. 3470. doi:10.1038/s41598-017-03687-9 (14 June 2017)
Payton L, Perrigault M, Hoede C, Massabuau JC, Sow M, Huvet A, Boullot F, Fabioux C, Hegaret H, Tran D. Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum Sci Rep, 7, pp. 3480. doi:10.1038/s41598-017-03797-4 (14 June 2017)
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SA, Holland PW, Sandve SR, Macqueen DJ. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification Genome Biol, 18, pp. 111. doi:10.1186/s13059-017-1241-z (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)
Luo S, Cao N, Tang Y, Gu W. Identification of key microRNAs and genes in preeclampsia by bioinformatics analysis PLoS One, 12(6), pp. e0178549. doi:10.1371/journal.pone.0178549 (8 June 2017)
Hao X, Zhong Y, Fu X, Lv Z, Shen Q, Yan T, Shi P, Ma Y, Chen M, Lv X, Wu Z, Zhao J, Sun X, Li L, Tang K. Transcriptome Analysis of Genes Associated with the Artemisinin Biosynthesis by Jasmonic Acid Treatment under the Light in Artemisia annua Front Plant Sci, 8, pp. 971. doi:10.3389/fpls.2017.00971 (8 June 2017)
He J, Kim D, Zhou X, Ahn SJ, Burne RA, Richards VP, Koo H. RNA-Seq Reveals Enhanced Sugar Metabolism in Streptococcus mutans Co-cultured with Candida albicans within Mixed-Species Biofilms Front Microbiol, 8, pp. 1036. doi:10.3389/fmicb.2017.01036 (8 June 2017)
Xu Y, Bernecky C, Lee CT, Maier KC, Schwalb B, Tegunov D, Plitzko JM, Urlaub H, Cramer P. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex Nat Commun, 8, pp. 15741. doi:10.1038/ncomms15741 (6 June 2017)
Forrest D, James K, Yuzenkova Y, Zenkin N. Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase Nat Commun, 8, pp. 15774. doi:10.1038/ncomms15774 (6 June 2017)
Axelsson AS, Mahdi T, Nenonen HA, Singh T, Hänzelmann S, Wendt A, Bagge A, Reinbothe TM, Millstein J, Yang X, Zhang B, Gusmao EG, Shu L, Szabat M, Tang Y, Wang J, Salö S, Eliasson L, Artner I, Fex M, Johnson JD, Wollheim CB, Derry JM, Mecham B, Spégel P, Mulder H, Costa IG, Zhang E, Rosengren AH. Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes Nat Commun, 8, pp. 15652. doi:10.1038/ncomms15652 (6 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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