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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 2016-08-24T10:20:09-04:00.

Abot A, Arnal G, Auer L, Lazuka A, Labourdette D, Lamarre S, Trouilh L, Laville E, Lombard V, Potocki-Veronese G, Henrissat B, O’Donohue M, Hernandez-Raquet G, Dumon C, Leberre VA. CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems BMC Genomics, 17(1), pp. 671. doi:10.1186/s12864-016-2988-4 (23 August 2016)
Zhan S, Dong Y, Zhao W, Guo J, Zhong T, Wang L, Li L, Zhang H. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat BMC Genomics, 17(1), pp. 666. doi:10.1186/s12864-016-3009-3 (22 August 2016)
Scheffold A, Holtman IR, Dieni S, Brouwer N, Katz SF, Jebaraj BM, Kahle PJ, Hengerer B, Lechel A, Stilgenbauer S, Boddeke EW, Eggen BJ, Rudolph KL, Biber K. Telomere shortening leads to an acceleration of synucleinopathy and impaired microglia response in a genetic mouse model Acta Neuropathol Commun, 4(1), pp. 87. doi:10.1186/s40478-016-0364-x (22 August 2016)
Vrahatis AG, Balomenos P, Tsakalidis AK, Bezerianos A. DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments. Bioinformatics. doi:10.1093/bioinformatics/btw544 (19 August 2016)
Manimaran S, Marie Selby H, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Corrada Bravo H, Evan Johnson W. BatchQC: Interactive software for evaluating sample and batch effects in genomic data. Bioinformatics. doi:10.1093/bioinformatics/btw538 (18 August 2016)
Joly Beauparlant C, Lamaze FC, Deschênes A, Samb R, Lemaçon A, Belleau P, Bilodeau S, Droit A. metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. PLoS Comput Biol, 12(8), pp. e1004751. doi:10.1371/journal.pcbi.1004751 (18 August 2016)
Rund SS, Yoo B, Alam C, Green T, Stephens MT, Zeng E, George GF, Sheppard AD, Duffield GE, Milenković T, Pfrender ME. Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation BMC Genomics, 17, pp. 653. doi:10.1186/s12864-016-2998-2 (18 August 2016)
Lewis Ames C, Ryan JF, Bely AE, Cartwright P, Collins AG. A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex BMC Genomics, 17, pp. 650. doi:10.1186/s12864-016-2944-3 (17 August 2016)
Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm Genome Biol, 17, pp. 173. doi:10.1186/s13059-016-1033-x (17 August 2016)
Islam MA, Große-Brinkhaus C, Pröll MJ, Uddin MJ, Rony SA, Tesfaye D, Tholen E, Hölker M, Schellander K, Neuhoff C. Deciphering transcriptome profiles of peripheral blood mononuclear cells in response to PRRSV vaccination in pigs BMC Genomics, 17, pp. 641. doi:10.1186/s12864-016-2849-1 (15 August 2016)
Ouattara B, Bissonnette N, Duplessis M, Girard CL. Supplements of vitamins B9 and B12 affect hepatic and mammary gland gene expression profiles in lactating dairy cows BMC Genomics, 17, pp. 640. doi:10.1186/s12864-016-2872-2 (15 August 2016)
Xu Z, Taylor JA, Leung YK, Ho SM, Niu L. oxBS-MLE: An efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. Bioinformatics. doi:10.1093/bioinformatics/btw527 (13 August 2016)
Parreira VR, Russell K, Athanasiadou S, Prescott JF. Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions BMC Microbiol, 16, pp. 186. doi:10.1186/s12866-016-0792-6 (12 August 2016)
Janky R, Binda MM, Allemeersch J, Van den broeck A, Govaere O, Swinnen JV, Roskams T, Aerts S, Topal B. Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma BMC Cancer, 16, pp. 632. doi:10.1186/s12885-016-2540-6 (12 August 2016)
Zhao K, Liang G, Sun X, Guan LL. Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes BMC Genomics, 17, pp. 630. doi:10.1186/s12864-016-2962-1 (12 August 2016)
Maboreke HR, Feldhahn L, Bönn M, Tarkka MT, Buscot F, Herrmann S, Menzel R, Ruess L. Transcriptome analysis in oak uncovers a strong impact of endogenous rhythmic growth on the interaction with plant-parasitic nematodes BMC Genomics, 17, pp. 627. doi:10.1186/s12864-016-2992-8 (12 August 2016)
Wijayawardena BK, Minchella DJ, DeWoody JA. The influence of trematode parasite burden on gene expression in a mammalian host BMC Genomics, 17, pp. 600. doi:10.1186/s12864-016-2950-5 (11 August 2016)
Rausch TK, Schillert A, Ziegler A, Lüking A, Zucht HD, Schulz-Knappe P. Comparison of pre-processing methods for multiplex bead-based immunoassays BMC Genomics, 17, pp. 601. doi:10.1186/s12864-016-2888-7 (11 August 2016)
Hickmott JW, Chen CY, Arenillas DJ, Korecki AJ, Lam SL, Molday LL, Bonaguro RJ, Zhou M, Chou AY, Mathelier A, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM. PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina Mol Ther Methods Clin Dev, 3, pp. 16051-. doi:10.1038/mtm.2016.51 (10 August 2016)
Michna A, Braselmann H, Selmansberger M, Dietz A, Hess J, Gomolka M, Hornhardt S, Blüthgen N, Zitzelsberger H, Unger K. Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data. PLoS One, 11(8), pp. e0160791. doi:10.1371/journal.pone.0160791 (9 August 2016)

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