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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 2016-02-12T05:20:07-05:00.

De Sano L, Caravagna G, Ramazzotti D, Graudenzi A, Mauri G, Mishra B, Antoniotti M. TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinformatics. doi:10.1093/bioinformatics/btw035 (9 February 2016)
Melloni GE, de Pretis S, Riva L, Pelizzola M, Céol A, Costanza J, Müller H, Zammataro L. LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. BMC Bioinformatics, 17(1), pp. 80. doi:10.1186/s12859-016-0935-7 (9 February 2016)
X Menezes R, Mohammadi L, J Goeman J, M Boer J. Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack. BMC Bioinformatics, 17(1), pp. 77. doi:10.1186/s12859-016-0926-8 (9 February 2016)
Li Z, Zhang J, Liu Y, Zhao J, Fu J, Ren X, Wang G, Wang J. Exogenous auxin regulates multi-metabolic network and embryo development, controlling seed secondary dormancy and germination in Nicotiana tabacum L. BMC Plant Biol, 16, pp. 41. doi:10.1186/s12870-016-0724-5 (9 February 2016)
Nyima T, Müller M, Hooiveld GJ, Morine MJ, Scotti M. Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice BMC Genomics, 17, pp. 106. doi:10.1186/s12864-016-2424-9 (9 February 2016)
Ibeagha-Awemu EM, Li R, Ammah AA, Dudemaine PL, Bissonnette N, Benchaar C, Zhao X. Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways BMC Genomics, 17, pp. 104. doi:10.1186/s12864-016-2423-x (9 February 2016)
Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, Tu Z, Zhu J. Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication Genome Med, 8, pp. 15. doi:10.1186/s13073-016-0268-1 (9 February 2016)
Kananen L, Marttila S, Nevalainen T, Jylhävä J, Mononen N, Kähönen M, Raitakari OT, Lehtimäki T, Hurme M. Aging-associated DNA methylation changes in middle-aged individuals: the Young Finns study BMC Genomics, 17, pp. 103. doi:10.1186/s12864-016-2421-z (9 February 2016)
Fukazawa T, Guo M, Ishida N, Yamatsuji T, Takaoka M, Yokota E, Haisa M, Miyake N, Ikeda T, Okui T, Takigawa N, Maeda Y, Naomoto Y. SOX2 suppresses CDKN1A to sustain growth of lung squamous cell carcinoma Sci Rep, 6, pp. 20113. doi:10.1038/srep20113 (5 February 2016)
Moslemi A, Mahjub H, Saidijam M, Poorolajal J, Soltanian AR. Bayesian Survival Analysis of High-Dimensional Microarray Data for Mantle Cell Lymphoma Patients. Asian Pac J Cancer Prev, 17(1), pp. 95-100. doi: (4 February 2016)
Liu L, Zhang SW, Gao F, Zhang Y, Huang Y, Chen R, Meng J. DRME: count-based differential RNA methylation analysis at small sample size scenario. Anal Biochem. doi:10.1016/j.ab.2016.01.014 (3 February 2016)
Ogando J, Tardáguila M, Díaz-Alderete A, Usategui A, Miranda-Ramos V, Martínez-Herrera DJ, de la Fuente L, García-León MJ, Moreno MC, Escudero S, Cañete JD, Toribio ML, Cases I, Pascual-Montano A, Pablos JL, Mañes S. Notch-regulated miR-223 targets the aryl hydrocarbon receptor pathway and increases cytokine production in macrophages from rheumatoid arthritis patients Sci Rep, 6, pp. 20223. doi:10.1038/srep20223 (3 February 2016)
Georgiadis P, Hebels DG, Valavanis I, Liampa I, Bergdahl IA, Johansson A, Palli D, Chadeau-Hyam M, Chatziioannou A, Jennen DG, Krauskopf J, Jetten MJ, Kleinjans JC, Vineis P, Kyrtopoulos SA. Omics for prediction of environmental health effects: Blood leukocyte-based cross-omic profiling reliably predicts diseases associated with tobacco smoking Sci Rep, 6, pp. 20544. doi:10.1038/srep20544 (3 February 2016)
Wang B, Zhao J, Zhang P. Gene signatures in osteoarthritic acetabular labrum using microarray analysis. Int J Rheum Dis. doi:10.1111/1756-185X.12810 (2 February 2016)
Park Y, Wu H. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics. doi:10.1093/bioinformatics/btw026 (27 January 2016)
Wright ES, Vetsigian KH. DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures. Bioinformatics. doi:10.1093/bioinformatics/btw047 (23 January 2016)
Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M. PAA: An R/Bioconductor package for biomarker discovery with protein microarrays. Bioinformatics. doi:10.1093/bioinformatics/btw037 (22 January 2016)
Rainer J, Taliun D, D'Elia Y, Pattaro C, Domingues FS, Weichenberger CX. FamAgg: an R Package to Evaluate Familial Aggregation of Traits in Large Pedigrees. Bioinformatics. doi:10.1093/bioinformatics/btw019 (22 January 2016)
Tan G, Lenhard B. TFBSTools: an R/Bioconductor package for transcription factor binding site analysis. Bioinformatics. doi:10.1093/bioinformatics/btw024 (21 January 2016)


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