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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 2016-07-25T03:00:12-04:00.

Nogales-Cadenas R, Cai Y, Lin JR, Zhang Q, Zhang W, Montagna C, Zhang ZD. MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice Breast Cancer Res, 18, pp. 75. doi:10.1186/s13058-016-0735-z (22 July 2016)
López-Úbeda R, Muñoz M, Vieira L, Hunter RH, Coy P, Canovas S. The oviductal transcriptome is influenced by a local ovarian effect in the sow J Ovarian Res, 9, pp. 44. doi:10.1186/s13048-016-0252-9 (22 July 2016)
Fan Y, Wang YF, Su HF, Fang N, Zou C, Li WF, Fei ZH. Decreased expression of the long noncoding RNA LINC00261 indicate poor prognosis in gastric cancer and suppress gastric cancer metastasis by affecting the epithelial–mesenchymal transition J Hematol Oncol, 9, pp. 57. doi:10.1186/s13045-016-0288-8 (21 July 2016)
Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KG. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network Genome Med, 8, pp. 76. doi:10.1186/s13073-016-0329-5 (19 July 2016)
Charng WL, Karaca E, Coban Akdemir Z, Gambin T, Atik MM, Gu S, Posey JE, Jhangiani SN, Muzny DM, Doddapaneni H, Hu J, Boerwinkle E, Gibbs RA, Rosenfeld JA, Cui H, Xia F, Manickam K, Yang Y, Faqeih EA, Al Asmari A, Saleh MA, El-Hattab AW, Lupski JR. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate BMC Med Genomics, 9, pp. 42. doi:10.1186/s12920-016-0208-3 (19 July 2016)
Miller CL, Romero M, Karna SL, Chen T, Heeb S, Leung KP. RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions BMC Microbiol, 16, pp. 155. doi:10.1186/s12866-016-0771-y (19 July 2016)
Atsumi S, Nosaka C, Adachi H, Kimura T, Kobayashi Y, Takada H, Watanabe T, Ohba SI, Inoue H, Kawada M, Shibasaki M, Shibuya M. New anti-cancer chemicals Ertredin and its derivatives, regulate oxidative phosphorylation and glycolysis and suppress sphere formation in vitro and tumor growth in EGFRvIII-transformed cells BMC Cancer, 16, pp. 496. doi:10.1186/s12885-016-2521-9 (19 July 2016)
Day SE, Coletta RL, Kim JY, Campbell LE, Benjamin TR, Roust LR, De Filippis EA, Dinu V, Shaibi GQ, Mandarino LJ, Coletta DK. Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes Clin Epigenetics, 8, pp. 77. doi:10.1186/s13148-016-0246-x (18 July 2016)
Lim AM, Wong NC, Pidsley R, Zotenko E, Corry J, Dobrovic A, Clark SJ, Rischin D, Solomon B. Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas Clin Epigenetics, 8, pp. 74. doi:10.1186/s13148-016-0235-0 (18 July 2016)
Lobo NC, Gedye C, Apostoli AJ, Brown KR, Paterson J, Stickle N, Robinette M, Fleshner N, Hamilton RJ, Kulkarni G, Zlotta A, Evans A, Finelli A, Moffat J, Jewett MA, Ailles L. Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine BMC Cancer, 16, pp. 485. doi:10.1186/s12885-016-2539-z (16 July 2016)
Cazaly E, Thomson R, Marthick JR, Holloway AF, Charlesworth J, Dickinson JL. Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses Clin Epigenetics, 8, pp. 75. doi:10.1186/s13148-016-0241-2 (16 July 2016)
Lewis J, Breeze CE, Charlesworth J, Maclaren OJ, Cooper J. Where next for the reproducibility agenda in computational biology? BMC Syst Biol, 10, pp. 52. doi:10.1186/s12918-016-0288-x (15 July 2016)
Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, dos Santos CC. Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness Sci Rep, 6, pp. 29334. doi:10.1038/srep29334 (14 July 2016)
Talukder AK, Agarwal M, Buetow KH, Denèfle PP. Tracking Cancer Genetic Evolution using OncoTrack Sci Rep, 6, pp. 29647. doi:10.1038/srep29647 (14 July 2016)
Arimappamagan A, Kruthika, Dawn R, Paturu K, Santosh V. 332 Molecular Characteristics of Tumor Infiltrating Front in Glioblastoma: Insights Into Molecular Heterogeneity and Implications on Targeted Therapy. Neurosurgery, 63 Suppl 1, pp. 197. doi:10.1227/01.neu.0000489821.05971.a8 (12 July 2016)
Backman TW, Girke T. bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. J Chem Inf Model. doi:10.1021/acs.jcim.6b00109 (12 July 2016)
Peña JF, Alié A, Richter DJ, Wang L, Funayama N, Nichols SA. Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges EvoDevo, 7, pp. 13. doi:10.1186/s13227-016-0050-x (12 July 2016)
Tian H. Identification of candidate genes for myeloma-induced osteocyte death based on microarray data J Orthop Surg Res, 11, pp. 81. doi:10.1186/s13018-016-0411-0 (12 July 2016)
Nguyen T, Diaz D, Tagett R, Draghici S. Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data Sci Rep, 6, pp. 29251. doi:10.1038/srep29251 (12 July 2016)
Chang HX, Yendrek CR, Caetano-Anolles G, Hartman GL. Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanses and polygalacturonases of Fusarium virguliforme BMC Microbiol, 16, pp. 147. doi:10.1186/s12866-016-0761-0 (12 July 2016)


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