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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 2017-04-24T02:40:10-04:00.

Skvortsova K, Zotenko E, Luu PL, Gould CM, Nair SS, Clark SJ, Stirzaker C. Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA Epigenetics Chromatin, 10, pp. 16. doi:10.1186/s13072-017-0123-7 (20 April 2017)
Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki S, Geiger T, Avraham KB, Shamir R. Reduced changes in protein compared to mRNA levels across non-proliferating tissues BMC Genomics, 18, pp. 305. doi:10.1186/s12864-017-3683-9 (18 April 2017)
MacManes MD, Austin SH, Lang AS, Booth A, Farrar V, Calisi RM. Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis Sci Rep, 7, pp. 45125. doi:10.1038/srep45125 (18 April 2017)
Okano K, Ozawa S, Sato H, Kodachi S, Ito M, Miyadai T, Takemura A, Okano T. Light- and circadian-controlled genes respond to a broad light spectrum in Puffer Fish-derived Fugu eye cells Sci Rep, 7, pp. 46150. doi:10.1038/srep46150 (18 April 2017)
Lehmann ML, Weigel TK, Elkahloun AG, Herkenham M. Chronic social defeat reduces myelination in the mouse medial prefrontal cortex Sci Rep, 7, pp. 46548. doi:10.1038/srep46548 (18 April 2017)
Sandén E, Dyberg C, Krona C, Gallo-Oller G, Olsen TK, Enríquez Pérez J, Wickström M, Estekizadeh A, Kool M, Visse E, Ekström TJ, Siesjö P, Inge Johnsen J, Darabi A. Establishment and characterization of an orthotopic patient-derived Group 3 medulloblastoma model for preclinical drug evaluation Sci Rep, 7, pp. 46366. doi:10.1038/srep46366 (18 April 2017)
Knutson TP, Truong TH, Ma S, Brady NJ, Sullivan ME, Raj G, Schwertfeger KL, Lange CA. Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs J Hematol Oncol, 10, pp. 89. doi:10.1186/s13045-017-0462-7 (17 April 2017)
Chen K, Franz CJ, Jiang H, Jiang Y, Wang D. An evolutionarily conserved transcriptional response to viral infection in Caenorhabditis nematodes BMC Genomics, 18, pp. 303. doi:10.1186/s12864-017-3689-3 (17 April 2017)
Kostidis S, Kokova D, Dementeva N, Saltykova IV, Kim HK, Choi YH, Mayboroda OA. 1H-NMR analysis of feces: new possibilities in the helminthes infections research BMC Infect Dis, 17, pp. 275. doi:10.1186/s12879-017-2351-7 (17 April 2017)
Pomiès L, Decourteix M, Franchel J, Moulia B, Leblanc-Fournier N. Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli BMC Genomics, 18, pp. 300. doi:10.1186/s12864-017-3670-1 (17 April 2017)
Sundar IK, Yin Q, Baier BS, Yan L, Mazur W, Li D, Susiarjo M, Rahman I. DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD Clin Epigenetics, 9, pp. 38. doi:10.1186/s13148-017-0335-5 (14 April 2017)
Kaushal A, Zhang H, Karmaus WJ, Ray M, Torres MA, Smith AK, Wang SL. Comparison of different cell type correction methods for genome-scale epigenetics studies BMC Bioinformatics, 18, pp. 216. doi:10.1186/s12859-017-1611-2 (14 April 2017)
Bennett BD, Bushel PR. goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med, 12, pp. 6. doi:10.1186/s13029-017-0066-1 (13 April 2017)
Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F. Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput Biol, 13(4), pp. e1005496. doi:10.1371/journal.pcbi.1005496 (13 April 2017)
Galbavy W, Lu Y, Kaczocha M, Puopolo M, Liu L, Rebecchi MJ. Transcriptomic evidence of a para-inflammatory state in the middle aged lumbar spinal cord Immun Ageing, 14, pp. 9. doi:10.1186/s12979-017-0091-6 (13 April 2017)
Zhang J, Schmidt CJ, Lamont SJ. Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress BMC Genomics, 18, pp. 295. doi:10.1186/s12864-017-3675-9 (13 April 2017)
Lu X, Wang X, Chen X, Shu N, Wang J, Wang D, Wang S, Fan W, Guo L, Guo X, Ye W. Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress BMC Genomics, 18, pp. 297. doi:10.1186/s12864-017-3681-y (13 April 2017)
Li L, Cai S, Liu S, Feng H, Zhang J. Bioinformatics analysis to screen the key prognostic genes in ovarian cancer J Ovarian Res, 10, pp. 27. doi:10.1186/s13048-017-0323-6 (13 April 2017)
Hewitt AW, Januar V, Sexton-Oates A, Joo JE, Franchina M, Wang JJ, Liang H, Craig JE, Saffery R. DNA methylation landscape of ocular tissue relative to matched peripheral blood Sci Rep, 7, pp. 46330. doi:10.1038/srep46330 (13 April 2017)
Pacini C, Ajioka JW, Micklem G. Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure BMC Bioinformatics, 18, pp. 213. doi:10.1186/s12859-017-1623-y (12 April 2017)

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