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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 2017-04-23T02:20:10-04:00.

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)
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)
Naake T, Gaquerel E. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data. Bioinformatics. doi:10.1093/bioinformatics/btx159 (11 April 2017)
Parodi AC, Sangalli LM, Vantini S, Amati B, Secchi P, Morelli MJ. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes. Bioinformatics. doi:10.1093/bioinformatics/btx201 (7 April 2017)
Zhou X, Meng G, Nardini C, Mei H. Systemic Evaluation of Cellular Reprogramming Processes exploiting a novel R-tool: eegc. Bioinformatics. doi:10.1093/bioinformatics/btx205 (7 April 2017)
Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe NM. GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. PLoS One, 12(4), pp. e0174744. doi:10.1371/journal.pone.0174744 (5 April 2017)
Ioannidis J, Donadeu FX. Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle PLoS One, 12(4), pp. e0174892. doi:10.1371/journal.pone.0174892 (5 April 2017)
Aleksandr I, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. doi:10.1093/bioinformatics/btx162 (4 April 2017)
Aleksandr I, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. doi:10.1093/bioinformatics/btx168 (4 April 2017)
Zhang JD, Hatje K, Sturm G, Broger C, Ebeling M, Burtin M, Terzi F, Pomposiello SI, Badi L. Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics, 18(1), pp. 277. doi:10.1186/s12864-017-3661-2 (4 April 2017)
Duchesne A, Vaiman A, Castille J, Beauvallet C, Gaignard P, Floriot S, Rodriguez S, Vilotte M, Boulanger L, Passet B, Albaric O, Guillaume F, Boukadiri A, Richard L, Bertaud M, Timsit E, Guatteo R, Jaffrézic F, Calvel P, Helary L, Mahla R, Esquerré D, Péchoux C, Liuu S, Vallat JM, Boichard D, Slama A, Vilotte JL. Bovine and murine models highlight novel roles for SLC25A46 in mitochondrial dynamics and metabolism, with implications for human and animal health PLoS Genet, 13(4), pp. e1006597. doi:10.1371/journal.pgen.1006597 (4 April 2017)
Salih MA, Fakiola M, Lyons PA, Younis BM, Musa AM, Elhassan AM, Anderson D, Syn G, Ibrahim ME, Blackwell JM, Mohamed HS. Expression profiling of Sudanese visceral leishmaniasis patients pre- and post-treatment with sodium stibogluconate. Parasite Immunol. doi:10.1111/pim.12431 (31 March 2017)


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