Publications

Featured

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).
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth, GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl. Acids Res; doi:10.1093/nar/gkv007
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 2015-07-04T21:20:10-07:00.

Sun S, Xuan F, Fu H, Zhu J, Ge X, Gu Z. Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia BMC Genomics, 16(1), pp. 491. doi:10.1186/s12864-015-1701-3 (3 July 2015)
Jia C, Guan W, Yang A, Xiao R, Tang WH, Moravec CS, Margulies KB, Cappola TP, Li M, Li C. MetaDiff: differential isoform expression analysis using random-effects meta-regression BMC Bioinformatics, 16(1), pp. 208. doi:10.1186/s12859-015-0623-z (2 July 2015)
Giannopoulou EG, Elemento O, Ivashkiv LB. Use of RNA sequencing to evaluate rheumatic disease patients Arthritis Res Ther, 17(1), pp. 167. doi:10.1186/s13075-015-0677-3 (1 July 2015)
Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing BMC Med Genomics, 8, pp. 35. doi:10.1186/s12920-015-0109-x (1 July 2015)
Valentini D, Ferrara G, Advani R, Hallander HO, Maeurer MJ. Serum reactome induced by Bordetella pertussis infection and Pertussis vaccines: qualitative differences in serum antibody recognition patterns revealed by peptide microarray analysis BMC Immunol, 16, pp. 40. doi:10.1186/s12865-015-0090-3 (1 July 2015)
Oláh P, Tombácz D, Póka N, Csabai Z, Prazsák I, Boldogkői Z. Characterization of pseudorabies virus transcriptome by Illumina sequencing BMC Microbiol, 15, pp. 130. doi:10.1186/s12866-015-0470-0 (1 July 2015)
Wagle P, Nikolić M, Frommolt P. QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation BMC Genomics, 16(1), pp. 487. doi:10.1186/s12864-015-1695-x (1 July 2015)
Richards EM, Rabaglino MB, Antolic A, Wood CE, Keller-Wood M. Patterns of Gene Expression in the Sheep Heart During the Perinatal Period Revealed by Transcriptomic Modeling. Physiol Genomics, pp. physiolgenomics.00027.2015. doi:10.1152/physiolgenomics.00027.2015 (30 June 2015)
Eijssen LM, Goelela VS, Kelder T, Adriaens ME, Evelo CT, Radonjic M. A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal. BMC Genomics, 16, pp. 482. doi:10.1186/s12864-015-1689-8 (30 June 2015)
Yang J, Fu Z, Hong Y, Wu H, Jin Y, Zhu C, Li H, Lu K, Shi Y, Yuan C, Cheng G, Feng X, Liu J, Lin J. The Differential Expression of Immune Genes between Water Buffalo and Yellow Cattle Determines Species-Specific Susceptibility to Schistosoma japonicum Infection PLoS One, 10(6), pp. e0130344. doi:10.1371/journal.pone.0130344 (30 June 2015)
Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M. Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data BMC Bioinformatics, 16(1), pp. 202. doi:10.1186/s12859-015-0607-z (30 June 2015)
Grilli A, Sciandra M, Terracciano M, Picci P, Scotlandi K. Integrated approaches to miRNAs target definition: time-series analysis in an osteosarcoma differentiative model BMC Med Genomics, 8, pp. 34. doi:10.1186/s12920-015-0106-0 (30 June 2015)
Wilson RL, Buckberry S, Spronk F, Laurence JA, Leemaqz S, O’Leary S, Bianco-Miotto T, Du J, Anderson PH, Roberts CT. Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome PLoS One, 10(6), pp. e0131287. doi:10.1371/journal.pone.0131287 (29 June 2015)
Choudhary P, Dodsworth BT, Sidders B, Gutteridge A, Michaelides C, Duckworth JK, Whiting PJ, Benn CL. A FOXM1 Dependent Mesenchymal-Epithelial Transition in Retinal Pigment Epithelium Cells PLoS One, 10(6), pp. e0130379. doi:10.1371/journal.pone.0130379 (29 June 2015)
Gutiérrez EE, Maldonado JE, Radosavljevic A, Molinari J, Patterson BD, Martínez-C. JM, Rutter AR, Hawkins MT, Garcia FJ, Helgen KM. The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela PLoS One, 10(6), pp. e0129113. doi:10.1371/journal.pone.0129113 (29 June 2015)
Son JS, Khair S, Pettet DW III, Ouyang N, Tian X, Zhang Y, Zhu W, Mackenzie GG, Robertson CE, Ir D, Frank DN, Rigas B, Li E. Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice PLoS One, 10(6), pp. e0127985. doi:10.1371/journal.pone.0127985 (29 June 2015)
Branco AF, Pereira SP, Gonzalez S, Gusev O, Rizvanov AA, Oliveira PJ. Gene Expression Profiling of H9c2 Myoblast Differentiation towards a Cardiac-Like Phenotype PLoS One, 10(6), pp. e0129303. doi:10.1371/journal.pone.0129303 (29 June 2015)
Duck G, Kovacevic A, Robertson DL, Stevens R, Nenadic G. Ambiguity and variability of database and software names in bioinformatics J Biomed Semantics, 6, pp. 29. doi:10.1186/s13326-015-0026-0 (29 June 2015)
Masotti A, Donninelli G, Da Sacco L, Varano B, Del Cornò M, Gessani S. HIV-1 gp120 influences the expression of microRNAs in human monocyte-derived dendritic cells via STAT3 activation BMC Genomics, 16(1), pp. 480. doi:10.1186/s12864-015-1673-3 (27 June 2015)
Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH. Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation BMC Genomics, 16(1), pp. 477. doi:10.1186/s12864-015-1708-9 (27 June 2015)

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