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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 2015-05-22T15:10:14-07:00.

Ryer EJ, Ronning KE, Erdman R, Schworer CM, Elmore JR, Peeler TC, Nevius CD, Lillvis JH, Garvin RP, Franklin DP, Kuivaniemi H, Tromp G. The Potential Role of DNA Methylation in Abdominal Aortic Aneurysms. Int J Mol Sci, 16(5), pp. 11259-11275. doi:10.3390/ijms160511259 (18 May 2015)
Wang B, Cunningham JM, Yang XH. Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics. doi:10.1093/bioinformatics/btv289 (15 May 2015)
Nicolle R, Radvanyi F, Elati M. COREGNET: reconstruction and integrated analysis of co-regulatory networks. Bioinformatics. doi:10.1093/bioinformatics/btv305 (14 May 2015)
Uziela K, Honkela A. Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability. PLoS One, 10(5), pp. e0126545. doi:10.1371/journal.pone.0126545 (12 May 2015)
Maia AF, Tanenbaum ME, Galli M, Lelieveld D, Egan DA, Gassmann R, Sunkel CE, van den Heuvel S, Medema RH. Genome-wide RNAi screen for synthetic lethal interactions with the C. elegans kinesin-5 homolog BMK-1 Sci Data, 2, pp. 150020. doi:10.1038/sdata.2015.20 (12 May 2015)
Alnasir J, Shanahan HP. Investigation into the annotation of protocol sequencing steps in the sequence read archive. Gigascience, 4, pp. 23. doi:10.1186/s13742-015-0064-7 (9 May 2015)
Wright RM, Aglyamova GV, Meyer E, Matz MV. Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus BMC Genomics, 16(1), pp. 371. doi:10.1186/s12864-015-1540-2 (9 May 2015)
Trovato A, Panelli S, Strozzi F, Cambulli C, Barbieri I, Martinelli N, Lombardi G, Capoferri R, Williams JL. Expression of genes involved in the T cell signalling pathway in circulating immune cells of cattle 24 months following oral challenge with Bovine Amyloidotic Spongiform Encephalopathy (BASE) BMC Vet Res, 11, pp. 105. doi:10.1186/s12917-015-0412-y (9 May 2015)
Dehman A, Ambroise C, Neuvial P. Performance of a blockwise approach in variable selection using linkage disequilibrium information BMC Bioinformatics, 16(1), pp. 148. doi:10.1186/s12859-015-0556-6 (8 May 2015)
de Pretis S, Kress T, Morelli MJ, Melloni GE, Riva L, Amati B, Pelizzola M. INSPEcT: a Computational Tool to Infer mRNA Synthesis, Processing and Degradation Dynamics from RNA- and 4sU-seq Time Course Experiments. Bioinformatics. doi:10.1093/bioinformatics/btv288 (7 May 2015)
Younis S, Javed Q, Blumenberg M. Transcriptional changes associated with resistance to inhibitors of epidermal growth factor receptor revealed using metaanalysis BMC Cancer, 15, pp. 369. doi:10.1186/s12885-015-1337-3 (7 May 2015)
Zhou Q, Jackson-Cook C, Lyon D, Perera R, Archer KJ. Identifying Molecular Features Associated with Psychoneurological Symptoms in Women with Breast Cancer Using Multivariate Mixed Models Cancer Inform, 14(Suppl 2), pp. 139-145. doi:10.4137/CIN.S17276 (7 May 2015)
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and Compositionally Robust Inference of Microbial Ecological Networks PLoS Comput Biol, 11(5), pp. e1004226. doi:10.1371/journal.pcbi.1004226 (7 May 2015)
Bourassa S, Fournier F, Nehmé B, Kelly I, Tremblay A, Lemelin V, Lamarche B, Couture P, Droit A. Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples PLoS One, 10(5), pp. e0125934. doi:10.1371/journal.pone.0125934 (7 May 2015)
Zhao L, Wit J, Svetec N, Begun DJ. Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans PLoS Genet, 11(5), pp. e1005184. doi:10.1371/journal.pgen.1005184 (7 May 2015)
Zhu W, Ausin I, Seleznev A, Méndez-Vigo B, Picó FX, Sureshkumar S, Sundaramoorthi V, Bulach D, Powell D, Seemann T, Alonso-Blanco C, Balasubramanian S. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana PLoS Genet, 11(5), pp. e1005085. doi:10.1371/journal.pgen.1005085 (7 May 2015)
Wang Y, MacKenzie KD, White AP. An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data BMC Genomics, 16(1), pp. 359. doi:10.1186/s12864-015-1555-8 (7 May 2015)
Lin P, Forêt S, Wilson SR, Burden CJ. Estimation of the methylation pattern distribution from deep sequencing data. BMC Bioinformatics, 16, pp. 145. doi:10.1186/s12859-015-0600-6 (6 May 2015)
Toufighi K, Yang JS, Luis NM, Aznar Benitah S, Lehner B, Serrano L, Kiel C. Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses PLoS Comput Biol, 11(5), pp. e1004256. doi:10.1371/journal.pcbi.1004256 (6 May 2015)
Kovalchuk A, Raffaello T, Jaber E, Keriö S, Ghimire R, Lorenz WW, Dean JF, Holopainen JK, Asiegbu FO. Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis) BMC Genomics, 16(1), pp. 352. doi:10.1186/s12864-015-1546-9 (6 May 2015)

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