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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 2017-10-17T00:40:09-04:00.

Lawrence M, Gentleman R. VariantTools: an extensible framework for developing and testing variant callers. Bioinformatics, 33(20), pp. 3311-3313. doi:10.1093/bioinformatics/btx450 (15 October 2017)
de Santiago I, Carroll T. Analysis of ChIP-seq Data in R/Bioconductor. Methods Mol Biol, 1689, pp. 195-226. doi:10.1007/978-1-4939-7380-4_17 (14 October 2017)
Yu Y, Mutlu AS, Liu H, Wang MC. High-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation Nat Commun, 8, pp. 865. doi:10.1038/s41467-017-00944-3 (11 October 2017)
Honda K, Kim SH, Kelly MC, Burns JC, Constance L, Li X, Zhou F, Hoa M, Kelley MW, Wangemann P, Morell RJ, Griffith AJ. Molecular architecture underlying fluid absorption by the developing inner ear eLife, 6, pp. e26851. doi:10.7554/eLife.26851 (10 October 2017)
Lee I, Rasoul BA, Holub AS, Lejeune A, Enke RA, Timp W. Whole genome DNA methylation sequencing of the chicken retina, cornea and brain Sci Data, 4, pp. 170148. doi:10.1038/sdata.2017.148 (10 October 2017)
Christopher MA, Myrick DA, Barwick BG, Engstrom AK, Porter-Stransky KA, Boss JM, Weinshenker D, Levey AI, Katz DJ. LSD1 protects against hippocampal and cortical neurodegeneration Nat Commun, 8, pp. 805. doi:10.1038/s41467-017-00922-9 (9 October 2017)
Antoniali G, Serra F, Lirussi L, Tanaka M, D’Ambrosio C, Zhang S, Radovic S, Dalla E, Ciani Y, Scaloni A, Li M, Piazza S, Tell G. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism Nat Commun, 8, pp. 797. doi:10.1038/s41467-017-00842-8 (6 October 2017)
Picart-Armada S, Thompson WK, Buil A, Perera-Lluna A. An R package to compute diffusion-based scores on biological networks: diffuStats. Bioinformatics. doi:10.1093/bioinformatics/btx632 (5 October 2017)
Persson H, Søkilde R, Häkkinen J, Pirona AC, Vallon-Christersson J, Kvist A, Mertens F, Borg Å, Mitelman F, Höglund M, Rovira C. Frequent miRNA-convergent fusion gene events in breast cancer Nat Commun, 8, pp. 788. doi:10.1038/s41467-017-01176-1 (5 October 2017)
Chen Z, Hagen DE, Ji T, Elsik CG, Rivera RM. Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome Sci Rep, 7, pp. 12667. doi:10.1038/s41598-017-13012-z (4 October 2017)
Liu Y, Wu P, Zhou J, Johnson-Pais TL, Lai Z, Chowdhury WH, Rodriguez R, Chen Y. XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. BMC Bioinformatics, 18(Suppl 11), pp. 384. doi:10.1186/s12859-017-1803-9 (3 October 2017)
Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics, 18(1), pp. 437. doi:10.1186/s12859-017-1847-x (3 October 2017)
Yang XH, Tang F, Shin J, Cunningham JM. Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma BMC Syst Biol, 11(Suppl 5), pp. 92. doi:10.1186/s12918-017-0466-5 (3 October 2017)
Liu Z, Zheng WJ, Allen GI, Liu Y, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools BMC Bioinformatics, 18(Suppl 11), pp. 405. doi:10.1186/s12859-017-1797-3 (3 October 2017)
Vangeel EB, Pishva E, Hompes T, van den Hove D, Lambrechts D, Allegaert K, Freson K, Izzi B, Claes S. Newborn genome-wide DNA methylation in association with pregnancy anxiety reveals a potential role for GABBR1 Clin Epigenetics, 9, pp. 107. doi:10.1186/s13148-017-0408-5 (3 October 2017)
Yang L, Liu L, Gao H, Pinnamaneni JP, Sanagasetti D, Singh VP, Wang K, Mathison M, Zhang Q, Chen F, Mo Q, Rosengart T, Yang J. The stem cell factor SALL4 is an essential transcriptional regulator in mixed lineage leukemia-rearranged leukemogenesis J Hematol Oncol, 10, pp. 159. doi:10.1186/s13045-017-0531-y (3 October 2017)
Karatzas E, Bourdakou MM, Kolios G, Spyrou GM. Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score Sci Rep, 7, pp. 12569. doi:10.1038/s41598-017-12849-8 (3 October 2017)
Salker MS, Singh Y, Zeng N, Chen H, Zhang S, Umbach AT, Fakhri H, Kohlhofer U, Quintanilla-Martinez L, Durairaj RR, Barros FS, Vrljicak P, Ott S, Brucker SY, Wallwiener D, Vrhovac Madunić I, Breljak D, Sabolić I, Koepsell H, Brosens JJ, Lang F. Loss of Endometrial Sodium Glucose Cotransporter SGLT1 is Detrimental to Embryo Survival and Fetal Growth in Pregnancy Sci Rep, 7, pp. 12612. doi:10.1038/s41598-017-11674-3 (3 October 2017)
Ballestrero A, Bedognetti D, Ferraioli D, Franceschelli P, Labidi-Galy SI, Leo E, Murai J, Pommier Y, Tsantoulis P, Vellone VG, Zoppoli G. Report on the first SLFN11 monothematic workshop: from function to role as a biomarker in cancer J Transl Med, 15, pp. 199. doi:10.1186/s12967-017-1296-3 (2 October 2017)
Chen Y, Dong J, Bennetzen JL, Zhong M, Yang J, Zhang J, Li S, Hao X, Zhang Z, Wang X. Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum Sci Rep, 7, pp. 12504. doi:10.1038/s41598-017-12249-y (2 October 2017)

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