Publications

Bioconductor F1000 Research Channel launched!

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). 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 2017-03-23T18:00:24-04:00.

Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD, Marconi VC. Oral microbiome in HIV-associated periodontitis. Medicine (Baltimore), 96(12), pp. e5821. doi:10.1097/MD.0000000000005821 (23 March 2017)
Zhen Y, Xinghui Z, Chao W, Yi Z, Jinwen C, Ruifang G, Chao Z, Min Z, Chunlei G, Yan F, Lingfang D, Long S, Wenzhi S, Xiaohe L, Rong X. Several microRNAs could predict survival in patients with hepatitis B-related liver cancer Sci Rep, 7, pp. 45195. doi:10.1038/srep45195 (21 March 2017)
Polaino S, Villalobos-Escobedo JM, Shakya VP, Miralles-Durán A, Chaudhary S, Sanz C, Shahriari M, Luque EM, Eslava AP, Corrochano LM, Herrera-Estrella A, Idnurm A. A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi Sci Rep, 7, pp. 44790. doi:10.1038/srep44790 (21 March 2017)
Cao W, Ma E, Zhou L, Yuan T, Zhang C. Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy World J Surg Oncol, 15, pp. 66. doi:10.1186/s12957-017-1125-4 (20 March 2017)
Prince DC, Rallapalli G, Xu D, Schoonbeek HJ, Çevik V, Asai S, Kemen E, Cruz-Mireles N, Kemen A, Belhaj K, Schornack S, Kamoun S, Holub EB, Halkier BA, Jones JD. Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana BMC Biol, 15, pp. 20. doi:10.1186/s12915-017-0360-z (20 March 2017)
Chen W, Xiong Y, Xu L, Zhang Q, Luo Z. An integrated analysis based on transcriptome and proteome reveals deastringency-related genes in CPCNA persimmon Sci Rep, 7, pp. 44671. doi:10.1038/srep44671 (17 March 2017)
Yu J, Ciaudo C. Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid Cells Sci Rep, 7, pp. 44736. doi:10.1038/srep44736 (17 March 2017)
Gao F, Liu P, Narayanan J, Yang M, Fish BL, Liu Y, Liang M, Jacobs ER, Medhora M. Changes in miRNA in the lung and whole blood after whole thorax irradiation in rats Sci Rep, 7, pp. 44132. doi:10.1038/srep44132 (17 March 2017)
Foroushani A, Agrahari R, Docking R, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications. BMC Med Genomics, 10(1), pp. 16. doi:10.1186/s12920-017-0253-6 (16 March 2017)
Park C, Yun SJ, Ryu SJ, Lee S, Lee YS, Yoon Y, Park SC. Systematic identification of an integrative network module during senescence from time-series gene expression BMC Syst Biol, 11, pp. 36. doi:10.1186/s12918-017-0417-1 (15 March 2017)
Lund AM, Kaas CS, Brandl J, Pedersen LE, Kildegaard HF, Kristensen C, Andersen MR. Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data BMC Syst Biol, 11, pp. 37. doi:10.1186/s12918-017-0414-4 (15 March 2017)
Kralova J, Kolar M, Kahle M, Truksa J, Lettlova S, Balusikova K, Bartunek P. Glycol porphyrin derivatives and temoporfin elicit resistance to photodynamic therapy by different mechanisms Sci Rep, 7, pp. 44497. doi:10.1038/srep44497 (15 March 2017)
Son HG, Seo M, Ham S, Hwang W, Lee D, An SW, Artan M, Seo K, Kaletsky R, Arey RN, Ryu Y, Ha CM, Kim YK, Murphy CT, Roh TY, Nam HG, Lee SJ. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans Nat Commun, 8, pp. 14749. doi:10.1038/ncomms14749 (9 March 2017)
Chopyk J, Chattopadhyay S, Kulkarni P, Smyth EM, Hittle LE, Paulson JN, Pop M, Buehler SS, Clark PI, Mongodin EF, Sapkota AR. Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions Front Microbiol, 8, pp. 358. doi:10.3389/fmicb.2017.00358 (7 March 2017)
Sandmann S, de Graaf AO, Dugas M. BBCAnalyzer: a visual approach to facilitate variant calling. BMC Bioinformatics, 18(1), pp. 133. doi:10.1186/s12859-017-1549-4 (28 February 2017)
Merino GA, Murua YA, Fresno C, Sendoya JM, Golubicki M, Iseas S, Coraglio M, Podhajcer OL, Llera AS, Fernández EA. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum Mutat. doi:10.1002/humu.23204 (24 February 2017)
Xu X, Jiang H, Li X, Wu P, Liu J, Wang T, Zhou X, Xiong J, Li W. Bioinformatics analysis on the differentiation of bone mesenchymal stem cells into osteoblasts and adipocytes. Mol Med Rep. doi:10.3892/mmr.2017.6178 (8 February 2017)
Parks DR, El Khettabi F, Chase E, Hoffman RA, Perfetto SP, Spidlen J, Wood JC, Moore WA, Brinkman RR. Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data. Cytometry A, 91(3), pp. 232-249. doi:10.1002/cyto.a.23052 (3 February 2017)
Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PLoS One, 12(2), pp. e0170181. doi:10.1371/journal.pone.0170181 (2 February 2017)

Books

Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers

Compendia

Literature Search »

 

Courses & Conferences »

Bioconductor courses and conferences explore R programming and the analysis of genomic data. View catalog of a recent course material.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.