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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
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).
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
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2018-05-26T07:00:09-04:00.

Stein-O’Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance Genome Med, 10, pp. 37. doi:10.1186/s13073-018-0545-2 (23 May 2018)
Zou LS, Erdos MR, Taylor DL, Chines PS, Varshney A, Parker SC, Collins FS, Didion JP. BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues BMC Genomics, 19, pp. 390. doi:10.1186/s12864-018-4766-y (23 May 2018)
Geng J, Huang SC, Chen YY, Chiu CH, Hu S, Chen YY. Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius BMC Genomics, 19, pp. 386. doi:10.1186/s12864-018-4781-z (23 May 2018)
Garate X, La Greca A, Neiman G, Blüguermann C, Santín Velazque NL, Moro LN, Luzzani C, Scassa ME, Sevlever GE, Romorini L, Miriuka SG. Identification of the miRNAome of early mesoderm progenitor cells and cardiomyocytes derived from human pluripotent stem cells Sci Rep, 8, pp. 8072. doi:10.1038/s41598-018-26156-3 (23 May 2018)
Yu G. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. doi:10.1093/bioinformatics/bty410 (22 May 2018)
Lin J, Gresham J, Wang T, Kim SY, Alvarez J, Damrauer JS, Floyd S, Granek J, Allen A, Chan C, Xie J, Owzar K. bcSeq: An R Package for Fast Sequence Mapping in High-throughput shRNA and CRISPR Screens. Bioinformatics. doi:10.1093/bioinformatics/bty402 (22 May 2018)
Frobel J, Rahmig S, Franzen J, Waskow C, Wagner W. Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice Clin Epigenetics, 10, pp. 67. doi:10.1186/s13148-018-0499-7 (22 May 2018)
Winge SB, Dalgaard MD, Belling KG, Jensen JM, Nielsen JE, Aksglaede L, Schierup MH, Brunak S, Skakkebæk NE, Juul A, Rajpert-De Meyts E, Almstrup K. Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells Cell Death Dis, 9(6), pp. 586. doi:10.1038/s41419-018-0671-1 (22 May 2018)
Luisier R, Tyzack GE, Hall CE, Mitchell JS, Devine H, Taha DM, Malik B, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM, Patani R. Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS Nat Commun, 9, pp. 2010. doi:10.1038/s41467-018-04373-8 (22 May 2018)
Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PF, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions Sci Rep, 8, pp. 7949. doi:10.1038/s41598-018-26170-5 (21 May 2018)
Armstrong AF, Grosberg RK. The developmental transcriptomes of two sea biscuit species with differing larval types BMC Genomics, 19, pp. 368. doi:10.1186/s12864-018-4768-9 (18 May 2018)
Lin HM, Nikolic I, Yang J, Castillo L, Deng N, Chan CL, Yeung NK, Dodson E, Elsworth B, Spielman C, Lee BY, Boyer Z, Simpson KJ, Daly RJ, Horvath LG, Swarbrick A. MicroRNAs as potential therapeutics to enhance chemosensitivity in advanced prostate cancer Sci Rep, 8, pp. 7820. doi:10.1038/s41598-018-26050-y (18 May 2018)
Chang JS, Ghosh S, Newman S, Salbaum JM. A map of the PGC-1α- and NT-PGC-1α-regulated transcriptional network in brown adipose tissue Sci Rep, 8, pp. 7876. doi:10.1038/s41598-018-26244-4 (18 May 2018)
Muramoto N, Oda A, Tanaka H, Nakamura T, Kugou K, Suda K, Kobayashi A, Yoneda S, Ikeuchi A, Sugimoto H, Kondo S, Ohto C, Shibata T, Mitsukawa N, Ohta K. Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks Nat Commun, 9, pp. 1995. doi:10.1038/s41467-018-04256-y (18 May 2018)
Im C, Sapkota Y, Moon W, Kawashima M, Nakamura M, Tokunaga K, Yasui Y. Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese Sci Rep, 8, pp. 7806. doi:10.1038/s41598-018-26112-1 (17 May 2018)
Liu Q, Yin X, Li M, Wan L, Liu L, Zhong X, Liu Z, Wang Q. Identification of potential crucial genes and pathways associated with vein graft restenosis based on gene expression analysis in experimental rabbits. PeerJ, 6, pp. e4704. doi:10.7717/peerj.4704 (16 May 2018)
Cao X, George EO, Wang M, Armstrong DB, Cheng C, Raimondi S, Rubnitz JE, Downing JR, Kundu M, Pounds SB. POST: a framework for set-based association analysis in high-dimensional data. Methods. doi:10.1016/j.ymeth.2018.05.011 (16 May 2018)
Zhang C, Dower K, Zhang B, Martinez RV, Lin LL, Zhao S. Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy Sci Rep, 8, pp. 7624. doi:10.1038/s41598-018-26035-x (16 May 2018)
Pan Y, Lu L, Chen J, Zhong Y, Dai Z. Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma. Hereditas, 155, pp. 21. doi:10.1186/s41065-018-0061-9 (9 May 2018)

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