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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 2016-12-04T11:20:09-05:00.

Lienhard M, Grasse S, Rolff J, Frese S, Schirmer U, Becker M, Börno S, Timmermann B, Chavez L, Sültmann H, Leschber G, Fichtner I, Schweiger MR, Herwig R. QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Res. doi:10.1093/nar/gkw1193 (1 December 2016)
Li CI, Shyr Y. Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data. Stat Appl Genet Mol Biol, 15(6), pp. 491-505. doi:10.1515/sagmb-2016-0008 (1 December 2016)
Handley N, Eide J, Taylor R, Wuertz B, Gaffney P, Ondrey F. PPARγ targeted oral cancer treatment and additional utility of genomics analytic techniques. Laryngoscope. doi:10.1002/lary.26423 (29 November 2016)
Hoffman GE, Schadt EE. variancePartition: interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics, 17(1), pp. 483. doi:10.1186/s12859-016-1323-z (25 November 2016)
Brereton MF, Rohm M, Shimomura K, Holland C, Tornovsky-Babeay S, Dadon D, Iberl M, Chibalina MV, Lee S, Glaser B, Dor Y, Rorsman P, Clark A, Ashcroft FM. Hyperglycaemia induces metabolic dysfunction and glycogen accumulation in pancreatic β-cells Nat Commun, 7, pp. 13496. doi:10.1038/ncomms13496 (24 November 2016)
Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, Nguyen JD, Salathia N, Shallcross J, Souaiaia T, Spaethling JM, Walker CP, Wang J, Wang K, Wang W, Wildberg A, Zheng L, Chow RH, Eberwine J, Knowles JA, Zhang K, Kim J. Assessing characteristics of RNA amplification methods for single cell RNA sequencing BMC Genomics, 17, pp. 966. doi:10.1186/s12864-016-3300-3 (24 November 2016)
Ikink GJ, Boer M, Bakker ER, Hilkens J. IRS4 induces mammary tumorigenesis and confers resistance to HER2-targeted therapy through constitutive PI3K/AKT-pathway hyperactivation Nat Commun, 7, pp. 13567. doi:10.1038/ncomms13567 (23 November 2016)
Mottawea W, Chiang CK, Mühlbauer M, Starr AE, Butcher J, Abujamel T, Deeke SA, Brandel A, Zhou H, Shokralla S, Hajibabaei M, Singleton R, Benchimol EI, Jobin C, Mack DR, Figeys D, Stintzi A. Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn's disease Nat Commun, 7, pp. 13419. doi:10.1038/ncomms13419 (23 November 2016)
Tandonnet S, Torres TT. Traditional versus 3′ RNA-seq in a non-model species Genom Data, 11, pp. 9-16. doi:10.1016/j.gdata.2016.11.002 (18 November 2016)
Dong S, Xia T, Wang L, Zhao Q, Tian J. Investigation of candidate genes for osteoarthritis based on gene expression profiles. Acta Orthop Traumatol Turc. doi:10.1016/j.aott.2016.04.002 (17 November 2016)
Maasalu K, Laius O, Zhytnik L, Kõks S, Prans E, Reimann E, Märtson A. Transcriptional landscape analysis identifies differently expressed genes involved in follicle-stimulating hormone induced postmenopausal osteoporosis. Exp Biol Med (Maywood). doi:10.1177/1535370216679899 (17 November 2016)
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters Cell, 167(5), pp. 1369-1384.e19. doi:10.1016/j.cell.2016.09.037 (17 November 2016)
Huang FC, Liu TS, Li SC, Shih MH, Shin JW, Lin WC. The effect of the disulfideisomerase domain containing protein in the defense against polyhexamethylene biguanide of highly tolerant Acanthamoeba at the trophozoite stage Int J Parasitol Drugs Drug Resist, 6(3), pp. 251-257. doi:10.1016/j.ijpddr.2016.11.001 (14 November 2016)
Hirano Y, Ihara K, Masuda T, Yamamoto T, Iwata I, Takahashi A, Awata H, Nakamura N, Takakura M, Suzuki Y, Horiuchi J, Okuno H, Saitoe M. Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies Nat Commun, 7, pp. 13471. doi:10.1038/ncomms13471 (14 November 2016)
Greer RL, Dong X, Moraes AC, Zielke RA, Fernandes GR, Peremyslova E, Vasquez-Perez S, Schoenborn AA, Gomes EP, Pereira AC, Ferreira SR, Yao M, Fuss IJ, Strober W, Sikora AE, Taylor GA, Gulati AS, Morgun A, Shulzhenko N. Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism Nat Commun, 7, pp. 13329. doi:10.1038/ncomms13329 (14 November 2016)
Suomi T, Elo LL. Accurate Detection of Differential Expression and Splicing Using Low-Level Features. Methods Mol Biol, 1507, pp. 141-151. doi:10.1007/978-1-4939-6518-2_11 (11 November 2016)
Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D. The pangenome of an agronomically important crop plant Brassica oleracea Nat Commun, 7, pp. 13390. doi:10.1038/ncomms13390 (11 November 2016)
Aka JA, Calvo EL, Lin SX. Genomic data on breast cancer transcript profile modulation by 17beta-hydroxysteroid dehydrogenase type 1 and 17-beta-estradiol Data Brief, 9, pp. 1000-1012. doi:10.1016/j.dib.2016.11.010 (9 November 2016)
Wang D, Zhu ZM, Tu YL, Dou CQ, Xu Y, Tan XL, Han MM, Yang ZJ, Jin X, Zhang B, Cai S, Liu ZW. Identfication of key miRNAs in pancreatitis using bioinformatics analysis of microarray data. Mol Med Rep. doi:10.3892/mmr.2016.5928 (7 November 2016)

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