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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). PMC4509590
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 2015-07-30T00:20:12-07:00.

Sharma A, Jamil MA, Nuesgen N, Schreiner F, Priebe L, Hoffmann P, Herns S, Nöthen MM, Fröhlich H, Oldenburg J, Woelfle J, El-Maarri O. DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations Clin Epigenetics, 7(1), pp. 76. doi:10.1186/s13148-015-0112-2 (28 July 2015)
Villacorta-Martin C, Núñez de Cáceres González FF, de Haan J, Huijben K, Passarinho P, Lugassi-Ben Hamo M, Zaccai M. Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs BMC Genomics, 16(1), pp. 550. doi:10.1186/s12864-015-1675-1 (28 July 2015)
McEvoy LM, O’Toole SA, Spillane CD, Martin CM, Gallagher MF, Stordal B, Blackshields G, Sheils O, O’Leary JJ. Identifying novel hypoxia-associated markers of chemoresistance in ovarian cancer BMC Cancer, 15, pp. 547. doi:10.1186/s12885-015-1539-8 (25 July 2015)
Mammana A, Chung HR. Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome Genome Biol, 16(1), pp. 151. doi:10.1186/s13059-015-0708-z (24 July 2015)
Jalbrzikowski M, Lazaro MT, Gao F, Huang A, Chow C, Geschwind DH, Coppola G, Bearden CE. Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and Autism Spectrum Disorder PLoS One, 10(7), pp. e0132542. doi:10.1371/journal.pone.0132542 (22 July 2015)
Caspeta L, Nielsen J. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses mBio, 6(4), pp. e00431-15. doi:10.1128/mBio.00431-15 (21 July 2015)
Zogo B, Djenontin A, Carolan K, Babonneau J, Guegan JF, Eyangoh S, Marion E. A Field Study in Benin to Investigate the Role of Mosquitoes and Other Flying Insects in the Ecology of Mycobacterium ulcerans PLoS Negl Trop Dis, 9(7), pp. e0003941. doi:10.1371/journal.pntd.0003941 (21 July 2015)
Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. doi:10.1093/nar/gkv715 (15 July 2015)
Murakawa Y, Hinz M, Mothes J, Schuetz A, Uhl M, Wyler E, Yasuda T, Mastrobuoni G, Friedel CC, Dölken L, Kempa S, Schmidt-Supprian M, Blüthgen N, Backofen R, Heinemann U, Wolf J, Scheidereit C, Landthaler M. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway Nat Commun, 6, pp. 7367. doi:10.1038/ncomms8367 (14 July 2015)
Gehring JS, Fischer B, Lawrence M, Huber W. SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants. Bioinformatics. doi:10.1093/bioinformatics/btv408 (10 July 2015)
Wang Y, Qian CY, Li XP, Zhang Y, He H, Wang J, Chen J, Cui JJ, Liu R, Zhou H, Xiao L, Xu XJ, Zheng Y, Fu YL, Chen ZY, Chen X, Zhang W, Ye CC, Zhou HH, Yin JY, Liu ZQ. Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer. Sci Rep, 5, pp. 11671. doi:10.1038/srep11671 (10 July 2015)
Constantinescu S, Szczurek E, Mohammadi P, Rahnenführer J, Beerenwinkel N. TiMEx: A Waiting Time Model for Mutually Exclusive Cancer Alterations. Bioinformatics. doi:10.1093/bioinformatics/btv400 (9 July 2015)
Cook DJ, Patra B, Kuttippurathu L, Hoek JB, Vadigepalli R. A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes Front Physiol, 6, pp. 189. doi:10.3389/fphys.2015.00189 (7 July 2015)
Araúzo-Bravo MJ. Computational Biology Methods for Characterization of Pluripotent Cells. Methods Mol Biol. doi:10.1007/7651_2015_279 (4 July 2015)
Richards EM, Rabaglino MB, Antolic A, Wood CE, Keller-Wood M. Patterns of Gene Expression in the Sheep Heart During the Perinatal Period Revealed by Transcriptomic Modeling. Physiol Genomics, pp. physiolgenomics.00027.2015. doi:10.1152/physiolgenomics.00027.2015 (30 June 2015)
Eijssen LM, Goelela VS, Kelder T, Adriaens ME, Evelo CT, Radonjic M. A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal. BMC Genomics, 16, pp. 482. doi:10.1186/s12864-015-1689-8 (30 June 2015)
Liefke R, Windhof-Jaidhauser IM, Gaedcke J, Salinas-Riester G, Wu F, Ghadimi M, Dango S. The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells Genome Med, 7(1), pp. 66. doi:10.1186/s13073-015-0180-0 (30 June 2015)
Fröhlich H. biRte: Bayesian inference of context-specific regulator activities and transcriptional networks. Bioinformatics. doi:10.1093/bioinformatics/btv379 (25 June 2015)
Moni MA, Liò P. How to build personalized multi-omics comorbidity profiles. Front Cell Dev Biol, 3, pp. 28. doi:10.3389/fcell.2015.00028 (24 June 2015)
Juliá M, Telenti A, Rausell A. Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. Bioinformatics. doi:10.1093/bioinformatics/btv368 (22 June 2015)

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