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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
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 2015-08-01T00:40:11-07:00.

Quigley D. Equalizer reduces SNP bias in Affymetrix microarrays BMC Bioinformatics, 16(1), pp. 238. doi:10.1186/s12859-015-0669-y (30 July 2015)
Benis N, Schokker D, Suarez-Diez M, Martins dos Santos VA, Smidt H, Smits MA. Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets BMC Genomics, 16(1), pp. 556. doi:10.1186/s12864-015-1733-8 (29 July 2015)
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)
Stephan-Otto Attolini C, Peña V, Rossell D. Designing alternative splicing RNA-seq studies. Beyond generic guidelines. Bioinformatics. doi:10.1093/bioinformatics/btv436 (27 July 2015)
Wang N, Zheng Y, Duan N, Zhang Z, Ji X, Jiang S, Sun S, Yang L, Bai Y, Fei Z, Chen X. Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica ‘Fuji’ PLoS One, 10(7), pp. e0133468. doi:10.1371/journal.pone.0133468 (24 July 2015)
Doggett K, Turkel N, Willoughby LF, Ellul J, Murray MJ, Richardson HE, Brumby AM. BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in Drosophila PLoS One, 10(7), pp. e0132987. doi:10.1371/journal.pone.0132987 (24 July 2015)
Pandey A, Misra P, Choudhary D, Yadav R, Goel R, Bhambhani S, Sanyal I, Trivedi R, Kumar Trivedi P. AtMYB12 expression in tomato leads to large scale differential modulation in transcriptome and flavonoid content in leaf and fruit tissues Sci Rep, 5, pp. 12412. doi:10.1038/srep12412 (24 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)
Zhang K, Xu Z, Sun Z. Identification of the key genes connected with plasma cells of multiple myeloma using expression profiles Onco Targets Ther, 8, pp. 1795-1803. doi:10.2147/OTT.S80075 (20 July 2015)
Argyropoulos C, Wang K, Bernardo J, Ellis D, Orchard T, Galas D, Johnson JP. Urinary MicroRNA Profiling Predicts the Development of Microalbuminuria in Patients with Type 1 Diabetes J Clin Med, 4(7), pp. 1498-1517. doi:10.3390/jcm4071498 (17 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)

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