Publications

Bioconductor F1000 Research Channel launched!

Featured

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 2018-07-22T21:00:09-04:00.

Kriss CL, Gregory-Lott E, Storey AJ, Tackett AJ, Wahls WP, Stevens SM Jr. In vivo metabolic tracing demonstrates the site-specific contribution of hepatic ethanol metabolism to histone acetylation. Alcohol Clin Exp Res. doi:10.1111/acer.13843 (21 July 2018)
Wang C, Tan Z, Niu B, Tsang KY, Tai A, Chan WC, Lo RL, Leung KK, Dung NW, Itoh N, Zhang MQ, Chan D, Cheah KS. Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia eLife, 7, pp. e37673. doi:10.7554/eLife.37673 (19 July 2018)
Valdeolivas A, Tichit L, Navarro C, Perrin S, Odelin G, Levy N, Cau P, Remy E, Baudot A. Random Walk with Restart on Multiplex and Heterogeneous Biological Networks. Bioinformatics. doi:10.1093/bioinformatics/bty637 (18 July 2018)
Quinn TP, Crowley TM, Richardson MF. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods BMC Bioinformatics, 19, pp. 274. doi:10.1186/s12859-018-2261-8 (18 July 2018)
Clissold RL, Ashfield B, Burrage J, Hannon E, Bingham C, Mill J, Hattersley A, Dempster EL. Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion Clin Epigenetics, 10, pp. 97. doi:10.1186/s13148-018-0530-z (18 July 2018)
Birkeland Å, ChyŻyńska K, Valen E. Shoelaces: an interactive tool for ribosome profiling processing and visualization BMC Genomics, 19, pp. 543. doi:10.1186/s12864-018-4912-6 (18 July 2018)
Kimes PK, Reyes A. Reproducible and replicable comparisons using SummarizedBenchmark. Bioinformatics. doi:10.1093/bioinformatics/bty627 (17 July 2018)
Ramos PI, Fernández Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM, Klein CC, Sagot MF, de Vasconcelos AT, Gales AC, Marti M, Turjanski AG, Nicolás MF. An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets Sci Rep, 8, pp. 10755. doi:10.1038/s41598-018-28916-7 (17 July 2018)
Hirose Y, Nagahashi M, Katsuta E, Yuza K, Miura K, Sakata J, Kobayashi T, Ichikawa H, Shimada Y, Kameyama H, McDonald KA, Takabe K, Wakai T. Generation of sphingosine-1-phosphate is enhanced in biliary tract cancer patients and is associated with lymphatic metastasis Sci Rep, 8, pp. 10814. doi:10.1038/s41598-018-29144-9 (17 July 2018)
Schlachetzki JC, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, Winner B, Glass CK, Winkler J. A monocyte gene expression signature in the early clinical course of Parkinson’s disease Sci Rep, 8, pp. 10757. doi:10.1038/s41598-018-28986-7 (17 July 2018)
Papale LA, Seltzer LJ, Madrid A, Pollak SD, Alisch RS. Differentially Methylated Genes in Saliva are linked to Childhood Stress Sci Rep, 8, pp. 10785. doi:10.1038/s41598-018-29107-0 (17 July 2018)
Stull VJ, Finer E, Bergmans RS, Febvre HP, Longhurst C, Manter DK, Patz JA, Weir TL. Impact of Edible Cricket Consumption on Gut Microbiota in Healthy Adults, a Double-blind, Randomized Crossover Trial Sci Rep, 8, pp. 10762. doi:10.1038/s41598-018-29032-2 (17 July 2018)
Livshits G, Alonso-Curbelo D, Morris JP IV, Koche R, Saborowski M, Wilkinson JE, Lowe SW. Arid1a restrains Kras-dependent changes in acinar cell identity eLife, 7, pp. e35216. doi:10.7554/eLife.35216 (17 July 2018)
Huang X, Guo B, Liu S, Wan J, Broxmeyer HE. Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment Nat Commun, 9, pp. 2741. doi:10.1038/s41467-018-05178-5 (16 July 2018)
Vidya SM, Kumar HS, Bhatt RM, Laxman RH, Ravishankar KV. Transcriptional profiling and genes involved in acquired thermotolerance in Banana: a non-model crop Sci Rep, 8, pp. 10683. doi:10.1038/s41598-018-27820-4 (16 July 2018)
Asada S, Goyama S, Inoue D, Shikata S, Takeda R, Fukushima T, Yonezawa T, Fujino T, Hayashi Y, Kawabata KC, Fukuyama T, Tanaka Y, Yokoyama A, Yamazaki S, Kozuka-Hata H, Oyama M, Kojima S, Kawazu M, Mano H, Kitamura T. Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis Nat Commun, 9, pp. 2733. doi:10.1038/s41467-018-05085-9 (16 July 2018)
Seal A, Wild DJ. Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links BMC Bioinformatics, 19, pp. 265. doi:10.1186/s12859-018-2254-7 (16 July 2018)
Krishnan P, Meile L, Plissonneau C, Ma X, Hartmann FE, Croll D, McDonald BA, Sánchez-Vallet A. Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat BMC Biol, 16, pp. 78. doi:10.1186/s12915-018-0543-2 (16 July 2018)
Weichenberger CX, Rainer J, Pattaro C, Pramstaller PP, Domingues FS. Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees. Bioinformatics. doi:10.1093/bioinformatics/bty541 (13 July 2018)

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.