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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 2018-11-19T06:20:08-05:00.

Ratnaparkhe M, Wong JK, Wei PC, Hlevnjak M, Kolb T, Simovic M, Haag D, Paul Y, Devens F, Northcott P, Jones DT, Kool M, Jauch A, Pastorczak A, Mlynarski W, Korshunov A, Kumar R, Downing SM, Pfister SM, Zapatka M, McKinnon PJ, Alt FW, Lichter P, Ernst A. Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors Nat Commun, 9, pp. 4760. doi:10.1038/s41467-018-06925-4 (12 November 2018)
Raborn RT, Brendel VP. Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes. Methods Mol Biol, 1858, pp. 99-116. doi:10.1007/978-1-4939-8775-7_9 (11 November 2018)
Yang SY, Lejault P, Chevrier S, Boidot R, Robertson AG, Wong JM, Monchaud D. Transcriptome-wide identification of transient RNA G-quadruplexes in human cells Nat Commun, 9, pp. 4730. doi:10.1038/s41467-018-07224-8 (9 November 2018)
Watanabe S, Sato M, Sawada Y, Tanaka M, Matsui A, Kanno Y, Hirai MY, Seki M, Sakamoto A, Seo M. Arabidopsis molybdenum cofactor sulfurase ABA3 contributes to anthocyanin accumulation and oxidative stress tolerance in ABA-dependent and independent ways Sci Rep, 8, pp. 16592. doi:10.1038/s41598-018-34862-1 (9 November 2018)
Roth R, Chiapello M, Montero H, Gehrig P, Grossmann J, O’Holleran K, Hartken D, Walters F, Yang SY, Hillmer S, Schumacher K, Bowden S, Craze M, Wallington EJ, Miyao A, Sawers R, Martinoia E, Paszkowski U. A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane Nat Commun, 9, pp. 4677. doi:10.1038/s41467-018-06865-z (8 November 2018)
Foroutan M, Bhuva DD, Lyu R, Horan K, Cursons J, Davis MJ. Single sample scoring of molecular phenotypes. BMC Bioinformatics, 19(1), pp. 404. doi:10.1186/s12859-018-2435-4 (6 November 2018)
Hunter ZR, Xu L, Tsakmaklis N, Demos MG, Kofides A, Jimenez C, Chan GG, Chen J, Liu X, Munshi M, Gustine J, Meid K, Patterson CJ, Yang G, Dubeau T, Samur MK, Castillo JJ, Anderson KC, Munshi NC, Treon SP. Insights into the genomic landscape of MYD88 wild-type Waldenström macroglobulinemia Blood Adv, 2(21), pp. 2937-2946. doi:10.1182/bloodadvances.2018022962 (6 November 2018)
Rizvi AA, Karaesmen E, Morgan M, Preus L, Wang J, Sovic M, Hahn T, Sucheston-Campbell LE. gwasurvivr : an R package for genome wide survival analysis. Bioinformatics. doi:10.1093/bioinformatics/bty920 (5 November 2018)
Zhu A, Ibrahim JG, Love MI. Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. doi:10.1093/bioinformatics/bty895 (3 November 2018)
Bacon WA, Hamilton RS, Yu Z, Kieckbusch J, Hawkes D, Krzak AM, Abell C, Colucci F, Charnock-Jones DS. Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice Front Immunol, 9, pp. 2523. doi:10.3389/fimmu.2018.02523 (1 November 2018)
Su Y, Pelz C, Huang T, Torkenczy K, Wang X, Cherry A, Daniel CJ, Liang J, Nan X, Dai MS, Adey A, Impey S, Sears RC. Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals Genes Dev, 32(21-22), pp. 1398-1419. doi:10.1101/gad.314377.118 (1 November 2018)
Hong HK, Maury E, Ramsey KM, Perelis M, Marcheva B, Omura C, Kobayashi Y, Guttridge DC, Barish GD, Bass J. Requirement for NF-κB in maintenance of molecular and behavioral circadian rhythms in mice Genes Dev, 32(21-22), pp. 1367-1379. doi:10.1101/gad.319228.118 (1 November 2018)
Hsu JI, Dayaram T, Tovy A, De Braekeleer E, Jeong M, Wang F, Zhang J, Heffernan TP, Gera S, Kovacs JJ, Marszalek JR, Bristow C, Yan Y, Garcia-Manero G, Kantarjian H, Vassiliou G, Futreal PA, Donehower LA, Takahashi K, Goodell MA. PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy Cell Stem Cell, 23(5), pp. 700-713.e6. doi:10.1016/j.stem.2018.10.004 (1 November 2018)
Blazquez L, Emmett W, Faraway R, Pineda JM, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J. Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing Mol Cell, 72(3), pp. 496-509.e9. doi:10.1016/j.molcel.2018.09.033 (1 November 2018)
Qiu Y, Milanes JE, Jones JA, Noorai RE, Shankar V, Morris JC. Glucose Signaling Is Important for Nutrient Adaptation during Differentiation of Pleomorphic African Trypanosomes mSphere, 3(5), pp. e00366-18. doi:10.1128/mSphere.00366-18 (31 October 2018)
Wacleche VS, Cattin A, Goulet JP, Gauchat D, Gosselin A, Cleret-Buhot A, Zhang Y, Tremblay CL, Routy JP, Ancuta P. CD16+ monocytes give rise to CD103+RALDH2+TCF4+ dendritic cells with unique transcriptional and immunological features Blood Adv, 2(21), pp. 2862-2878. doi:10.1182/bloodadvances.2018020123 (31 October 2018)
Verhagen FH, Hiddingh S, Rijken R, Pandit A, Leijten E, Olde Nordkamp M, ten Dam-van Loon NH, Nierkens S, Imhof SM, de Boer JH, Radstake TR, Kuiper JJ. High-Dimensional Profiling Reveals Heterogeneity of the Th17 Subset and Its Association With Systemic Immunomodulatory Treatment in Non-infectious Uveitis Front Immunol, 9, pp. 2519. doi:10.3389/fimmu.2018.02519 (31 October 2018)
Lee LH, Halu A, Morgan S, Iwata H, Aikawa M, Singh SA. XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis. J Proteome Res. doi:10.1021/acs.jproteome.8b00615 (29 October 2018)
Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics. doi:10.1093/bioinformatics/bty902 (26 October 2018)
Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME. pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra. Bioinformatics. doi:10.1093/bioinformatics/bty837 (23 October 2018)

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