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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 2017-11-19T10:00:10-05:00.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. doi:10.1093/nar/gkx1126 (13 November 2017)
Peng Z, Wang J, Shan B, Yuan F, Li B, Dong Y, Peng W, Shi W, Cheng Y, Gao Y, Zhang C, Duan C. Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma. Sci Rep, 7(1), pp. 15331. doi:10.1038/s41598-017-15712-y (10 November 2017)
Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H, Lawley TD. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota Nat Commun, 8, pp. 1367. doi:10.1038/s41467-017-01449-9 (8 November 2017)
Wang T, Wang G, Zhang X, Wu D, Yang L, Wang G, Hao D. The expression of miRNAs is associated with tumour genome instability and predicts the outcome of ovarian cancer patients treated with platinum agents Sci Rep, 7, pp. 14736. doi:10.1038/s41598-017-12259-w (7 November 2017)
Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JG, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries Sci Rep, 7, pp. 14626. doi:10.1038/s41598-017-14892-x (7 November 2017)
Penberthy KK, Rival C, Shankman LS, Raymond MH, Zhang J, Perry JS, Lee CS, Han CZ, Onengut-Gumuscu S, Palczewski K, Lysiak JJ, Ravichandran KS. Context-dependent compensation among phosphatidylserine-recognition receptors Sci Rep, 7, pp. 14623. doi:10.1038/s41598-017-15191-1 (7 November 2017)
Domínguez-Soto Á, Usategui A, Casas-Engel MD, Simón-Fuentes M, Nieto C, Cuevas VD, Vega MA, Luis Pablos J, Corbí ÁL. Serotonin drives the acquisition of a profibrotic and anti-inflammatory gene profile through the 5-HT7R-PKA signaling axis Sci Rep, 7, pp. 14761. doi:10.1038/s41598-017-15348-y (7 November 2017)
Tangtanatakul P, Thammasate B, Jacquet A, Reantragoon R, Pisitkun T, Avihingsanon Y, Leelahavanichkul A, Hirankarn N. Transcriptomic profiling in human mesangial cells using patient-derived lupus autoantibodies identified miR-10a as a potential regulator of IL8 Sci Rep, 7, pp. 14517. doi:10.1038/s41598-017-15160-8 (6 November 2017)
Rausch V, Krieg A, Camps J, Behrens B, Beier M, Wangsa D, Heselmeyer-Haddad K, Baldus SE, Knoefel WT, Ried T, Stoecklein NH. Array comparative genomic hybridization of 18 pancreatic ductal adenocarcinomas and their autologous metastases BMC Res Notes, 10, pp. 560. doi:10.1186/s13104-017-2886-0 (6 November 2017)
Marabita F, Almgren M, Sjöholm LK, Kular L, Liu Y, James T, Kiss NB, Feinberg AP, Olsson T, Kockum I, Alfredsson L, Ekström TJ, Jagodic M. Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship Sci Rep, 7, pp. 14589. doi:10.1038/s41598-017-14788-w (6 November 2017)
Maitre D, Selmoni OM, Uppal A, Marques da Cunha L, Wilkins LG, Roux J, Mobley KB, Castro I, Knörr S, Robinson-Rechavi M, Wedekind C. Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster Sci Rep, 7, pp. 15024. doi:10.1038/s41598-017-14905-9 (3 November 2017)
Wang S, Zhang J, Sui L, Xu H, Piao Q, Liu Y, Qu X, Sun Y, Song L, Li D, Peng L, Hua S, Hu G, Chen J. Antibiotics induce polarization of pleural macrophages to M2-like phenotype in patients with tuberculous pleuritis Sci Rep, 7, pp. 14982. doi:10.1038/s41598-017-14808-9 (3 November 2017)
Ruzicka WB, Subburaju S, Coyle JT, Benes FM. Location Matters: Distinct DNA Methylation Patterns in GABAergic Interneuronal Populations from Separate Microcircuits within the Human Hippocampus. Hum Mol Genet. doi:10.1093/hmg/ddx395 (2 November 2017)
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res, 77(21), pp. e39-e42. doi:10.1158/0008-5472.CAN-17-0344 (1 November 2017)
Hon J, Martínek T, Zendulka J, Lexa M. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics, 33(21), pp. 3373-3379. doi:10.1093/bioinformatics/btx413 (1 November 2017)
Almugbel R, Hung LH, Hu J, Almutairy A, Ortogero N, Tamta Y, Yeung KY. Reproducible Bioconductor workflows using browser-based interactive notebooks and containers. J Am Med Inform Assoc. doi:10.1093/jamia/ocx120 (28 October 2017)
Signal B, Gloss BS, Dinger ME, Mercer TR. Machine learning annotation of human branchpoints. Bioinformatics. doi:10.1093/bioinformatics/btx688 (28 October 2017)
Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. ndexr - an R package to interface with the Network Data Exchange. Bioinformatics. doi:10.1093/bioinformatics/btx683 (26 October 2017)
Dirmeier S, Fuchs C, Mueller NS, Theis FJ. netReg: Network-regularized linear models for biological association studies. Bioinformatics. doi:10.1093/bioinformatics/btx677 (25 October 2017)
Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M. GRcalculator: an online tool for calculating and mining dose-response data. BMC Cancer, 17(1), pp. 698. doi:10.1186/s12885-017-3689-3 (24 October 2017)

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