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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 2018-11-13T04:20:07-05:00.

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)

Iracane E, Donovan PD, Ola M, Butler G, Holland LM. Identification of an Exceptionally Long Intron in the HAC1 Gene of Candida parapsilosis mSphere, 3(6), pp. e00532-18. doi:10.1128/mSphere.00532-18 (7 November 2018)

Wang L, Ozark PA, Smith ER, Zhao Z, Marshall SA, Rendleman EJ, Piunti A, Ryan C, Whelan AL, Helmin KA, Morgan MA, Zou L, Singer BD, Shilatifard A. TET2 coactivates gene expression through demethylation of enhancers Sci Adv, 4(11), pp. eaau6986. doi:10.1126/sciadv.aau6986 (7 November 2018)

Valdecantos MP, Ruiz L, Pardo V, Castro-Sanchez L, García-Monzón C, Lanzón B, Rupérez J, Barbas C, Naylor J, Trevaskis JL, Grimsby J, Rondinone CM, Valverde ÁM. Differential Effects of a Glucagon-Like Peptide 1 Receptor Agonist in Non-Alcoholic Fatty Liver Disease and in Response to Hepatectomy Sci Rep, 8, pp. 16461. doi:10.1038/s41598-018-33949-z (7 November 2018)

Revinski DR, Zaragosi LE, Boutin C, Ruiz-Garcia S, Deprez M, Thomé V, Rosnet O, Gay AS, Mercey O, Paquet A, Pons N, Ponzio G, Marcet B, Kodjabachian L, Barbry P. CDC20B is required for deuterosome-mediated centriole production in multiciliated cells Nat Commun, 9, pp. 4668. doi:10.1038/s41467-018-06768-z (7 November 2018)

Tamminen M, Betz A, Pereira AL, Thali M, Matthews B, Suter MJ, Narwani A. Proteome evolution under non-substitutable resource limitation Nat Commun, 9, pp. 4650. doi:10.1038/s41467-018-07106-z (7 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)

Salomon MP, Orozco JI, Wilmott JS, Hothi P, Manughian-Peter AO, Cobbs CS, Scolyer RA, Hoon DS, Marzese DM. Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features Sci Data, 5, pp. 180245. doi:10.1038/sdata.2018.245 (6 November 2018)

Smith MR, Yevoo P, Sadahiro M, Austin C, Amarasiriwardena C, Awawda M, Arora M, Dudley JT, Morishita H. Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity Sci Rep, 8, pp. 16388. doi:10.1038/s41598-018-34592-4 (6 November 2018)

Tessier L, Côté O, Clark ME, Viel L, Diaz-Méndez A, Anders S, Bienzle D. Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma Sci Rep, 8, pp. 16408. doi:10.1038/s41598-018-34636-9 (6 November 2018)

Orozco JI, Knijnenburg TA, Manughian-Peter AO, Salomon MP, Barkhoudarian G, Jalas JR, Wilmott JS, Hothi P, Wang X, Takasumi Y, Buckland ME, Thompson JF, Long GV, Cobbs CS, Shmulevich I, Kelly DF, Scolyer RA, Hoon DS, Marzese DM. Epigenetic profiling for the molecular classification of metastatic brain tumors Nat Commun, 9, pp. 4627. doi:10.1038/s41467-018-06715-y (6 November 2018)

Daniel S, Nylander V, Ingerslev LR, Zhong L, Fabre O, Clifford B, Johnston K, Cohn RJ, Barres R, Simar D. T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors Clin Epigenetics, 10, pp. 138. doi:10.1186/s13148-018-0561-5 (6 November 2018)

Kumar MS, Slud EV, Okrah K, Hicks SC, Hannenhalli S, Corrada Bravo H. Analysis and correction of compositional bias in sparse sequencing count data BMC Genomics, 19, pp. 799. doi:10.1186/s12864-018-5160-5 (6 November 2018)

Duan W, Zhang R, Zhao Y, Shen S, Wei Y, Chen F, Christiani DC. Bayesian variable selection for parametric survival model with applications to cancer omics data Hum Genomics, 12, pp. 49. doi:10.1186/s40246-018-0179-x (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)

Aden K, Tran F, Ito G, Sheibani-Tezerji R, Lipinski S, Kuiper JW, Tschurtschenthaler M, Saveljeva S, Bhattacharyya J, Häsler R, Bartsch K, Luzius A, Jentzsch M, Falk-Paulsen M, Stengel ST, Welz L, Schwarzer R, Rabe B, Barchet W, Krautwald S, Hartmann G, Pasparakis M, Blumberg RS, Schreiber S, Kaser A, Rosenstiel P. ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING J Exp Med, 215(11), pp. 2868-2886. doi:10.1084/jem.20171029 (5 November 2018)

Kvaløy K, Page CM, Holmen TL. Epigenome-wide methylation differences in a group of lean and obese women – A HUNT Study Sci Rep, 8, pp. 16330. doi:10.1038/s41598-018-34003-8 (5 November 2018)

Cambré I, Gaublomme D, Burssens A, Jacques P, Schryvers N, De Muynck A, Meuris L, Lambrecht S, Carter S, de Bleser P, Saeys Y, Van Hoorebeke L, Kollias G, Mack M, Simoens P, Lories R, Callewaert N, Schett G, Elewaut D. Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis Nat Commun, 9, pp. 4613. doi:10.1038/s41467-018-06933-4 (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)

Caballero-Solares A, Xue X, Parrish CC, Foroutani MB, Taylor RG, Rise ML. Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil BMC Genomics, 19, pp. 796. doi:10.1186/s12864-018-5188-6 (3 November 2018)