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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 2018-09-18T13:00:10-04:00.

Rabaglino MB, Keller-Wood M, Wood CE. A transcriptomics model of estrogen action in the ovine fetal hypothalamus: evidence for estrogenic effects of ICI 182,780. Physiol Rep, 6(18), pp. e13871. doi:10.14814/phy2.13871 (18 September 2018)
Yang HB, Jiang J, Li LL, Yang HQ, Zhang XY. Biomarker identification of thyroid associated ophthalmopathy using microarray data Int J Ophthalmol, 11(9), pp. 1482-1488. doi:10.18240/ijo.2018.09.09 (18 September 2018)
Borys S, Ludwig-Slomczynska AH, Seweryn M, Hohendorff J, Koblik T, Machlowska J, Kiec-Wilk B, Wolkow P, Malecki MT. Negative pressure wound therapy in the treatment of diabetic foot ulcers may be mediated through differential gene expression. Acta Diabetol. doi:10.1007/s00592-018-1223-y (17 September 2018)
Brown SM, Bush SJ, Summers KM, Hume DA, Lawrence AB. Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity Behav Brain Res, 350, pp. 6-15. doi:10.1016/j.bbr.2018.05.015 (17 September 2018)
Luijk R, Wu H, Ward-Caviness CK, Hannon E, Carnero-Montoro E, Min JL, Mandaviya P, Müller-Nurasyid M, Mei H, van der Maarel SM, Relton C, Mill J, Waldenberger M, Bell JT, Jansen R, Zhernakova A, Franke L, ‘t Hoen PA, Boomsma DI, van Duijn CM, van Greevenbroek MM, Veldink JH, Wijmenga C, van Meurs J, Daxinger L, Slagboom PE, van Zwet EW, Heijmans BT. Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation Nat Commun, 9, pp. 3738. doi:10.1038/s41467-018-05714-3 (14 September 2018)
Bortoluzzi A, Salum GA, da Rosa ED, Chagas VD, Castro MA, Manfro GG. DNA methylation in adolescents with anxiety disorder: a longitudinal study Sci Rep, 8, pp. 13800. doi:10.1038/s41598-018-32090-1 (14 September 2018)
Skakkebæk A, Nielsen MM, Trolle C, Vang S, Hornshøj H, Hedegaard J, Wallentin M, Bojesen A, Hertz JM, Fedder J, Østergaard JR, Pedersen JS, Gravholt CH. DNA hypermethylation and differential gene expression associated with Klinefelter syndrome Sci Rep, 8, pp. 13740. doi:10.1038/s41598-018-31780-0 (13 September 2018)
Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, Ming C, Neff R, Ma W, Fullard JF, Hauberg ME, Bendl J, Peters MA, Logsdon B, Wang P, Mahajan M, Mangravite LM, Dammer EB, Duong DM, Lah JJ, Seyfried NT, Levey AI, Buxbaum JD, Ehrlich M, Gandy S, Katsel P, Haroutunian V, Schadt E, Zhang B. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease Sci Data, 5, pp. 180185. doi:10.1038/sdata.2018.185 (11 September 2018)
Sales G, Calura E, Romualdi C. metaGraphite - a new layer of pathway annotation to get metabolite networks. Bioinformatics. doi:10.1093/bioinformatics/bty719 (4 September 2018)
Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E. clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets. PLoS Comput Biol, 14(9), pp. e1006378. doi:10.1371/journal.pcbi.1006378 (4 September 2018)
Hu Z, Glicksberg BS, Butte AJ. Robust prediction of clinical outcomes using cytometry data. Bioinformatics. doi:10.1093/bioinformatics/bty768 (31 August 2018)
Jose V, Fumagalli D, Rothé F, Majjaj S, Loi S, Michiels S, Sotiriou C. Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays PLoS One, 13(8), pp. e0203346. doi:10.1371/journal.pone.0203346 (31 August 2018)
Terrigno M, Bertacchi M, Pandolfini L, Baumgart M, Calvello M, Cellerino A, Studer M, Cremisi F. The microRNA miR-21 Is a Mediator of FGF8 Action on Cortical COUP-TFI Translation Stem Cell Reports, 11(3), pp. 756-769. doi:10.1016/j.stemcr.2018.08.002 (30 August 2018)
Hoorntje ET, Posafalvi A, Syrris P, van der Velde KJ, Bolling MC, Protonotarios A, Boven LG, Amat-Codina N, Groeneweg JA, Wilde AA, Sobreira N, Calkins H, Hauer RN, Jonkman MF, McKenna WJ, Elliott PM, Sinke RJ, van den Berg MP, Chelko SP, James CA, van Tintelen JP, Judge DP, Jongbloed JD. No major role for rare plectin variants in arrhythmogenic right ventricular cardiomyopathy PLoS One, 13(8), pp. e0203078. doi:10.1371/journal.pone.0203078 (30 August 2018)
Espín-Pérez A, Portier C, Chadeau-Hyam M, van Veldhoven K, Kleinjans JC, de Kok TM. Comparison of statistical methods and the use of quality control samples for batch effect correction in human transcriptome data PLoS One, 13(8), pp. e0202947. doi:10.1371/journal.pone.0202947 (30 August 2018)
Nilsson E, King SE, McBirney M, Kubsad D, Pappalardo M, Beck D, Sadler-Riggleman I, Skinner MK. Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases PLoS One, 13(8), pp. e0202662. doi:10.1371/journal.pone.0202662 (29 August 2018)
Kim ST, Lee YJ, Tasaki T, Hwang J, Kang MJ, Yi EC, Kim BY, Kwon YT. The N-recognin UBR4 of the N-end rule pathway is required for neurogenesis and homeostasis of cell surface proteins PLoS One, 13(8), pp. e0202260. doi:10.1371/journal.pone.0202260 (29 August 2018)
Kim JC, Ha YJ, Tak KH, Roh SA, Kwon YH, Kim CW, Yoon YS, Lee JL, Park Y, Kim SK, Kim SY, Cho DH, Kim YS. Opposite functions of GSN and OAS2 on colorectal cancer metastasis, mediating perineural and lymphovascular invasion, respectively PLoS One, 13(8), pp. e0202856. doi:10.1371/journal.pone.0202856 (27 August 2018)
Jabbari K, Bobbili DR, Lal D, Reinthaler EM, Schubert J, Wolking S, Sinha V, Motameny S, Thiele H, Kawalia A, Altmüller J, Toliat MR, Kraaij R, van Rooij J, Uitterlinden AG, Ikram MA, Zara F, Lehesjoki AE, Krause R, Zimprich F, Sander T, Neubauer BA, May P, Lerche H, Nürnberg P. Rare gene deletions in genetic generalized and Rolandic epilepsies PLoS One, 13(8), pp. e0202022. doi:10.1371/journal.pone.0202022 (27 August 2018)
Erkenbrack EM, Maziarz JD, Griffith OW, Liang C, Chavan AR, Nnamani MC, Wagner GP. The mammalian decidual cell evolved from a cellular stress response PLoS Biol, 16(8), pp. e2005594. doi:10.1371/journal.pbio.2005594 (24 August 2018)

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