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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 2018-09-24T14:40:06-04:00.

Page CM, Vos L, Rounge TB, Harbo HF, Andreassen BK. Assessing genome-wide significance for the detection of differentially methylated regions. Stat Appl Genet Mol Biol. doi:10.1515/sagmb-2017-0050 (19 September 2018)
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)
Brockman KL, Azzari PN, Branstool MT, Atack JM, Schulz BL, Jen FE, Jennings MP, Bakaletz LO. Epigenetic Regulation Alters Biofilm Architecture and Composition in Multiple Clinical Isolates of Nontypeable Haemophilus influenzae mBio, 9(5), pp. e01682-18. doi:10.1128/mBio.01682-18 (18 September 2018)
Fabre PJ, Leleu M, Mascrez B, Lo Giudice Q, Cobb J, Duboule D. Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development BMC Biol, 16, pp. 101. doi:10.1186/s12915-018-0570-z (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)
Long X, Deng Z, Li G, Wang Z. Identification of critical genes to predict recurrence and death in colon cancer: integrating gene expression and bioinformatics analysis Cancer Cell Int, 18, pp. 139. doi:10.1186/s12935-018-0640-x (17 September 2018)
Peripolli E, Metzger J, de Lemos MV, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FL, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CD, Di Croce F, Osterstock J, Denise S, Pereira AS, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits BMC Genomics, 19, pp. 680. doi:10.1186/s12864-018-5060-8 (17 September 2018)
Johnson EK, Matkovich SJ, Nerbonne JM. Regional Differences in mRNA and lncRNA Expression Profiles in Non-Failing Human Atria and Ventricles Sci Rep, 8, pp. 13919. doi:10.1038/s41598-018-32154-2 (17 September 2018)
Ulanska-Poutanen J, Mieczkowski J, Zhao C, Konarzewska K, Kaza B, Pohl HB, Bugajski L, Kaminska B, Franklin RJ, Zawadzka M. Injury-induced perivascular niche supports alternative differentiation of adult rodent CNS progenitor cells eLife, 7, pp. e30325. doi:10.7554/eLife.30325 (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)
Barham C, Fil D, Byrum SD, Rahmatallah Y, Glazko G, Kiaei M. RNA-Seq Analysis of Spinal Cord Tissues from hPFN1G118V Transgenic Mouse Model of ALS at Pre-symptomatic and End-Stages of Disease Sci Rep, 8, pp. 13737. doi:10.1038/s41598-018-31132-y (13 September 2018)
de Souza MM, Zerlotini A, Geistlinger L, Tizioto PC, Taylor JF, Rocha MI, Diniz WJ, Coutinho LL, Regitano LC. A comprehensive manually-curated compendium of bovine transcription factors Sci Rep, 8, pp. 13747. doi:10.1038/s41598-018-32146-2 (13 September 2018)
Keller RF, Dragomir A, Yantao F, Akay YM, Akay M. Investigating the genetic profile of dopaminergic neurons in the VTA in response to perinatal nicotine exposure using mRNA-miRNA analyses Sci Rep, 8, pp. 13769. doi:10.1038/s41598-018-31882-9 (13 September 2018)
Sun X, St John JC. Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours Epigenetics Chromatin, 11, pp. 53. doi:10.1186/s13072-018-0223-z (12 September 2018)
Klau S, Jurinovic V, Hornung R, Herold T, Boulesteix AL. Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data BMC Bioinformatics, 19, pp. 322. doi:10.1186/s12859-018-2344-6 (12 September 2018)
Rib L, Villeneuve D, Minocha S, Praz V, Hernandez N, Guex N, Herr W. Cycles of gene expression and genome response during mammalian tissue regeneration Epigenetics Chromatin, 11, pp. 52. doi:10.1186/s13072-018-0222-0 (12 September 2018)

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