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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 2018-05-22T06:00:09-04:00.

Cao X, George EO, Wang M, Armstrong DB, Cheng C, Raimondi S, Rubnitz JE, Downing JR, Kundu M, Pounds SB. POST: a framework for set-based association analysis in high-dimensional data. Methods. doi:10.1016/j.ymeth.2018.05.011 (16 May 2018)
Carreras-Torres R, Johansson M, Haycock PC, Relton CL, Davey Smith G, Brennan P, Martin RM. Role of obesity in smoking behaviour: Mendelian randomisation study in UK Biobank BMJ, 361, pp. k1767. doi:10.1136/bmj.k1767 (16 May 2018)
Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages Nat Commun, 9, pp. 1910. doi:10.1038/s41467-018-04295-5 (15 May 2018)
Kagoya Y, Nakatsugawa M, Saso K, Guo T, Anczurowski M, Wang CH, Butler MO, Arrowsmith CH, Hirano N. DOT1L inhibition attenuates graft-versus-host disease by allogeneic T cells in adoptive immunotherapy models Nat Commun, 9, pp. 1915. doi:10.1038/s41467-018-04262-0 (15 May 2018)
Barwick BG, Scharer CD, Martinez RJ, Price MJ, Wein AN, Haines RR, Bally AP, Kohlmeier JE, Boss JM. B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation Nat Commun, 9, pp. 1900. doi:10.1038/s41467-018-04234-4 (15 May 2018)
Mackay A, Burford A, Molinari V, Jones DT, Izquierdo E, Brouwer-Visser J, Giangaspero F, Haberler C, Pietsch T, Jacques TS, Figarella-Branger D, Rodriguez D, Morgan PS, Raman P, Waanders AJ, Resnick AC, Massimino M, Garrè ML, Smith H, Capper D, Pfister SM, Würdinger T, Tam R, Garcia J, Thakur MD, Vassal G, Grill J, Jaspan T, Varlet P, Jones C. Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial Cancer Cell, 33(5), pp. 829-842.e5. doi:10.1016/j.ccell.2018.04.004 (14 May 2018)
Zhang C, Xiang T, Li S, Ye L, Feng Y, Pei L, Li L, Wang X, Sun R, Tao Q, Ren G. The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β-catenin signalling Cell Death Dis, 9(5), pp. 573. doi:10.1038/s41419-018-0604-z (14 May 2018)
Vértesy Á, Arindrarto W, Roost MS, Reinius B, Torrens-Juaneda V, Bialecka M, Moustakas I, Ariyurek Y, Kuijk E, Mei H, Sandberg R, van Oudenaarden A, Chuva de Sousa Lopes SM. Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells Nat Commun, 9, pp. 1873. doi:10.1038/s41467-018-04215-7 (14 May 2018)
Iglesias AI, Mishra A, Vitart V, Bykhovskaya Y, Höhn R, Springelkamp H, Cuellar-Partida G, Gharahkhani P, Bailey JN, Willoughby CE, Li X, Yazar S, Nag A, Khawaja AP, Polašek O, Siscovick D, Mitchell P, Tham YC, Haines JL, Kearns LS, Hayward C, Shi Y, van Leeuwen EM, Taylor KD, Bonnemaijer P, Rotter JI, Martin NG, Zeller T, Mills RA, Staffieri SE, Jonas JB, Schmidtmann I, Boutin T, Kang JH, Lucas SE, Wong TY, Beutel ME, Wilson JF, Uitterlinden AG, Vithana EN, Foster PJ, Hysi PG, Hewitt AW, Khor CC, Pasquale LR, Montgomery GW, Klaver CC, Aung T, Pfeiffer N, Mackey DA, Hammond CJ, Cheng CY, Craig JE, Rabinowitz YS, Wiggs JL, Burdon KP, van Duijn CM, MacGregor S. Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases Nat Commun, 9, pp. 1864. doi:10.1038/s41467-018-03646-6 (14 May 2018)
Chuang JH, Yarmishyn AA, Hwang DK, Hsu CC, Wang ML, Yang YP, Chien KH, Chiou SH, Peng CH, Chen SJ. Expression profiling of cell-intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages Stem Cell Res Ther, 9, pp. 140. doi:10.1186/s13287-018-0848-7 (11 May 2018)
Biase FH, Kimble KM. Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells BMC Genomics, 19, pp. 351. doi:10.1186/s12864-018-4738-2 (10 May 2018)
Walter RB, Boswell M, Chang J, Boswell WT, Lu Y, Navarro K, Walter SM, Walter DJ, Salinas R, Savage M. Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus) BMC Genomics, 19, pp. 355. doi:10.1186/s12864-018-4735-5 (10 May 2018)
Tsoucas D, Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection Genome Biol, 19, pp. 58. doi:10.1186/s13059-018-1431-3 (10 May 2018)
Ottaviani S, Stebbing J, Frampton AE, Zagorac S, Krell J, de Giorgio A, Trabulo SM, Nguyen VT, Magnani L, Feng H, Giovannetti E, Funel N, Gress TM, Jiao LR, Lombardo Y, Lemoine NR, Heeschen C, Castellano L. TGF-β induces miR-100 and miR-125b but blocks let-7a through LIN28B controlling PDAC progression Nat Commun, 9, pp. 1845. doi:10.1038/s41467-018-03962-x (10 May 2018)
Muri J, Heer S, Matsushita M, Pohlmeier L, Tortola L, Fuhrer T, Conrad M, Zamboni N, Kisielow J, Kopf M. The thioredoxin-1 system is essential for fueling DNA synthesis during T-cell metabolic reprogramming and proliferation Nat Commun, 9, pp. 1851. doi:10.1038/s41467-018-04274-w (10 May 2018)
Rozenbaum M, Rajman M, Rishal I, Koppel I, Koley S, Medzihradszky KF, Oses-Prieto JA, Kawaguchi R, Amieux PS, Burlingame AL, Coppola G, Fainzilber M. Translatome Regulation in Neuronal Injury and Axon Regrowth eNeuro, 5(2), pp. ENEURO.0276-17.2018. doi:10.1523/ENEURO.0276-17.2018 (10 May 2018)
Olde Loohuis LM, Mangul S, Ori AP, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA. Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia Transl Psychiatry, 8, pp. 96. doi:10.1038/s41398-018-0107-9 (10 May 2018)
Pan Y, Lu L, Chen J, Zhong Y, Dai Z. Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma. Hereditas, 155, pp. 21. doi:10.1186/s41065-018-0061-9 (9 May 2018)
Li Z, Li SP, Li RY, Zhu H, Liu X, Guo XL, Mu LL, Cai JJ, Bai F, Chen GQ, Hong DL. Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes Cell Death Dis, 9(5), pp. 526. doi:10.1038/s41419-018-0600-3 (9 May 2018)
Parry AJ, Hoare M, Bihary D, Hänsel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D’Santos P, Russell IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence Nat Commun, 9, pp. 1840. doi:10.1038/s41467-018-04283-9 (9 May 2018)

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