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Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

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). PMC4509590

Kannan L, et al. (2015). Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform. doi:10.1093/bib/bbv080

Love M, Huber W, and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550; doi:10.1186/s13059-014-0550-8

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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2017-08-22T10:00:10-04:00.

Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications Genome Med, 9, pp. 75. doi:10.1186/s13073-017-0467-4 (18 August 2017)

Brüwer JD, Agrawal S, Liew YJ, Aranda M, Voolstra CR. Association of coral algal symbionts with a diverse viral community responsive to heat shock BMC Microbiol, 17, pp. 174. doi:10.1186/s12866-017-1084-5 (17 August 2017)

Udhane SS, Legeza B, Marti N, Hertig D, Diserens G, Nuoffer JM, Vermathen P, Flück CE. Combined transcriptome and metabolome analyses of metformin effects reveal novel links between metabolic networks in steroidogenic systems Sci Rep, 7, pp. 8652. doi:10.1038/s41598-017-09189-y (17 August 2017)

Correia C, Koshkin A, Duarte P, Hu D, Teixeira A, Domian I, Serra M, Alves PM. Distinct carbon sources affect structural and functional maturation of cardiomyocytes derived from human pluripotent stem cells Sci Rep, 7, pp. 8590. doi:10.1038/s41598-017-08713-4 (17 August 2017)

Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems Sci Rep, 7, pp. 8637. doi:10.1038/s41598-017-08320-3 (17 August 2017)

Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL. CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo Sci Rep, 7, pp. 8642. doi:10.1038/s41598-017-08094-8 (17 August 2017)

Banos G, Bramis G, Bush SJ, Clark EL, McCulloch ME, Smith J, Schulze G, Arsenos G, Hume DA, Psifidi A. The genomic architecture of mastitis resistance in dairy sheep BMC Genomics, 18, pp. 624. doi:10.1186/s12864-017-3982-1 (16 August 2017)

Rotllant G, Nguyen TV, Sbragaglia V, Rahi L, Dudley KJ, Hurwood D, Ventura T, Company JB, Chand V, Aguzzi J, Mather PB. Sex and tissue specific gene expression patterns identified following de novo transcriptomic analysis of the Norway lobster, Nephrops norvegicus BMC Genomics, 18, pp. 622. doi:10.1186/s12864-017-3981-2 (16 August 2017)

Su S, Hou Z, Liu D, Jia C, Wang L, Xu J, Tao J. Comparative transcriptome analysis of second- and third-generation merozoites of Eimeria necatrix Parasit Vectors, 10, pp. 388. doi:10.1186/s13071-017-2325-z (16 August 2017)

Li S, Kim E, Wong EM, Joo JH, Nguyen TL, Stone J, Song YM, Flander LB, Saffery R, Giles GG, Southey MC, Sung J, Hopper JL. Twin birth changes DNA methylation of subsequent siblings Sci Rep, 7, pp. 8463. doi:10.1038/s41598-017-08595-6 (16 August 2017)

Jenull S, Tscherner M, Gulati M, Nobile CJ, Chauhan N, Kuchler K. The Candida albicans HIR histone chaperone regulates the yeast-to-hyphae transition by controlling the sensitivity to morphogenesis signals Sci Rep, 7, pp. 8308. doi:10.1038/s41598-017-08239-9 (16 August 2017)

Niu X, Guan Y, Chen S, Li H. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon BMC Genomics, 18, pp. 619. doi:10.1186/s12864-017-4044-4 (15 August 2017)

Kresovich JK, Zheng Y, Cardenas A, Joyce BT, Rifas-Shiman SL, Oken E, Gillman MW, Hivert MF, Baccarelli AA, Hou L. Cord blood DNA methylation and adiposity measures in early and mid-childhood Clin Epigenetics, 9, pp. 86. doi:10.1186/s13148-017-0384-9 (15 August 2017)

Nalluri JJ, Rana P, Barh D, Azevedo V, Dinh TN, Vladimirov V, Ghosh P. Determining causal miRNAs and their signaling cascade in diseases using an influence diffusion model Sci Rep, 7, pp. 8133. doi:10.1038/s41598-017-08125-4 (15 August 2017)

Li S, Christiansen L, Christensen K, Kruse TA, Redmond P, Marioni RE, Deary IJ, Tan Q. Identification, replication and characterization of epigenetic remodelling in the aging genome: a cross population analysis Sci Rep, 7, pp. 8183. doi:10.1038/s41598-017-08346-7 (15 August 2017)

Scheel TK, Moore MJ, Luna JM, Nishiuchi E, Fak J, Darnell RB, Rice CM. Global mapping of miRNA-target interactions in cattle (Bos taurus) Sci Rep, 7, pp. 8190. doi:10.1038/s41598-017-07880-8 (15 August 2017)

Duan N, Bai Y, Sun H, Wang N, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, Liu J, Wang D, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong GY, Cheng L, Fei Z, Chen X. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement Nat Commun, 8, pp. 249. doi:10.1038/s41467-017-00336-7 (15 August 2017)

Wong LL, Rademaker MT, Saw EL, Lew KS, Ellmers LJ, Charles CJ, Richards AM, Wang P. Identification of novel microRNAs in the sheep heart and their regulation in heart failure Sci Rep, 7, pp. 8250. doi:10.1038/s41598-017-08574-x (15 August 2017)

Huang C, Cun Y, Yu H, Tong Z, Xiao B, Song Z, Wang B, Li Y, Liu Y. Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection Virol J, 14, pp. 153. doi:10.1186/s12985-017-0821-6 (14 August 2017)

Beauvais-Flück R, Slaveykova VI, Cosio C. Cellular toxicity pathways of inorganic and methyl mercury in the green microalga Chlamydomonas reinhardtii Sci Rep, 7, pp. 8034. doi:10.1038/s41598-017-08515-8 (14 August 2017)