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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 2017-09-25T18:40:11-04:00.

Van Bortle K, Phanstiel DH, Snyder MP. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation Genome Biol, 18, pp. 180. doi:10.1186/s13059-017-1310-3 (20 September 2017)
Lawlor N, Youn A, Kursawe R, Ucar D, Stitzel ML. Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts Sci Rep, 7, pp. 11959. doi:10.1038/s41598-017-12335-1 (20 September 2017)
Lewis S, Kennedy J, Burgner D, McLachlan R, Ranganathan S, Hammarberg K, Saffery R, Amor DJ, Cheung MM, Doyle LW, Juonala M, Donath S, McBain J, Halliday J. Clinical review of 24–35 year olds conceived with and without in vitro fertilization: study protocol Reprod Health, 14, pp. 117. doi:10.1186/s12978-017-0377-3 (20 September 2017)
Bain CC, Montgomery J, Scott CL, Kel JM, Girard-Madoux MJ, Martens L, Zangerle-Murray TF, Ober-Blöbaum J, Lindenbergh-Kortleve D, Samsom JN, Henri S, Lawrence T, Saeys Y, Malissen B, Dalod M, Clausen BE, Mowat AM. TGFβR signalling controls CD103+CD11b+ dendritic cell development in the intestine Nat Commun, 8, pp. 620. doi:10.1038/s41467-017-00658-6 (20 September 2017)
Mroczek S, Chlebowska J, Kuliński TM, Gewartowska O, Gruchota J, Cysewski D, Liudkovska V, Borsuk E, Nowis D, Dziembowski A. The non-canonical poly(A) polymerase FAM46C acts as an onco-suppressor in multiple myeloma Nat Commun, 8, pp. 619. doi:10.1038/s41467-017-00578-5 (20 September 2017)
Pirhaji L, Milani P, Dalin S, Wassie BT, Dunn DE, Fenster RJ, Avila-Pacheco J, Greengard P, Clish CB, Heiman M, Lo DC, Fraenkel E. Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements Nat Commun, 8, pp. 623. doi:10.1038/s41467-017-00353-6 (20 September 2017)
Birnbaum DJ, Finetti P, Lopresti A, Gilabert M, Poizat F, Raoul JL, Delpero JR, Moutardier V, Birnbaum D, Mamessier E, Bertucci F. A 25-gene classifier predicts overall survival in resectable pancreatic cancer BMC Med, 15, pp. 170. doi:10.1186/s12916-017-0936-z (20 September 2017)
Cao Y, Han Y, Meng D, Li D, Jiao C, Jin Q, Lin Y, Cai Y. B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.) BMC Plant Biol, 17, pp. 156. doi:10.1186/s12870-017-1105-4 (19 September 2017)
Singh G, Singh G, Singh P, Parmar R, Paul N, Vashist R, Swarnkar MK, Kumar A, Singh S, Singh AK, Kumar S, Sharma RK. Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert Sci Rep, 7, pp. 11835. doi:10.1038/s41598-017-12025-y (19 September 2017)
Trabanelli S, Chevalier MF, Martinez-Usatorre A, Gomez-Cadena A, Salomé B, Lecciso M, Salvestrini V, Verdeil G, Racle J, Papayannidis C, Morita H, Pizzitola I, Grandclément C, Bohner P, Bruni E, Girotra M, Pallavi R, Falvo P, Leibundgut EO, Baerlocher GM, Carlo-Stella C, Taurino D, Santoro A, Spinelli O, Rambaldi A, Giarin E, Basso G, Tresoldi C, Ciceri F, Gfeller D, Akdis CA, Mazzarella L, Minucci S, Pelicci PG, Marcenaro E, McKenzie AN, Vanhecke D, Coukos G, Mavilio D, Curti A, Derré L, Jandus C. Tumour-derived PGD2 and NKp30-B7H6 engagement drives an immunosuppressive ILC2-MDSC axis Nat Commun, 8, pp. 593. doi:10.1038/s41467-017-00678-2 (19 September 2017)
Huang HT, Seo HS, Zhang T, Wang Y, Jiang B, Li Q, Buckley DL, Nabet B, Roberts JM, Paulk J, Dastjerdi S, Winter GE, McLauchlan H, Moran J, Bradner JE, Eck MJ, Dhe-Paganon S, Zhao JJ, Gray NS. MELK is not necessary for the proliferation of basal-like breast cancer cells eLife, 6, pp. e26693. doi:10.7554/eLife.26693 (19 September 2017)
Tamiru M, Natsume S, Takagi H, White B, Yaegashi H, Shimizu M, Yoshida K, Uemura A, Oikawa K, Abe A, Urasaki N, Matsumura H, Babil P, Yamanaka S, Matsumoto R, Muranaka S, Girma G, Lopez-Montes A, Gedil M, Bhattacharjee R, Abberton M, Kumar PL, Rabbi I, Tsujimura M, Terachi T, Haerty W, Corpas M, Kamoun S, Kahl G, Takagi H, Asiedu R, Terauchi R. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination BMC Biol, 15, pp. 86. doi:10.1186/s12915-017-0419-x (19 September 2017)
Hernandez MX, Jiang S, Cole TA, Chu SH, Fonseca MI, Fang MJ, Hohsfield LA, Torres MD, Green KN, Wetsel RA, Mortazavi A, Tenner AJ. Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss Mol Neurodegener, 12, pp. 66. doi:10.1186/s13024-017-0210-z (18 September 2017)
Hardcastle TJ. Methods for discovering genomic loci exhibiting complex patterns of differential methylation BMC Bioinformatics, 18, pp. 416. doi:10.1186/s12859-017-1836-0 (18 September 2017)
Yokoyama T, Yanagihara T, Suzuki K, Hamada N, Tsubouchi K, Ogata-Suetsugu S, Mikumo H, Ikeda-Harada C, Maeyama T, Kuwano K, Nakanishi Y. Depletion of club cells attenuates bleomycin-induced lung injury and fibrosis in mice J Inflamm (Lond), 14, pp. 20. doi:10.1186/s12950-017-0168-1 (18 September 2017)
Spiers H, Hannon E, Schalkwyk LC, Bray NJ, Mill J. 5-hydroxymethylcytosine is highly dynamic across human fetal brain development BMC Genomics, 18, pp. 738. doi:10.1186/s12864-017-4091-x (18 September 2017)
Fournier M, Monin A, Ferrari C, Baumann PS, Conus P, Do K. Implication of the glutamate–cystine antiporter xCT in schizophrenia cases linked to impaired GSH synthesis NPJ Schizophr, 3, pp. 31. doi:10.1038/s41537-017-0035-3 (18 September 2017)
Berdasco M, Gómez A, Rubio MJ, Català-Mora J, Zanón-Moreno V, Lopez M, Hernández C, Yoshida S, Nakama T, Ishikawa K, Ishibashi T, Boubekeur AM, Louhibi L, Pujana MA, Sayols S, Setien F, Corella D, de Torres C, Parareda A, Mora J, Zhao L, Zhang K, Lleonart ME, Alonso J, Simó R, Caminal JM, Esteller M. DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated Disorders Sci Rep, 7, pp. 11762. doi:10.1038/s41598-017-12084-1 (18 September 2017)
Sowpati DT, Srivastava S, Dhawan J, Mishra RK. C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search BMC Bioinformatics, 18(Suppl 10), pp. 392. doi:10.1186/s12859-017-1786-6 (13 September 2017)
Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA sequencing data. Genome Biol, 18(1), pp. 174. doi:10.1186/s13059-017-1305-0 (12 September 2017)

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