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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 2018-02-20T13:00:10-05:00.

Rahman RU, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder DS, Capece V, Shomroni O, Bonn S. Oasis 2: improved online analysis of small RNA-seq data BMC Bioinformatics, 19, pp. 54. doi:10.1186/s12859-018-2047-z (14 February 2018)
Schenkel LC, Aref-Eshghi E, Skinner C, Ainsworth P, Lin H, Paré G, Rodenhiser DI, Schwartz C, Sadikovic B. Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C Clin Epigenetics, 10, pp. 21. doi:10.1186/s13148-018-0453-8 (14 February 2018)
Metwally AA, Yang J, Ascoli C, Dai Y, Finn PW, Perkins DL. MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies Microbiome, 6, pp. 32. doi:10.1186/s40168-018-0402-y (13 February 2018)
Mohan V, Radha V, Nguyen TT, Stawiski EW, Pahuja KB, Goldstein LD, Tom J, Anjana RM, Kong-Beltran M, Bhangale T, Jahnavi S, Chandni R, Gayathri V, George P, Zhang N, Murugan S, Phalke S, Chaudhuri S, Gupta R, Zhang J, Santhosh S, Stinson J, Modrusan Z, Ramprasad VL, Seshagiri S, Peterson AS. Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India BMC Med Genet, 19, pp. 22. doi:10.1186/s12881-018-0528-6 (13 February 2018)
Meng F, Yuan G, Zhu X, Zhou Y, Wang D, Guo Y. Functional Variants Identified Efficiently through an Integrated Transcriptome and Epigenome Analysis Sci Rep, 8, pp. 2959. doi:10.1038/s41598-018-21024-6 (13 February 2018)
Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R. The effects of death and post-mortem cold ischemia on human tissue transcriptomes Nat Commun, 9, pp. 490. doi:10.1038/s41467-017-02772-x (13 February 2018)
Deng G, Yang J, Zhang Q, Xiao ZX, Cai H. MethCNA: a database for integrating genomic and epigenomic data in human cancer BMC Genomics, 19, pp. 138. doi:10.1186/s12864-018-4525-0 (13 February 2018)
Shabalin AA, Hattab MW, Clark SL, Chan RF, Kumar G, Aberg KA, van den Oord EJCG, Birol I. RaMWAS: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms. Bioinformatics. doi:10.1093/bioinformatics/bty069 (12 February 2018)
Sanford T, Meng MV, Railkar R, Agarwal PK, Porten SP. Integrative analysis of the epigenetic basis of muscle-invasive urothelial carcinoma Clin Epigenetics, 10, pp. 19. doi:10.1186/s13148-018-0451-x (12 February 2018)
Egea I, Albaladejo I, Meco V, Morales B, Sevilla A, Bolarin MC, Flores FB. The drought-tolerant Solanum pennellii regulates leaf water loss and induces genes involved in amino acid and ethylene/jasmonate metabolism under dehydration Sci Rep, 8, pp. 2791. doi:10.1038/s41598-018-21187-2 (12 February 2018)
Ahrazem O, Argandoña J, Fiore A, Aguado C, Luján R, Rubio-Moraga Á, Marro M, Araujo-Andrade C, Loza-Alvarez P, Diretto G, Gómez-Gómez L. Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis Sci Rep, 8, pp. 2843. doi:10.1038/s41598-018-21225-z (12 February 2018)
Sana J, Busek P, Fadrus P, Besse A, Radova L, Vecera M, Reguli S, Stollinova Sromova L, Hilser M, Lipina R, Lakomy R, Kren L, Smrcka M, Sedo A, Slaby O. Identification of microRNAs differentially expressed in glioblastoma stem-like cells and their association with patient survival Sci Rep, 8, pp. 2836. doi:10.1038/s41598-018-20929-6 (12 February 2018)
Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs Nat Commun, 9, pp. 619. doi:10.1038/s41467-018-02866-0 (12 February 2018)
Eilebrecht S, Hotz-Wagenblatt A, Sarachaga V, Burk A, Falida K, Chakraborty D, Nikitina E, Tessmer C, Whitley C, Sauerland C, Gunst K, Grewe I, Bund T. Expression and replication of virus-like circular DNA in human cells Sci Rep, 8, pp. 2851. doi:10.1038/s41598-018-21317-w (12 February 2018)
Karakashev S, Zhu H, Wu S, Yokoyama Y, Bitler BG, Park PH, Lee JH, Kossenkov AV, Gaonkar KS, Yan H, Drapkin R, Conejo-Garcia JR, Speicher DW, Ordog T, Zhang R. CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity Nat Commun, 9, pp. 631. doi:10.1038/s41467-018-03031-3 (12 February 2018)
Jessa S, Kleinman CL, Hancock J. chromswitch: A flexible method to detect chromatin state switches. Bioinformatics. doi:10.1093/bioinformatics/bty075 (9 February 2018)
Li S, Wong EM, Bui M, Nguyen TL, Joo JH, Stone J, Dite GS, Giles GG, Saffery R, Southey MC, Hopper JL. Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study Clin Epigenetics, 10, pp. 18. doi:10.1186/s13148-018-0452-9 (9 February 2018)
Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo Genome Biol, 19, pp. 19. doi:10.1186/s13059-018-1398-0 (9 February 2018)
Kebede AZ, Johnston A, Schneiderman D, Bosnich W, Harris LJ. Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes BMC Genomics, 19, pp. 131. doi:10.1186/s12864-018-4513-4 (9 February 2018)
Dickinson SE, Griffin BA, Elmore MF, Kriese-Anderson L, Elmore JB, Dyce PW, Rodning SP, Biase FH. Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential BMC Genomics, 19, pp. 129. doi:10.1186/s12864-018-4505-4 (9 February 2018)

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