Publications

Featured

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).
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth, GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl. Acids Res; doi:10.1093/nar/gkv007
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 2015-04-17T14:04:16-07:00.

Siebourg-Polster J, Mudrak D, Emmenlauer M, Rämö P, Dehio C, Greber U, Fröhlich H, Beerenwinkel N. NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Comput Biol, 11(4), pp. e1004078. doi:10.1371/journal.pcbi.1004078 (16 April 2015)
Liu Y, Fang Y, Huang M, Jin Y, Sun J, Tao X, Zhang G, He K, Zhao Y, Zhao H. Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) II: transcriptome alterations of pathways involved in carbohydrate metabolism and endogenous hormone crosstalk Biotechnol Biofuels, 8, pp. 64. doi:10.1186/s13068-015-0245-8 (11 April 2015)
Falgreen S, Dybkær K, Young KH, Xu-Monette ZY, El-Galaly TC, Laursen MB, Bødker JS, Kjeldsen MK, Schmitz A, Nyegaard M, Johnsen HE, Bøgsted M. Predicting response to multidrug regimens in cancer patients using cell line experiments and regularised regression models BMC Cancer, 15, pp. 235. doi:10.1186/s12885-015-1237-6 (8 April 2015)
Sörensen T, Baumgart S, Durek P, Grützkau A, Häupl T. immunoClust-An automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A. doi:10.1002/cyto.a.22626 (7 April 2015)
Musella V, Callari M, Di Buduo E, Scuro M, Dugo M, Miodini P, Bianchini G, Paolini B, Gianni L, Daidone MG, Cappelletti V. Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients PLoS One, 10(4), pp. e0123194. doi:10.1371/journal.pone.0123194 (6 April 2015)
McAdams RM, McPherson RJ, Beyer RP, Bammler TK, Farin FM, Juul SE. Dose-Dependent Effects of Morphine Exposure on mRNA and microRNA (miR) Expression in Hippocampus of Stressed Neonatal Mice PLoS One, 10(4), pp. e0123047. doi:10.1371/journal.pone.0123047 (6 April 2015)
Leng N, Li Y, Mcintosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey C, Stewart R, Kendziorski C. EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinformatics. doi:10.1093/bioinformatics/btv193 (5 April 2015)
Zhang J, Ren A, Chen H, Zhao M, Shi L, Chen M, Wang H, Feng Z. Transcriptome Analysis and Its Application in Identifying Genes Associated with Fruiting Body Development in Basidiomycete Hypsizygus marmoreus PLoS One, 10(4), pp. e0123025. doi:10.1371/journal.pone.0123025 (2 April 2015)
Hedjazi L, Gauguier D, Zalloua PA, Nicholson JK, Dumas ME, Cazier JB. mQTL.NMR: An Integrated Suite for Genetic Mapping of Quantitative Variations of 1H NMR-Based Metabolic Profiles. Anal Chem. doi:10.1021/acs.analchem.5b00145 (2 April 2015)
Ollikainen M, Ismail K, Gervin K, Kyllönen A, Hakkarainen A, Lundbom J, Järvinen EA, Harris JR, Lundbom N, Rissanen A, Lyle R, Pietiläinen KH, Kaprio J. Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat Clin Epigenetics, 7(1), pp. 39. doi:10.1186/s13148-015-0073-5 (2 April 2015)
Serrano M, Gao J, Bota J, Bate AR, Meisner J, Eichenberger P, Moran CP Jr, Henriques AO. Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in Bacillus subtilis PLoS Genet, 11(4), pp. e1005104. doi:10.1371/journal.pgen.1005104 (2 April 2015)
Dobón A, Canet JV, García-Andrade J, Angulo C, Neumetzler L, Persson S, Vera P. Novel Disease Susceptibility Factors for Fungal Necrotrophic Pathogens in Arabidopsis PLoS Pathog, 11(4), pp. e1004800. doi:10.1371/journal.ppat.1004800 (1 April 2015)
Blanco I, Kuchenbaecker K, Cuadras D, Wang X, Barrowdale D, de Garibay GR, Librado P, Sánchez-Gracia A, Rozas J, Bonifaci N, McGuffog L, Pankratz VS, Islam A, Mateo F, Berenguer A, Petit A, Català I, Brunet J, Feliubadaló L, Tornero E, Benítez J, Osorio A, Cajal TR, Nevanlinna H, Aittomäki K, Arun BK, Toland AE, Karlan BY, Walsh C, Lester J, Greene MH, Mai PL, Nussbaum RL, Andrulis IL, Domchek SM, Nathanson KL, Rebbeck TR, Barkardottir RB, Jakubowska A, Lubinski J, Durda K, Jaworska-Bieniek K, Claes K, Van Maerken T, Díez O, Hansen TV, Jønson L, Gerdes AM, Ejlertsen B, de la Hoya M, Caldés T, Dunning AM, Oliver C, Fineberg E, Cook M, Peock S, McCann E, Murray A, Jacobs C, Pichert G, Lalloo F, Chu C, Dorkins H, Paterson J, Ong KR, Teixeira MR, Hogervorst FB, van der Hout AH, Seynaeve C, van der Luijt RB, Ligtenberg MJ, Devilee P, Wijnen JT, Rookus MA, Meijers-Heijboer HE, Blok MJ, van den Ouweland AM, Aalfs CM, Rodriguez GC, Phillips KA, Piedmonte M, Nerenstone SR, Bae-Jump VL, O'Malley DM, Ratner ES, Schmutzler RK, Wappenschmidt B, Rhiem K, Engel C, Meindl A, Ditsch N, Arnold N, Plendl HJ, Niederacher D, Sutter C, Wang-Gohrke S, Steinemann D, Preisler-Adams S, Kast K, Varon-Mateeva R, Gehrig A, Bojesen A, Pedersen IS, Sunde L, Jensen UB, Thomassen M, Kruse TA, Foretova L, Peterlongo P, Bernard L, Peissel B, Scuvera G, Manoukian S, Radice P, Ottini L, Montagna M, Agata S, Maugard C, Simard J, Soucy P, Berger A, Fink-Retter A, Singer CF, Rappaport C, Geschwantler-Kaulich D, Tea MK, Pfeiler G, John EM, Miron A, Neuhausen SL, Terry MB, Chung WK, Daly MB, Goldgar DE, Janavicius R, Dorfling CM, van Rensburg EJ, Fostira F, Konstantopoulou I, Garber J, Godwin AK, Olah E, Narod SA, Rennert G, Paluch SS, Laitman Y, Friedman E, Liljegren A, Rantala J, Stenmark-Askmalm M, Loman N, Imyanitov EN, Hamann U, Spurdle AB, Healey S, Weitzel JN, Herzog J, Margileth D, Gorrini C, Esteller M, Gómez A, Sayols S, Vidal E, Heyn H, Stoppa-Lyonnet D, Léoné M, Barjhoux L, Fassy-Colcombet M, de Pauw A, Lasset C, Ferrer SF, Castera L, Berthet P, Cornelis F, Bignon YJ, Damiola F, Mazoyer S, Sinilnikova OM, Maxwell CA, Vijai J, Robson M, Kauff N, Corines MJ, Villano D, Cunningham J, Lee A, Lindor N, Lázaro C, Easton DF, Offit K, Chenevix-Trench G, Couch FJ, Antoniou AC, Pujana MA. Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers PLoS One, 10(4), pp. e0120020. doi:10.1371/journal.pone.0120020 (1 April 2015)
Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, Krishna S, Rayner JC, Cox-Singh J. Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism PLoS One, 10(4), pp. e0121303. doi:10.1371/journal.pone.0121303 (1 April 2015)
Seo M, Yoon J, Park T. GRACOMICS: software for graphical comparison of multiple results with omics data BMC Genomics, 16(1), pp. 256. doi:10.1186/s12864-015-1461-0 (1 April 2015)
Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, ten Hoopen R, Ibrahim AE, Fuks F, Murrell A. 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer Genome Biol, 16(1), pp. 69. doi:10.1186/s13059-015-0605-5 (1 April 2015)
Sanhueza M, Chai A, Smith C, McCray BA, Simpson TI, Taylor JP, Pennetta G. Network Analyses Reveal Novel Aspects of ALS Pathogenesis PLoS Genet, 11(3), pp. e1005107. doi:10.1371/journal.pgen.1005107 (31 March 2015)
Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, Janga SC. Uncovering RNA binding proteins associated with age and gender during liver maturation Sci Rep, 5, pp. 9512. doi:10.1038/srep09512 (31 March 2015)
Artigaud S, Lacroix C, Richard J, Flye-Sainte-Marie J, Bargelloni L, Pichereau V. Proteomic responses to hypoxia at different temperatures in the great scallop (Pecten maximus) PeerJ, 3, pp. e871. doi:10.7717/peerj.871 (31 March 2015)
Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, Waldner MJ, Bindea G, Mlecnik B, Galon J, Trajanoski Z. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy Genome Biol, 16(1), pp. 64. doi:10.1186/s13059-015-0620-6 (31 March 2015)

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