Publications

Featured

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
Tippmann, S. (2015) Programming tools: Adventures with R. Nature 517: 109–110.
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 2015-03-05T06:50:08-08:00.

Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. miR-10b-5p expression in Huntington’s disease brain relates to age of onset and the extent of striatal involvement BMC Med Genomics, 8, pp. 10. doi:10.1186/s12920-015-0083-3 (1 March 2015)
Zmienko A, Samelak-Czajka A, Goralski M, Sobieszczuk-Nowicka E, Kozlowski P, Figlerowicz M. Selection of Reference Genes for qPCR- and ddPCR-Based Analyses of Gene Expression in Senescing Barley Leaves PLoS One, 10(2), pp. e0118226. doi:10.1371/journal.pone.0118226 (27 February 2015)
Simbulan RK, Di Santo M, Liu X, Lin W, Donjacour A, Maltepe E, Shenoy A, Borini A, Rinaudo P. Embryonic Stem Cells Derived from In Vivo or In Vitro-Generated Murine Blastocysts Display Similar Transcriptome and Differentiation Potential PLoS One, 10(2), pp. e0117422. doi:10.1371/journal.pone.0117422 (27 February 2015)
Pelle KG, Oh K, Buchholz K, Narasimhan V, Joice R, Milner DA, Brancucci NM, Ma S, Voss TS, Ketman K, Seydel KB, Taylor TE, Barteneva NS, Huttenhower C, Marti M. Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection Genome Med, 7(1), pp. 19. doi:10.1186/s13073-015-0133-7 (27 February 2015)
Iversen H, Lindbäck T, L’Abée-Lund TM, Roos N, Aspholm M, Stenfors Arnesen L. The Gut Bacterium Bacteroides thetaiotaomicron Influences the Virulence Potential of the Enterohemorrhagic Escherichia coli O103:H25 PLoS One, 10(2), pp. e0118140. doi:10.1371/journal.pone.0118140 (26 February 2015)
Chen J, Nolte V, Schlötterer C. Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster PLoS Genet, 11(2), pp. e1004883. doi:10.1371/journal.pgen.1004883 (26 February 2015)
Navarro SL, White E, Kantor ED, Zhang Y, Rho J, Song X, Milne GL, Lampe PD, Lampe JW. Randomized Trial of Glucosamine and Chondroitin Supplementation on Inflammation and Oxidative Stress Biomarkers and Plasma Proteomics Profiles in Healthy Humans PLoS One, 10(2), pp. e0117534. doi:10.1371/journal.pone.0117534 (26 February 2015)
Leal Valentim F, van Mourik S, Posé D, Kim MC, Schmid M, van Ham RC, Busscher M, Sanchez-Perez GF, Molenaar J, Angenent GC, Immink RG, van Dijk AD. A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network PLoS One, 10(2), pp. e0116973. doi:10.1371/journal.pone.0116973 (26 February 2015)
Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DG. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population Genome Biol, 16(1), pp. 23. doi:10.1186/s13059-015-0590-8 (25 February 2015)
Frey FP, Urbany C, Hüttel B, Reinhardt R, Stich B. Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress BMC Genomics, 16(1), pp. 123. doi:10.1186/s12864-015-1282-1 (25 February 2015)
von der Heyde S, Wagner S, Czerny A, Nietert M, Ludewig F, Salinas-Riester G, Arlt D, Beißbarth T. mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer PLoS One, 10(2), pp. e0117818. doi:10.1371/journal.pone.0117818 (24 February 2015)
Herrmann US, Sonati T, Falsig J, Reimann RR, Dametto P, O’Connor T, Li B, Lau A, Hornemann S, Sorce S, Wagner U, Sanoudou D, Aguzzi A. Prion Infections and Anti-PrP Antibodies Trigger Converging Neurotoxic Pathways PLoS Pathog, 11(2), pp. e1004662. doi:10.1371/journal.ppat.1004662 (24 February 2015)
Postnikova OA, Hult M, Shao J, Skantar A, Nemchinov LG. Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root-Knot Nematode Meloidogyne incognita PLoS One, 10(2), pp. e0118269. doi:10.1371/journal.pone.0118269 (24 February 2015)
Panse C, Trachsel C, Grossmann J, Schlapbach R. specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics. doi:10.1093/bioinformatics/btv105 (23 February 2015)
Nakayama J, Watanabe K, Jiang J, Matsuda K, Chao SH, Haryono P, La-ongkham O, Sarwoko MA, Sujaya IN, Zhao L, Chen KT, Chen YP, Chiu HH, Hidaka T, Huang NX, Kiyohara C, Kurakawa T, Sakamoto N, Sonomoto K, Tashiro K, Tsuji H, Chen MJ, Leelavatcharamas V, Liao CC, Nitisinprasert S, Rahayu ES, Ren FZ, Tsai YC, Lee YK. Diversity in gut bacterial community of school-age children in Asia Sci Rep, 5, pp. 8397. doi:10.1038/srep08397 (23 February 2015)
Rossmann FS, Racek T, Wobser D, Puchalka J, Rabener EM, Reiger M, Hendrickx AP, Diederich AK, Jung K, Klein C, Huebner J. Phage-mediated Dispersal of Biofilm and Distribution of Bacterial Virulence Genes Is Induced by Quorum Sensing PLoS Pathog, 11(2), pp. e1004653. doi:10.1371/journal.ppat.1004653 (23 February 2015)
Zhou J, Cheng Y, Yin M, Yang E, Gong W, Liu C, Zheng X, Deng K, Ren Z, Zhang Y. Identification of Novel miRNAs and miRNA Expression Profiling in Wheat Hybrid Necrosis PLoS One, 10(2), pp. e0117507. doi:10.1371/journal.pone.0117507 (23 February 2015)
Amorim CE, Acuña-Alonzo V, Salzano FM, Bortolini MC, Hünemeier T. Differing Evolutionary Histories of the ACTN3*R577X Polymorphism among the Major Human Geographic Groups PLoS One, 10(2), pp. e0115449. doi:10.1371/journal.pone.0115449 (23 February 2015)
Lau C, Nygård S, Fure H, Olstad OK, Holden M, Lappegård KT, Brekke OL, Espevik T, Hovig E, Mollnes TE. CD14 and Complement Crosstalk and Largely Mediate the Transcriptional Response to Escherichia coli in Human Whole Blood as Revealed by DNA Microarray PLoS One, 10(2), pp. e0117261. doi:10.1371/journal.pone.0117261 (23 February 2015)
Lin IH, Chen DT, Chang YF, Lee YL, Su CH, Cheng C, Tsai YC, Ng SC, Chen HT, Lee MC, Chen HW, Suen SH, Chen YC, Liu TT, Chang CH, Hsu MT. Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes PLoS One, 10(2), pp. e0118453. doi:10.1371/journal.pone.0118453 (23 February 2015)

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