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 2015-04-26T15:40:08-07:00.

Cai Y, Dai X, Zhang Q, Dai Z. Gene expression of OCT4, SOX2, KLF4 and MYC (OSKM) induced pluripotent stem cells: identification for potential mechanisms. Diagn Pathol, 10(1), pp. 35. doi:10.1186/s13000-015-0263-7 (24 April 2015)
Forster L, McCooke J, Bellgard M, Joske D, Finlayson J, Ghassemifar R. Differential gene expression analysis in early and late erythroid progenitor cells in β-thalassaemia. Br J Haematol. doi:10.1111/bjh.13432 (19 April 2015)
Keermann M, Kõks S, Reimann E, Prans E, Abram K, Kingo K. Transcriptional landscape of psoriasis identifies the involvement of IL36 and IL36RN BMC Genomics, 16(1), pp. 322. doi:10.1186/s12864-015-1508-2 (19 April 2015)
Yang Y, Zhou QJ, Chen XQ, Yan BL, Guo XL, Zhang HL, Du AF. Profiling of differentially expressed genes in sheep T lymphocytes response to an artificial primary Haemonchus contortus infection Parasit Vectors, 8, pp. 235. doi:10.1186/s13071-015-0844-z (18 April 2015)
Mitra A, Luo J, He Y, Gu Y, Zhang H, Zhao K, Cui K, Song J. Histone modifications induced by MDV infection at early cytolytic and latency phases BMC Genomics, 16(1), pp. 311. doi:10.1186/s12864-015-1492-6 (18 April 2015)
Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML. Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts PLoS Comput Biol, 11(4), pp. e1004130. doi:10.1371/journal.pcbi.1004130 (17 April 2015)
Kemper KE, Reich CM, Bowman PJ, vander Jagt CJ, Chamberlain AJ, Mason BA, Hayes BJ, Goddard ME. Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions Genet Sel Evol, 47(1), pp. 29. doi:10.1186/s12711-014-0074-4 (17 April 2015)
Hou J, Wang F, Kong P, Yu PK, Wang H, Han W. Gene Profiling Characteristics of Radioadaptive Response in AG01522 Normal Human Fibroblasts PLoS One, 10(4), pp. e0123316. doi:10.1371/journal.pone.0123316 (17 April 2015)
Reinhold AK, Batti L, Bilbao D, Buness A, Rittner HL, Heppenstall PA. Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain PLoS One, 10(4), pp. e0123342. doi:10.1371/journal.pone.0123342 (16 April 2015)
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)
Yan L, Lai X, Li X, Wei C, Tan X, Zhang Y. Analyses of the Complete Genome and Gene Expression of Chloroplast of Sweet Potato [Ipomoea batata] PLoS One, 10(4), pp. e0124083. doi:10.1371/journal.pone.0124083 (15 April 2015)
Qin J, Wang X, Wang L, Zhu B, Zhang X, Yao Q, Xu P. Comparative Transcriptome Analysis Reveals Different Molecular Mechanisms of Bacillus coagulans 2-6 Response to Sodium Lactate and Calcium Lactate during Lactic Acid Production PLoS One, 10(4), pp. e0124316. doi:10.1371/journal.pone.0124316 (15 April 2015)
Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling PLoS Genet, 11(4), pp. e1004953. doi:10.1371/journal.pgen.1004953 (15 April 2015)
Świątek-Połatyńska MA, Bucca G, Laing E, Gubbens J, Titgemeyer F, Smith CP, Rigali S, van Wezel GP. Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets PLoS One, 10(4), pp. e0122479. doi:10.1371/journal.pone.0122479 (15 April 2015)
Xu C, Zeng B, Huang J, Huang W, Liu Y. Genome-Wide Transcriptome and Expression Profile Analysis of Phalaenopsis during Explant Browning PLoS One, 10(4), pp. e0123356. doi:10.1371/journal.pone.0123356 (14 April 2015)
Çalışkan M, Baker SW, Gilad Y, Ober C. Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection PLoS Genet, 11(4), pp. e1005111. doi:10.1371/journal.pgen.1005111 (13 April 2015)
Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P. Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses PLoS One, 10(4), pp. e0124360. doi:10.1371/journal.pone.0124360 (13 April 2015)
Sangket U, Vijasika S, Noh H, Chantratita W, Klungthong C, Yoon IK, Fernandez S, Rutvisuttinunt W. SNPer: An R Library for Quantitative Variant Analysis on Single Nucleotide Polymorphisms among Influenza Virus Populations PLoS One, 10(4), pp. e0122812. doi:10.1371/journal.pone.0122812 (13 April 2015)
Zanette DL, Lorenzi JC, Panepucci RA, Palma PV, dos Santos DF, Prata KL, Silva WA Jr. Simvastatin Modulates Mesenchymal Stromal Cell Proliferation and Gene Expression PLoS One, 10(4), pp. e0120137. doi:10.1371/journal.pone.0120137 (13 April 2015)
Laurent A, Calabrese M, Warnatz HJ, Yaspo ML, Tkachuk V, Torres M, Blasi F, Penkov D. ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells PLoS One, 10(4), pp. e0122518. doi:10.1371/journal.pone.0122518 (13 April 2015)

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