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 2015-03-27T10:40:11-07:00.

Gavai AK, Supandi F, Hettling H, Murrell P, Leunissen JA, van Beek JH. Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain. PLoS One, 10(3), pp. e0119016. doi:10.1371/journal.pone.0119016 (25 March 2015)
Hedjazi L, Gauguier D, Zalloua P, 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 (24 March 2015)
Matos I, Machado MP, Schartl M, Coelho MM. Gene Expression Dosage Regulation in an Allopolyploid Fish PLoS One, 10(3), pp. e0116309. doi:10.1371/journal.pone.0116309 (19 March 2015)
Bae SH, Han HW, Moon J. Functional Analysis of the Molecular Interactions of TATA Box-Containing Genes and Essential Genes PLoS One, 10(3), pp. e0120848. doi:10.1371/journal.pone.0120848 (19 March 2015)
Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M. Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53 PLoS Genet, 11(3), pp. e1005053. doi:10.1371/journal.pgen.1005053 (19 March 2015)
Yang Z, Peng Z, Wei S, Liao M, Yu Y, Jang Z. Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.) BMC Genomics, 16(1), pp. 211. doi:10.1186/s12864-015-1453-0 (19 March 2015)
Wang L, Yang L, Peng Z, Lu D, Jin Y, McNutt M, Yin Y. cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. BMC Syst Biol, 9(1), pp. 1416. doi:10.1186/1752-0509-9-S1-S1 (18 March 2015)
Fortney K, Griesman J, Kotlyar M, Pastrello C, Angeli M, Sound-Tsao M, Jurisica I. Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data PLoS Comput Biol, 11(3), pp. e1004068. doi:10.1371/journal.pcbi.1004068 (18 March 2015)
Edwards-Jones B, Aw R, Barton GR, Tredwell GD, Bundy JG, Leak DJ. Translational Arrest Due to Cytoplasmic Redox Stress Delays Adaptation to Growth on Methanol and Heterologous Protein Expression in a Typical Fed-Batch Culture of Pichia pastoris PLoS One, 10(3), pp. e0119637. doi:10.1371/journal.pone.0119637 (18 March 2015)
Mi G, Di Y, Schafer DW. Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data PLoS One, 10(3), pp. e0119254. doi:10.1371/journal.pone.0119254 (18 March 2015)
Debowski K, Warthemann R, Lentes J, Salinas-Riester G, Dressel R, Langenstroth D, Gromoll J, Sasaki E, Behr R. Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach PLoS One, 10(3), pp. e0118424. doi:10.1371/journal.pone.0118424 (18 March 2015)
Dong Y, Dai F, Ren Y, Liu H, Chen L, Yang P, Liu Y, Li X, Wang W, Xiang H. Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration BMC Genomics, 16(1), pp. 203. doi:10.1186/s12864-015-1420-9 (17 March 2015)
Avramopoulos D, Pearce BD, McGrath J, Wolyniec P, Wang R, Eckart N, Hatzimanolis A, Goes FS, Nestadt G, Mulle J, Coneely K, Hopkins M, Ruczinski I, Yolken R, Pulver AE. Infection and Inflammation in Schizophrenia and Bipolar Disorder: A Genome Wide Study for Interactions with Genetic Variation PLoS One, 10(3), pp. e0116696. doi:10.1371/journal.pone.0116696 (17 March 2015)
Li Z, Wang J, Zhang X, Xu L. Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant PLoS One, 10(3), pp. e0119027. doi:10.1371/journal.pone.0119027 (17 March 2015)
Lamikanra AA, Merryweather-Clarke AT, Tipping AJ, Roberts DJ. Distinct Mechanisms of Inadequate Erythropoiesis Induced by Tumor Necrosis Factor Alpha or Malarial Pigment PLoS One, 10(3), pp. e0119836. doi:10.1371/journal.pone.0119836 (17 March 2015)
Smith SD, Kawash JK, Grigoriev A. GROM-RD: resolving genomic biases to improve read depth detection of copy number variants PeerJ, 3, pp. e836. doi:10.7717/peerj.836 (17 March 2015)
Alanazi I, Hoffmann P, Adelson DL. MicroRNAs Are Part of the Regulatory Network that Controls EGF Induced Apoptosis, Including Elements of the JAK/STAT Pathway, in A431 Cells PLoS One, 10(3), pp. e0120337. doi:10.1371/journal.pone.0120337 (17 March 2015)
Tedder A, Helling M, Pannell JR, Shimizu-Inatsugi R, Kawagoe T, van Campen J, Sese J, Shimizu KK. Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae) Ann Bot, 115(5), pp. 763-776. doi:10.1093/aob/mcv006 (16 March 2015)
Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I. A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts. Birth Defects Res A Clin Mol Teratol. doi:10.1002/bdra.23362 (16 March 2015)
Fesenko IA, Arapidi GP, Skripnikov AY, Alexeev DG, Kostryukova ES, Manolov AI, Altukhov IA, Khazigaleeva RA, Seredina AV, Kovalchuk SI, Ziganshin RH, Zgoda VG, Novikova SE, Semashko TA, Slizhikova DK, Ptushenko VV, Gorbachev AY, Govorun VM, Ivanov VT. Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens BMC Plant Biol, 15, pp. 87. doi:10.1186/s12870-015-0468-7 (15 March 2015)

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