Orchestrating high-throughput genomic analysis with Bioconductor
Wolfgang Huber,Vincent J. Carey,Robert Gentleman,Simon Anders,Marc R. J. Carlson,Benilton S. Carvalho,Héctor Corrada Bravo,Sean Davis,Laurent Gatto,Thomas Girke,Raphael Gottardo,Florian Hahne,Kasper D. Hansen,Rafael A. Irizarry,Michael S. Lawrence,Michael I. Love,James W. MacDonald,Valerie Obenchain,Andrzej K. Oleś,Hervé Pagès,Alejandro Reyes,Paul Shannon,Gordon K. Smyth,Dan Tenenbaum,Levi Waldron,Martin Morgan +25 more
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TLDR
An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.Abstract:
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.read more
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Differential Susceptibility to T Cell-Induced Colitis in Mice: Role of the Intestinal Microbiota.
Cynthia Reinoso Webb,Hendrik den Bakker,Iurii Koboziev,Yava L. Jones-Hall,Kameswara Rao Kottapalli,Dmitry V. Ostanin,Kathryn L. Furr,Qinghui Mu,Xin M. Luo,Matthew B. Grisham +9 more
TL;DR: The data demonstrate that specific microbial communities determine disease susceptibility and that manipulation of the intestinal microbiota alters the induction and/or perpetuation of chronic colitis.
Journal ArticleDOI
3-D nasal cultures: Systems toxicological assessment of a candidate modified-risk tobacco product.
Anita R. Iskandar,Carole Mathis,Florian Martin,Patrice Leroy,Alain Sewer,Shoaib Majeed,Diana Kuehn,Keyur Trivedi,Davide Grandolfo,Maciej Cabanski,Emmanuel Guedj,Celine Merg,Stefan Frentzel,Nikolai V. Ivanov,Manuel C. Peitsch,Julia Hoeng +15 more
TL;DR: For all tested concentrations the impact of 3R4F smoke was substantially greater than that of THS2.2 aerosol in terms of cytotoxicity levels, alterations in tissue morphology, secretion of pro-inflammatory mediators, impaired ciliary function, and increased perturbed transcriptomes and miRNA expression profiles.
Journal ArticleDOI
Overexpression of Rice Expansin7 (Osexpa7) Confers Enhanced Tolerance to Salt Stress in Rice.
TL;DR: The results suggest that OsEXPA7 plays an important role in increasing salt stress tolerance by coordinating sodium transport, ROS scavenging, and cell-wall loosening.
Posted ContentDOI
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
TL;DR: Rsubread is faster, uses less memory and produces read count summaries that more accurately correlate with true values, and the results show that users can adopt the R environment for alignment and quantification without suffering any loss of performance.
Journal ArticleDOI
Enabling precision medicine by unravelling disease pathophysiology: quantifying signal transduction pathway activity across cell and tissue types.
TL;DR: A method enabling quantitative measurement of functional pathway activity based on Bayesian computational model inference of pathway activity from measurements of mRNA levels of target genes of the pathway-associated transcription factor is developed.
References
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Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Benjamin M. Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,Kurt Hornik,Torsten Hothorn,Wolfgang Huber,Stefano Maria Iacus,Rafael A. Irizarry,Friedrich Leisch,Cheng Li,Martin Maechler,A. J. Rossini,Günther Sawitzki,Colin A. Smith,Gordon K. Smyth,Luke Tierney,Jean Yang,Jianhua Zhang +24 more
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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
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