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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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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Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
TL;DR: A high rate of multinucleotide mutation events at both short and long genomic distances is shown, showing that mutation drives GC content lower in already GC-poor regions, and using the precise context-dependent mutation rates to predict long-term evolutionary patterns at synonymous sites.
Journal ArticleDOI
Unraveling negative biotic interactions determining soil microbial community assembly and functioning.
Sana Romdhane,Aymé Spor,Julie Aubert,David Bru,Marie-Christine Breuil,Sara Hallin,Arnaud Mounier,Sarah Ouadah,Myrto Tsiknia,Laurent Philippot +9 more
TL;DR: In this paper, a top-down manipulation approach based on the removal of various populations in a natural soil microbial community was used to address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota.
Journal ArticleDOI
Genome-wide transcriptome analysis of Aspergillus fumigatus exposed to osmotic stress reveals regulators of osmotic and cell wall stresses that are SakAHOG1 and MpkC dependent
Leila Pereira Silva,Patrícia Alves de Castro,Thaila Fernanda dos Reis,Mario Henrique Paziani,Marcia Regina von Zeska Kress,Diego Mauricio Riaño-Pachón,Daisuke Hagiwara,Laure Nicolas Annick Ries,Neil Andrew Brown,Gustavo H. Goldman +9 more
TL;DR: The results strongly indicate that MpkC and SakA have independent and collaborative functions during the transcriptional response to transient osmotic stress, which is a prerequisite for the survival and virulence strategies of the pathogen.
Journal ArticleDOI
Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling
Fang-Ke Huang,Guoan Zhang,Kevin Lawlor,Arpi Nazarian,John Philip,Paul Tempst,Noah Dephoure,Thomas A. Neubert +7 more
TL;DR: The data show that MS2-based quantitation using TMT can be successfully used for large-scale multiplexed quantitative proteomics, and demonstrates the ratios calculated using an MS2 method are highly correlated with ratios obtained using MS3- based quantitation with reduced ratio suppression.
Journal ArticleDOI
Exosomes for Wound Healing: Purification Optimization and Identification of Bioactive Components
TL;DR: The extent of the bioactivity of these exosomal components is found to be dependent on the target cell type, and this work specifically assesses the involvement of lipids and the transmembrane enzyme CD73 in the exosomes’ biological activity in stimulating the cutaneous wound healing process.
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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Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
Bioconductor: open software development for computational biology and bioinformatics
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
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