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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HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor
Lucas Schiffer,Rimsha Azhar,Lori Shepherd,Marcel Ramos,Marcel Ramos,Ludwig Geistlinger,Curtis Huttenhower,Curtis Huttenhower,Jennifer Beam Dowd,Jennifer Beam Dowd,Nicola Segata,Levi Waldron +11 more
TL;DR: The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects.
Journal ArticleDOI
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.
Fedor A. Kolpakov,Ilya R. Akberdin,Timur A. Kashapov,llya Kiselev,Semyon K. Kolmykov,Yury V. Kondrakhin,Elena Kutumova,Nikita Mandrik,S. S. Pintus,Anna S. Ryabova,Ruslan N. Sharipov,Ivan S. Yevshin,Alexander E. Kel +12 more
TL;DR: This work has developed several predefined perspectives that display only those web interface elements that are needed for a specific task, to facilitate a user focus on a particular task or database.
Journal ArticleDOI
Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes
Yoshihiro Hayashi,Yue Zhang,Asumi Yokota,Xiaomei Yan,Jinqin Liu,Kwangmin Choi,Bing Li,Goro Sashida,Yanyan Peng,Zefeng Xu,Rui Huang,Lulu Zhang,George M. Freudiger,Jingya Wang,Yunzhu Dong,Yile Zhou,Jieyu Wang,Lingyun Wu,Lingyun Wu,Jiachen Bu,Jiachen Bu,Aili Chen,Xinghui Zhao,Xiujuan Sun,Kashish Chetal,Andre Olsson,Miki Watanabe,Lindsey E. Romick-Rosendale,Hironori Harada,Lee Yung Shih,William Tse,James P. Bridges,Michael A. Caligiuri,Taosheng Huang,Yi Zheng,David P. Witte,Qianfei Wang,Cheng-Kui Qu,Nathan Salomonis,H. Leighton Grimes,Stephen D. Nimer,Zhijian Xiao,Gang Huang,Gang Huang +43 more
TL;DR: It is shown that dysregulation of HIF1A signaling could generate the clinically relevant diversity of MDS phenotypes by functioning as a signaling funnel for MDS driver mutations, which could resolve the disconnection between genotypes and phenotypes and provide a new clue as to how a variety of driver mutations cause common M DS phenotypes.
Journal ArticleDOI
Transcriptomic profiling and genetic analyses reveal novel key regulators of cellulase and xylanase gene expression in Penicillium oxalicum
Yu-Si Yan,Shuai Zhao,Lu-Sheng Liao,Qi-Peng He,Ya-Ru Xiong,Long Wang,Cheng-Xi Li,Jia-Xun Feng +7 more
TL;DR: Three key new regulatory genes are detected and identified that directly and indirectly regulate the expression of cellulase and xylanase genes in P. oxalicum, but the mode of regulation changes dynamically during the growth of fungal cells in the presence of cellulose.
Journal ArticleDOI
Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25.
TL;DR: The results of this study increase knowledge and understanding of the regulatory effects imposed by ethanol on cellulose biosynthesis, providing new opportunities for directed strain improvement, scaled-up bionanocellulose production, and wider industrial exploitation of the Komagataeibacter species as bacterial cellulose producers.
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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Bioconductor: open software development for computational biology and bioinformatics
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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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