Literature DB >> 16939789

Bioconductor: an open source framework for bioinformatics and computational biology.

Mark Reimers1, Vincent J Carey.   

Abstract

This chapter describes the Bioconductor project and details of its open source facilities for analysis of microarray and other high-throughput biological experiments. Particular attention is paid to concepts of container and workflow design, connections of biological metadata to statistical analysis products, support for statistical quality assessment, and calibration of inference uncertainty measures when tens of thousands of simultaneous statistical tests are performed.

Mesh：

Year:  2006        PMID： 16939789     DOI： 10.1016/S0076-6879(06)11008-3

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN： 0076-6879            Impact factor:   1.600


  107 in total

1.  The role of the E2F1 transcription factor in the innate immune response to systemic LPS.

Authors:  Laura A Warg; Judy L Oakes; Rachel Burton; Amanda J Neidermyer; Holly R Rutledge; Steve Groshong; David A Schwartz; Ivana V Yang
Journal:  Am J Physiol Lung Cell Mol Physiol       Date:  2012-06-15       Impact factor: 5.464

2.  Simplifying complexity.

Authors:  Nicole Cloonan; Sean M Grimmond
Journal:  Nat Methods       Date:  2010-09-29       Impact factor: 28.547

Review 3.  Toward a complete in silico, multi-layered embryonic stem cell regulatory network.

Authors:  Huilei Xu; Christoph Schaniel; Ihor R Lemischka; Avi Ma'ayan
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

4.  Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression.

Authors:  Xuezheng Sun; Patricia Casbas-Hernandez; Carol Bigelow; Liza Makowski; D Joseph Jerry; Sallie Smith Schneider; Melissa A Troester
Journal:  Breast Cancer Res Treat       Date:  2011-10-15       Impact factor: 4.872

Review 5.  Using genomics to understand intestinal biology.

Authors:  J C Fleet
Journal:  J Physiol Biochem       Date:  2007-03       Impact factor: 4.158

6.  Identification of commonly dysregulated genes in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation.

Authors:  W H Xiao; X L Qu; X M Li; Y L Sun; H X Zhao; S Wang; X Zhou
Journal:  Cancer Gene Ther       Date:  2015-04-24       Impact factor: 5.987

7.  Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers.

Authors:  Xinan Yang; Younghee Lee; Hong Fan; Xiao Sun; Yves A Lussier
Journal:  Chin Sci Bull       Date:  2010-11

8.  Circadian oscillation of gibberellin signaling in Arabidopsis.

Authors:  María Verónica Arana; Nora Marín-de la Rosa; Julin N Maloof; Miguel A Blázquez; David Alabadí
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-16       Impact factor: 11.205

9.  Temporal transcriptional response during infection of type II alveolar epithelial cells with Francisella tularensis live vaccine strain (LVS) supports a general host suppression and bacterial uptake by macropinocytosis.

Authors:  Christopher E Bradburne; Anne B Verhoeven; Ganiraju C Manyam; Saira A Chaudhry; Eddie L Chang; Dzung C Thach; Charles L Bailey; Monique L van Hoek
Journal:  J Biol Chem       Date:  2013-01-15       Impact factor: 5.157

10.  RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica serovar Typhimurium.

Authors:  Andrew M Bailey; Al Ivens; Rob Kingsley; Jennifer L Cottell; John Wain; Laura J V Piddock
Journal:  J Bacteriol       Date:  2010-01-15       Impact factor: 3.490
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