Literature DB >> 15297301

Network structures and algorithms in Bioconductor.

Vincent J Carey1, Jeff Gentry, Elizabeth Whalen, Robert Gentleman.   

Abstract

UNLABELLED: In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology. AVAILABILITY: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org).

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Year:  2004        PMID： 15297301     DOI： 10.1093/bioinformatics/bth458

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  30 in total

1.  Dynamics of global transcriptome in bovine matured oocytes and preimplantation embryos.

Authors:  M Misirlioglu; G P Page; H Sagirkaya; A Kaya; J J Parrish; N L First; E Memili
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-01       Impact factor: 11.205

2.  A graphical approach to tracking and reporting target status in structural genomics.

Authors:  Xiaokang Pan; Gary E Wesenberg; John L Markley; Brian G Fox; George N Phillips; Craig A Bingman
Journal:  J Struct Funct Genomics       Date:  2008-01-31

3.  Identification of genetically mediated cortical networks: a multivariate study of pediatric twins and siblings.

Authors:  J E Schmitt; R K Lenroot; G L Wallace; S Ordaz; K N Taylor; N Kabani; D Greenstein; J P Lerch; K S Kendler; M C Neale; J N Giedd
Journal:  Cereb Cortex       Date:  2008-01-29       Impact factor: 5.357

4.  A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.

Authors:  Tony Chiang; Denise Scholtens
Journal:  Nat Protoc       Date:  2009-03-26       Impact factor: 13.491

5.  Using scale and feather traits for module construction provides a functional approach to chicken epidermal development.

Authors:  Weier Bao; Matthew J Greenwold; Roger H Sawyer
Journal:  Funct Integr Genomics       Date:  2017-05-05       Impact factor: 3.410

6.  minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information.

Authors:  Patrick E Meyer; Frédéric Lafitte; Gianluca Bontempi
Journal:  BMC Bioinformatics       Date:  2008-10-29       Impact factor: 3.169

7.  Advanced data-mining strategies for the analysis of direct-infusion ion trap mass spectrometry data from the association of perennial ryegrass with its endophytic fungus, Neotyphodium lolii.

Authors:  Mingshu Cao; Albert Koulman; Linda J Johnson; Geoffrey A Lane; Susanne Rasmussen
Journal:  Plant Physiol       Date:  2008-02-20       Impact factor: 8.340

8.  Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis.

Authors:  Henning Redestig; Miyako Kusano; Atsushi Fukushima; Fumio Matsuda; Kazuki Saito; Masanori Arita
Journal:  BMC Bioinformatics       Date:  2010-04-29       Impact factor: 3.169

9.  Multimodality vaccination against clade C SHIV: partial protection against mucosal challenges with a heterologous tier 2 virus.

Authors:  Samir K Lakhashe; Siddappa N Byrareddy; Mingkui Zhou; Barbara C Bachler; Girish Hemashettar; Shiu-Lok Hu; Francois Villinger; James G Else; Shannon Stock; Sandra J Lee; Diego A Vargas-Inchaustegui; Egidio Brocca Cofano; Marjorie Robert-Guroff; Welkin E Johnson; Victoria R Polonis; Donald N Forthal; Erwann P Loret; Robert A Rasmussen; Ruth M Ruprecht
Journal:  Vaccine       Date:  2014-09-20       Impact factor: 3.641

10.  Identifying functional modules in protein-protein interaction networks: an integrated exact approach.

Authors:  Marcus T Dittrich; Gunnar W Klau; Andreas Rosenwald; Thomas Dandekar; Tobias Müller
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937
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