Literature DB >> 17903289

Graphs in molecular biology.

Wolfgang Huber1, Vincent J Carey, Li Long, Seth Falcon, Robert Gentleman.   

Abstract

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network.

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Year:  2007        PMID： 17903289      PMCID： PMC1995545          DOI： 10.1186/1471-2105-8-S6-S8

Source DB:  PubMed          Journal:  BMC Bioinformatics        ISSN： 1471-2105            Impact factor:   3.169


  11 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Pathways database system: an integrated system for biological pathways.

Authors:  L Krishnamurthy; J Nadeau; G Ozsoyoglu; M Ozsoyoglu; G Schaeffer; M Tasan; W Xu
Journal:  Bioinformatics       Date:  2003-05-22       Impact factor: 6.937

3.  Minimal cut sets in biochemical reaction networks.

Authors:  Steffen Klamt; Ernst Dieter Gilles
Journal:  Bioinformatics       Date:  2004-01-22       Impact factor: 6.937

4.  A graph-theoretic approach to testing associations between disparate sources of functional genomics data.

Authors:  Raji Balasubramanian; Thomas LaFramboise; Denise Scholtens; Robert Gentleman
Journal:  Bioinformatics       Date:  2004-07-15       Impact factor: 6.937

5.  The MeSH translation maintenance system: structure, interface design, and implementation.

Authors:  Stuart J Nelson; Michael Schopen; Allan G Savage; Jacque-Lynne Schulman; Natalie Arluk
Journal:  Stud Health Technol Inform       Date:  2004

6.  Making sense of high-throughput protein-protein interaction data.

Authors:  Denise Scholtens; Robert Gentleman
Journal:  Stat Appl Genet Mol Biol       Date:  2005-01-03

7.  Vertex similarity in networks.

Authors:  E A Leicht; Petter Holme; M E J Newman
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-02-17

8.  Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.

Authors:  H Ge; Z Liu; G M Church; M Vidal
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

9.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

10.  Reactome: a knowledgebase of biological pathways.

Authors:  G Joshi-Tope; M Gillespie; I Vastrik; P D'Eustachio; E Schmidt; B de Bono; B Jassal; G R Gopinath; G R Wu; L Matthews; S Lewis; E Birney; L Stein
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971
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  41 in total

1.  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

2.  A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection.

Authors:  Michelle Carey; Juan Camilo Ramírez; Shuang Wu; Hulin Wu
Journal:  Stat Methods Med Res       Date:  2018-07       Impact factor: 3.021

3.  A quick guide to large-scale genomic data mining.

Authors:  Curtis Huttenhower; Oliver Hofmann
Journal:  PLoS Comput Biol       Date:  2010-05-27       Impact factor: 4.475

4.  Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model.

Authors:  Feng Chen; Hai-Hong Zhu; Lin-Fu Zhou; Jie Li; Li-Ying Zhao; Shan-Shan Wu; Jing Wang; Wei Liu; Zhi Chen
Journal:  BMC Genomics       Date:  2010-04-15       Impact factor: 3.969

5.  Finding sRNA generative locales from high-throughput sequencing data with NiBLS.

Authors:  Daniel MacLean; Vincent Moulton; David J Studholme
Journal:  BMC Bioinformatics       Date:  2010-02-18       Impact factor: 3.169

6.  Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern.

Authors:  Binhua Tang; Xuechen Wu; Ge Tan; Su-Shing Chen; Qing Jing; Bairong Shen
Journal:  BMC Syst Biol       Date:  2010-09-13

7.  Novel topological descriptors for analyzing biological networks.

Authors:  Matthias M Dehmer; Nicola N Barbarini; Kurt K Varmuza; Armin A Graber
Journal:  BMC Struct Biol       Date:  2010-06-17

8.  SubpathwayMiner: a software package for flexible identification of pathways.

Authors:  Chunquan Li; Xia Li; Yingbo Miao; Qianghu Wang; Wei Jiang; Chun Xu; Jing Li; Junwei Han; Fan Zhang; Binsheng Gong; Liangde Xu
Journal:  Nucleic Acids Res       Date:  2009-08-25       Impact factor: 16.971

9.  Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases.

Authors:  Elsa Chacko; Shoba Ranganathan
Journal:  BMC Genomics       Date:  2009-12-03       Impact factor: 3.969

10.  Computing paths and cycles in biological interaction graphs.

Authors:  Steffen Klamt; Axel von Kamp
Journal:  BMC Bioinformatics       Date:  2009-06-15       Impact factor: 3.169
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