Literature DB >> 20650822

A survey of current software for network analysis in molecular biology.

Sterling Thomas1, Danail Bonchev.   

Abstract

Software for network motifs and modules is briefly reviewed, along with programs for network comparison. The three major software packages for network analysis, CYTOSCAPE, INGENUITY and PATHWAY STUDIO, and their associated databases, are compared in detail. A comparative test evaluated how these software packages perform the search for key terms and the creation of network from those terms and from experimental expression data.

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Year:  2010        PMID： 20650822      PMCID： PMC3500165          DOI： 10.1186/1479-7364-4-5-353

Source DB:  PubMed          Journal:  Hum Genomics        ISSN： 1473-9542            Impact factor:   4.639


  19 in total

1.  Network motifs in the transcriptional regulation network of Escherichia coli.

Authors:  Shai S Shen-Orr; Ron Milo; Shmoolik Mangan; Uri Alon
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

Review 2.  Computational systems biology.

Authors:  Hiroaki Kitano
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

3.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

Review 4.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

5.  Modular organization of cellular networks.

Authors:  Alexander W Rives; Timothy Galitski
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-21       Impact factor: 11.205

6.  Hierarchical organization of modularity in metabolic networks.

Authors:  E Ravasz; A L Somera; D A Mongru; Z N Oltvai; A L Barabási
Journal:  Science       Date:  2002-08-30       Impact factor: 47.728

Review 7.  Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

Authors:  Jason A Papin; Jennifer L Reed; Bernhard O Palsson
Journal:  Trends Biochem Sci       Date:  2004-12       Impact factor: 13.807

8.  Functional cartography of complex metabolic networks.

Authors:  Roger Guimerà; Luís A Nunes Amaral
Journal:  Nature       Date:  2005-02-24       Impact factor: 49.962

9.  Finding community structure in networks using the eigenvectors of matrices.

Authors:  M E J Newman
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-09-11

10.  Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks.

Authors:  Mathieu Clément-Ziza; Christophe Malabat; Christian Weber; Ivan Moszer; Tero Aittokallio; Catherine Letondal; Sandrine Rousseau
Journal:  Bioinformatics       Date:  2009-08-03       Impact factor: 6.937
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  91 in total

Review 1.  Computational tools for prioritizing candidate genes: boosting disease gene discovery.

Authors:  Yves Moreau; Léon-Charles Tranchevent
Journal:  Nat Rev Genet       Date:  2012-07-03       Impact factor: 53.242

Review 2.  Genome-Wide Approaches to Defining Macrophage Identity and Function.

Authors:  Gregory J Fonseca; Jason S Seidman; Christopher K Glass
Journal:  Microbiol Spectr       Date:  2016-10

3.  Glucocorticoid receptor ChIP-sequencing of subcutaneous fat reveals modulation of inflammatory pathways.

Authors:  Puneet Singh; Clifton O Brock; Paul A Volden; Kyle Hernandez; Maxwell Skor; Masha Kocherginsky; Julie E Park; Matthew J Brady; Suzanne D Conzen
Journal:  Obesity (Silver Spring)       Date:  2015-09-26       Impact factor: 5.002

4.  SILAC-Based Quantitative Proteomic Analysis Unveils Arsenite-Induced Perturbation of Multiple Pathways in Human Skin Fibroblast Cells.

Authors:  Fan Zhang; Yongsheng Xiao; Yinsheng Wang
Journal:  Chem Res Toxicol       Date:  2017-02-14       Impact factor: 3.739

5.  A Network Approach to Wound Healing.

Authors:  Tomasz Arodz; Danail Bonchev; Robert F Diegelmann
Journal:  Adv Wound Care (New Rochelle)       Date:  2013-11       Impact factor: 4.730

6.  Transcriptional Pathways Altered in Response to Vibration in a Model of Hand-Arm Vibration Syndrome.

Authors:  Stacey Waugh; Michael L Kashon; Shengqiao Li; Gerome R Miller; Claud Johnson; Kristine Krajnak
Journal:  J Occup Environ Med       Date:  2016-04       Impact factor: 2.162

7.  Transgenerational transmission and modification of pathological traits induced by prenatal immune activation.

Authors:  U Weber-Stadlbauer; J Richetto; M A Labouesse; J Bohacek; I M Mansuy; U Meyer
Journal:  Mol Psychiatry       Date:  2016-03-29       Impact factor: 15.992

8.  Oxalate upregulates expression of IL-2Rβ and activates IL-2R signaling in HK-2 cells, a line of human renal epithelial cells.

Authors:  Sweaty Koul; Lakshmipathi Khandrika; Thomas J Pshak; Naoko Iguchi; Mintu Pal; Joshua J Steffan; Hari K Koul
Journal:  Am J Physiol Renal Physiol       Date:  2014-02-12

9.  6-thioguanine induces mitochondrial dysfunction and oxidative DNA damage in acute lymphoblastic leukemia cells.

Authors:  Fan Zhang; Lijuan Fu; Yinsheng Wang
Journal:  Mol Cell Proteomics       Date:  2013-09-16       Impact factor: 5.911

10.  RNA sequencing and pathway analysis identify tumor necrosis factor alpha driven small proline-rich protein dysregulation in chronic rhinosinusitis.

Authors:  Vijay R Ramakrishnan; Joseph R Gonzalez; Sarah E Cooper; Henry P Barham; Catherine B Anderson; Eric D Larson; Carlyne D Cool; John D Diller; Kenneth Jones; Sue C Kinnamon
Journal:  Am J Rhinol Allergy       Date:  2017-09-01       Impact factor: 2.467
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