Literature DB >> 17040977

Resources for integrative systems biology: from data through databases to networks and dynamic system models.

Aylwin Ng1, Borisas Bursteinas, Qiong Gao, Ewan Mollison, Marketa Zvelebil.   

Abstract

In systems biology, biologically relevant quantitative modelling of physiological processes requires the integration of experimental data from diverse sources. Recent developments in high-throughput methodologies enable the analysis of the transcriptome, proteome, interactome, metabolome and phenome on a previously unprecedented scale, thus contributing to the deluge of experimental data held in numerous public databases. In this review, we describe some of the databases and simulation tools that are relevant to systems biology and discuss a number of key issues affecting data integration and the challenges these pose to systems-level research.

Mesh：

Year:  2006        PMID： 17040977     DOI： 10.1093/bib/bbl036

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  27 in total

Review 1.  Systems immunology: a survey of modeling formalisms, applications and simulation tools.

Authors:  Vipin Narang; James Decraene; Shek-Yoon Wong; Bindu S Aiswarya; Andrew R Wasem; Shiang Rong Leong; Alexandre Gouaillard
Journal:  Immunol Res       Date:  2012-09       Impact factor: 2.829

2.  Identification and treatment of symptoms associated with inflammation in medically ill patients.

Authors:  Robert Dantzer; Lucile Capuron; Michael R Irwin; Andrew H Miller; Helene Ollat; Victor Hugh Perry; Sarah Rousey; Raz Yirmiya
Journal:  Psychoneuroendocrinology       Date:  2007-12-03       Impact factor: 4.905

3.  A computational-experimental approach to designing a polyfunctional genosensor derived from the Escherichia coli gene yfiA promoter.

Authors:  N V Tikunova; T M Khlebodarova; A V Kachko; I L Stepanenko; N A Kolchanov
Journal:  Dokl Biochem Biophys       Date:  2007 Nov-Dec       Impact factor: 0.788

Review 4.  Designing and encoding models for synthetic biology.

Authors:  Lukas Endler; Nicolas Rodriguez; Nick Juty; Vijayalakshmi Chelliah; Camille Laibe; Chen Li; Nicolas Le Novère
Journal:  J R Soc Interface       Date:  2009-04-01       Impact factor: 4.118

Review 5.  Integrating computational and biochemical studies to explore mechanisms in NF-{kappa}B signaling.

Authors:  Jeffrey D Kearns; Alexander Hoffmann
Journal:  J Biol Chem       Date:  2008-10-20       Impact factor: 5.157

6.  The new biology: a bridge to clinical cardiology.

Authors:  Ge Louridas; Kg Lourida
Journal:  Hippokratia       Date:  2012-04       Impact factor: 0.471

Review 7.  Antiviral innate immunity through the lens of systems biology.

Authors:  Shashank Tripathi; Adolfo Garcia-Sastre
Journal:  Virus Res       Date:  2015-12-03       Impact factor: 3.303

Review 8.  Cellular senescence: unravelling complexity.

Authors:  João F Passos; Cedric Simillion; Jennifer Hallinan; Anil Wipat; Thomas von Zglinicki
Journal:  Age (Dordr)       Date:  2009-12

Review 9.  Systems glycobiology: biochemical reaction networks regulating glycan structure and function.

Authors:  Sriram Neelamegham; Gang Liu
Journal:  Glycobiology       Date:  2011-03-24       Impact factor: 4.313

10.  An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions.

Authors:  Shizuka Uchida; André Schneider; Marion Wiesnet; Benno Jungblut; Polina Zarjitskaya; Katharina Jenniches; Karsten Grosse Kreymborg; Werner Seeger; Thomas Braun
Journal:  BMC Genomics       Date:  2009-03-06       Impact factor: 3.969
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