Literature DB >> 18757046

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks.

William J R Longabaugh1, Eric H Davidson, Hamid Bolouri.   

Abstract

Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on software tools for building GRN models, and so there is a need for custom tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for building GRN models. We also outline our future development plans, and give some examples of current applications of BioTapestry.

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Mesh：

Year:  2008        PMID： 18757046      PMCID： PMC2762351          DOI： 10.1016/j.bbagrm.2008.07.014

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN： 0006-3002


  18 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

Review 3.  Gene regulatory networks for development.

Authors:  Michael Levine; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-23       Impact factor: 11.205

4.  Evolutionary plasticity of developmental gene regulatory network architecture.

Authors:  Veronica F Hinman; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-27       Impact factor: 11.205

Review 5.  Gene regulatory networks and the evolution of animal body plans.

Authors:  Eric H Davidson; Douglas H Erwin
Journal:  Science       Date:  2006-02-10       Impact factor: 47.728

6.  Understanding the dynamic behavior of genetic regulatory networks by functional decomposition.

Authors:  William Longabaugh; Hamid Bolouri
Journal:  Curr Genomics       Date:  2006-11       Impact factor: 2.236

7.  Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo.

Authors:  Paola Oliveri; Katherine D Walton; Eric H Davidson; David R McClay
Journal:  Development       Date:  2006-11       Impact factor: 6.868

Review 8.  Developmental gene regulatory networks in the zebrafish embryo.

Authors:  Tzu-Min Chan; William Longabaugh; Hamid Bolouri; Hua-Ling Chen; Wen-Fang Tseng; Chung-Hao Chao; Te-Hsuan Jang; Yu-I Lin; Shao-Chin Hung; Horng-Dar Wang; Chiou-Hwa Yuh
Journal:  Biochim Biophys Acta       Date:  2008-10-08

9.  Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.

Authors:  Steven A Vokes; Hongkai Ji; Scott McCuine; Toyoaki Tenzen; Shane Giles; Sheng Zhong; William J R Longabaugh; Eric H Davidson; Wing H Wong; Andrew P McMahon
Journal:  Development       Date:  2007-04-18       Impact factor: 6.868

10.  Genome-wide analysis of gene expression during early Arabidopsis flower development.

Authors:  Frank Wellmer; Márcio Alves-Ferreira; Annick Dubois; José Luis Riechmann; Elliot M Meyerowitz
Journal:  PLoS Genet       Date:  2006-06-12       Impact factor: 5.917
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  45 in total

Review 1.  Computational tools for metabolic engineering.

Authors:  Wilbert B Copeland; Bryan A Bartley; Deepak Chandran; Michal Galdzicki; Kyung H Kim; Sean C Sleight; Costas D Maranas; Herbert M Sauro
Journal:  Metab Eng       Date:  2012-05       Impact factor: 9.783

2.  Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo.

Authors:  Enhu Li; Stefan C Materna; Eric H Davidson
Journal:  Dev Biol       Date:  2012-07-06       Impact factor: 3.582

3.  The Systems Biology Graphical Notation.

Authors:  Nicolas Le Novère; Michael Hucka; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Anatoly Sorokin; Emek Demir; Katja Wegner; Mirit I Aladjem; Sarala M Wimalaratne; Frank T Bergman; Ralph Gauges; Peter Ghazal; Hideya Kawaji; Lu Li; Yukiko Matsuoka; Alice Villéger; Sarah E Boyd; Laurence Calzone; Melanie Courtot; Ugur Dogrusoz; Tom C Freeman; Akira Funahashi; Samik Ghosh; Akiya Jouraku; Sohyoung Kim; Fedor Kolpakov; Augustin Luna; Sven Sahle; Esther Schmidt; Steven Watterson; Guanming Wu; Igor Goryanin; Douglas B Kell; Chris Sander; Herbert Sauro; Jacky L Snoep; Kurt Kohn; Hiroaki Kitano
Journal:  Nat Biotechnol       Date:  2009-08-07       Impact factor: 54.908

4.  A gene regulatory network controlling the embryonic specification of endoderm.

Authors:  Isabelle S Peter; Eric H Davidson
Journal:  Nature       Date:  2011-05-29       Impact factor: 49.962

Review 5.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

Review 6.  Built shallow to maintain homeostasis and persistent infection: insight into the transcriptional regulatory network of the gastric human pathogen Helicobacter pylori.

Authors:  Alberto Danielli; Gabriele Amore; Vincenzo Scarlato
Journal:  PLoS Pathog       Date:  2010-06-10       Impact factor: 6.823

7.  A curated online resource for SOX10 and pigment cell molecular genetic pathways.

Authors:  Laura L Baxter; R Travis Moreland; Anh-Dao Nguyen; Tyra G Wolfsberg; William J Pavan
Journal:  Database (Oxford)       Date:  2010-10-25       Impact factor: 3.451

8.  Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network.

Authors:  Clemens Kühn; Christoph Wierling; Alexander Kühn; Edda Klipp; Georgia Panopoulou; Hans Lehrach; Albert J Poustka
Journal:  BMC Syst Biol       Date:  2009-08-23

9.  phiSITE: database of gene regulation in bacteriophages.

Authors:  Lubos Klucar; Matej Stano; Matus Hajduk
Journal:  Nucleic Acids Res       Date:  2009-11-09       Impact factor: 16.971

10.  myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks.

Authors:  Jamil Bacha; James S Brodie; Matthew W Loose
Journal:  BMC Dev Biol       Date:  2009-06-06       Impact factor: 1.978
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