Literature DB >> 21938637

BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks.

William J R Longabaugh1.   

Abstract

BioTapestry is an open source, freely available software tool that has been developed to handle the -challenges of modeling genetic regulatory networks (GRNs). Using BioTapestry, a researcher can -construct a network model and use it to visualize and understand the dynamic behavior of a complex, spatially and temporally distributed GRN. Here we provide a step-by-step example of a way to use BioTapestry to build a GRN model and discuss some common issues that can arise during this process.

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Year:  2012        PMID: 21938637     DOI: 10.1007/978-1-61779-292-2_21

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  27 in total

Review 1.  Photoreceptor cell fate specification in vertebrates.

Authors:  Joseph A Brzezinski; Thomas A Reh
Journal:  Development       Date:  2015-10-01       Impact factor: 6.868

2.  Developmental effector gene regulation: Multiplexed strategies for functional analysis.

Authors:  Lijun Wang; Kari Koppitch; Ann Cutting; Ping Dong; Parul Kudtarkar; Jenny Zeng; R Andrew Cameron; Eric H Davidson
Journal:  Dev Biol       Date:  2018-10-28       Impact factor: 3.582

3.  Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis.

Authors:  Arielle Woznica; Maximilian Haeussler; Ella Starobinska; Jessica Jemmett; Younan Li; David Mount; Brad Davidson
Journal:  Dev Biol       Date:  2012-05-14       Impact factor: 3.582

4.  Geometric control of ciliated band regulatory states in the sea urchin embryo.

Authors:  Julius C Barsi; Enhu Li; Eric H Davidson
Journal:  Development       Date:  2015-02-05       Impact factor: 6.868

5.  How Does the Regulatory Genome Work?

Authors:  Sorin Istrail; Isabelle S Peter
Journal:  J Comput Biol       Date:  2019-06-04       Impact factor: 1.479

Review 6.  Regulatory states in the developmental control of gene expression.

Authors:  Isabelle S Peter
Journal:  Brief Funct Genomics       Date:  2017-09-01       Impact factor: 4.241

Review 7.  Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors:  Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal:  Pharmacol Ther       Date:  2013-02-04       Impact factor: 12.310

8.  Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids.

Authors:  Eric M Erkenbrack; Eric H Davidson; Isabelle S Peter
Journal:  Development       Date:  2018-12-18       Impact factor: 6.868

9.  Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis.

Authors:  Brenna S McCauley; Eda Akyar; H Rosa Saad; Veronica F Hinman
Journal:  Development       Date:  2015-01-01       Impact factor: 6.868

10.  A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma.

Authors:  Boris Aguilar; David L Gibbs; David J Reiss; Mark McConnell; Samuel A Danziger; Andrew Dervan; Matthew Trotter; Douglas Bassett; Robert Hershberg; Alexander V Ratushny; Ilya Shmulevich
Journal:  Gigascience       Date:  2020-07-01       Impact factor: 6.524

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