Literature DB >> 10998591

The visual display of regulatory information and networks.

I Pirson1, N Fortemaison, C Jacobs, S Dremier, J E Dumont, C Maenhaut.   

Abstract

Cell regulation and signal transduction are becoming increasingly complex, with reports of new cross-signalling, feedback, and feedforward regulations between pathways and between the multiple isozymes discovered at each step of these pathways. However, this information, which requires pages of text for its description, can be summarized in very simple schemes, although there is no consensus on the drawing of such schemes. This article presents a simple set of rules that allows a lot of information to be inserted in easily understandable displays.

Mesh:

Year:  2000        PMID: 10998591     DOI: 10.1016/s0962-8924(00)01817-1

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN: 0962-8924            Impact factor:   20.808


  9 in total

1.  CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

Authors:  Hiroyuki Kurata; Nana Matoba; Natsumi Shimizu
Journal:  Nucleic Acids Res       Date:  2003-07-15       Impact factor: 16.971

2.  Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.

Authors:  Kurt W Kohn; Mirit I Aladjem; John N Weinstein; Yves Pommier
Journal:  Mol Biol Cell       Date:  2005-11-02       Impact factor: 4.138

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.  Communicating Structure and Function in Synthetic Biology Diagrams.

Authors:  Jacob Beal; Tramy Nguyen; Thomas E Gorochowski; Angel Goñi-Moreno; James Scott-Brown; James Alastair McLaughlin; Curtis Madsen; Benjamin Aleritsch; Bryan Bartley; Shyam Bhakta; Mike Bissell; Sebastian Castillo Hair; Kevin Clancy; Augustin Luna; Nicolas Le Novère; Zach Palchick; Matthew Pocock; Herbert Sauro; John T Sexton; Jeffrey J Tabor; Christopher A Voigt; Zach Zundel; Chris Myers; Anil Wipat
Journal:  ACS Synth Biol       Date:  2019-08-05       Impact factor: 5.110

5.  Incremental and unifying modelling formalism for biological interaction networks.

Authors:  Anastasia Yartseva; Hanna Klaudel; Raymond Devillers; François Képès
Journal:  BMC Bioinformatics       Date:  2007-11-08       Impact factor: 3.169

6.  CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Authors:  Emanuel Gonçalves; Martijn van Iersel; Julio Saez-Rodriguez
Journal:  BMC Bioinformatics       Date:  2013-01-16       Impact factor: 3.169

7.  A comprehensive pathway map of epidermal growth factor receptor signaling.

Authors:  Kanae Oda; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano
Journal:  Mol Syst Biol       Date:  2005-05-25       Impact factor: 11.429

8.  Presenting and exploring biological pathways with PathVisio.

Authors:  Martijn P van Iersel; Thomas Kelder; Alexander R Pico; Kristina Hanspers; Susan Coort; Bruce R Conklin; Chris Evelo
Journal:  BMC Bioinformatics       Date:  2008-09-25       Impact factor: 3.169

9.  VisANT: an online visualization and analysis tool for biological interaction data.

Authors:  Zhenjun Hu; Joseph Mellor; Jie Wu; Charles DeLisi
Journal:  BMC Bioinformatics       Date:  2004-02-19       Impact factor: 3.169

  9 in total

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