Literature DB >> 14997004

Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks.

Mirit I Aladjem1, Stefania Pasa, Silvio Parodi, John N Weinstein, Yves Pommier, Kurt W Kohn.   

Abstract

Molecular interaction maps (MIMs) use a clear, accurate, and versatile graphical language to depict complex biological processes. Here, we discuss the main features of the MIM language and its potential uses. MIMs can be used as database resources and simulation guides, and can serve to generate new hypotheses regarding the roles of specific molecules in the bioregulatory networks that control progression through the cell cycle, differentiation, and cell death.

Mesh：

Year:  2004        PMID： 14997004     DOI： 10.1126/stke.2222004pe8

Source DB:  PubMed          Journal:  Sci STKE        ISSN： 1525-8882


  11 in total

1.  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

Review 2.  Chromatin challenges during DNA replication: a systems representation.

Authors:  Kurt W Kohn; Mirit I Aladjem; John N Weinstein; Yves Pommier
Journal:  Mol Biol Cell       Date:  2007-10-24       Impact factor: 4.138

3.  Phosphorylation of BLM, dissociation from topoisomerase IIIalpha, and colocalization with gamma-H2AX after topoisomerase I-induced replication damage.

Authors:  V Ashutosh Rao; Angela M Fan; Linghua Meng; Christopher F Doe; Phillip S North; Ian D Hickson; Yves Pommier
Journal:  Mol Cell Biol       Date:  2005-10       Impact factor: 4.272

4.  Rule-based cell systems model of aging using feedback loop motifs mediated by stress responses.

Authors:  Andres Kriete; William J Bosl; Glenn Booker
Journal:  PLoS Comput Biol       Date:  2010-06-17       Impact factor: 4.475

5.  Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis.

Authors:  Kurt W Kohn; Mirit I Aladjem; John N Weinstein; Yves Pommier
Journal:  Cell Cycle       Date:  2009-07-26       Impact factor: 4.534

6.  A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

Authors:  Augustin Luna; Evrim I Karac; Margot Sunshine; Lucas Chang; Ruth Nussinov; Mirit I Aladjem; Kurt W Kohn
Journal:  BMC Bioinformatics       Date:  2011-05-17       Impact factor: 3.169

Review 7.  Depicting combinatorial complexity with the molecular interaction map notation.

Authors:  Kurt W Kohn; Mirit I Aladjem; Sohyoung Kim; John N Weinstein; Yves Pommier
Journal:  Mol Syst Biol       Date:  2006-10-03       Impact factor: 11.429

8.  SPIKE--a database, visualization and analysis tool of cellular signaling pathways.

Authors:  Ran Elkon; Rita Vesterman; Nira Amit; Igor Ulitsky; Idan Zohar; Mali Weisz; Gilad Mass; Nir Orlev; Giora Sternberg; Ran Blekhman; Jackie Assa; Yosef Shiloh; Ron Shamir
Journal:  BMC Bioinformatics       Date:  2008-02-20       Impact factor: 3.169

9.  Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies.

Authors:  Lorenzo Tortolina; David J Duffy; Massimo Maffei; Nicoletta Castagnino; Aimée M Carmody; Walter Kolch; Boris N Kholodenko; Cristina De Ambrosi; Annalisa Barla; Elia M Biganzoli; Alessio Nencioni; Franco Patrone; Alberto Ballestrero; Gabriele Zoppoli; Alessandro Verri; Silvio Parodi
Journal:  Oncotarget       Date:  2015-03-10

10.  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
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