scholarly journals Depicting combinatorial complexity with the molecular interaction map notation

2006 ◽  
Vol 2 (1) ◽  
pp. 51 ◽  
Author(s):  
Kurt W Kohn ◽  
Mirit I Aladjem ◽  
Sohyoung Kim ◽  
John N Weinstein ◽  
Yves Pommier
Keyword(s):  
Molecular Interaction ◽  
Combinatorial Complexity ◽  
Interaction Map

Cell Cycle Control: Molecular Interaction Map

2006 ◽  
Author(s):  
Kurt W Kohn ◽  
Mirit I Aladjem ◽  
Stefania Pasa ◽  
Silvio Parodi ◽  
Yves Pommier
Keyword(s):  
Cell Cycle ◽  
Molecular Interaction ◽  
Cell Cycle Control ◽  
Interaction Map

Systematic Elucidation and Validation of OncoProtein-Centric Molecular Interaction Maps

2018 ◽  
Author(s):  
Joshua Broyde ◽  
David R. Simpson ◽  
Diana Murray ◽  
Federico M. Giorgi ◽  
Alexander Lachmann ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
De Novo ◽  
Synthetic Lethality ◽  
Specific Nature ◽  
Cancer Pathways ◽  
Binding Partners ◽  
Algorithm Validation ◽  
Cancer Phenotypes ◽  
Interaction Map ◽  
Context Specific

ABSTRACTThe largely incomplete and tissue-independent nature of cancer pathways represents a key limitation to the ability to elucidate mechanistic determinants of cancer phenotypes and to predict adaptive response to targeted therapy. To address these challenges, we propose replacing canonical cancer pathways with a more accurate, comprehensive, and context-specific architecture – dubbed a Protein-Centric molecular interaction Map (PC-Map) – representing modulators, effectors, and cognate binding-partners of any oncoprotein of interest. To reconstruct these complex molecular architectures de novo, we introduce a novel OncoSig algorithm. Validation of a lung adenocarcinoma specific (LUAD) KRAS-centric PC-Map recapitulated known KRAS biology and, more critically, identified a novel repertoire of proteins eliciting synthetic lethality in KRASG12D LUAD organoid cultures. Showing the generalizable nature of the algorithm, we elucidated PC-Maps for ten recurrently mutated oncoproteins, including KRAS, in distinct tumor contexts. This revealed a highly context-specific nature of cancer’s regulatory and signaling architectures to an unprecedented degree of resolution.

scholarly journals A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis

PLoS ONE ◽  
2010 ◽  
Vol 5 (4) ◽  
pp. e10137 ◽  
Author(s):  
Gang Wu ◽  
Lisha Zhu ◽  
Jennifer E. Dent ◽  
Christine Nardini
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Interaction ◽  
Interaction Map

scholarly journals Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology

2006 ◽  
Vol 17 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Kurt W. Kohn ◽  
Mirit I. Aladjem ◽  
John N. Weinstein ◽  
Yves Pommier
Keyword(s):  
Computer Simulation ◽  
Systems Biology ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Structure And Function ◽  
Graphical Notations ◽  
Interaction Map ◽  
And Function ◽  
Network Diagrams

A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. “Heuristic” MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. “Explicit” MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.

scholarly journals Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

2013 ◽  
Vol 49 (1) ◽  
pp. 88-102 ◽  
Author(s):  
Kazuhiro A. Fujita ◽  
Marek Ostaszewski ◽  
Yukiko Matsuoka ◽  
Samik Ghosh ◽  
Enrico Glaab ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Interaction ◽  
Interaction Map

Chk2 Molecular Interaction Map and Rationale for Chk2 Inhibitors: Fig. 1.

2006 ◽  
Vol 12 (9) ◽  
pp. 2657-2661 ◽  
Author(s):  
Yves Pommier ◽  
John N. Weinstein ◽  
Mirit I. Aladjem ◽  
Kurt W. Kohn
Keyword(s):  
Molecular Interaction ◽  
Interaction Map

scholarly journals A comprehensive molecular interaction map of the budding yeast cell cycle

2010 ◽  
Vol 6 (1) ◽  
pp. 415 ◽  
Author(s):  
Kazunari Kaizu ◽  
Samik Ghosh ◽  
Yukiko Matsuoka ◽  
Hisao Moriya ◽  
Yuki Shimizu‐Yoshida ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Yeast Cell ◽  
Molecular Interaction ◽  
Budding Yeast ◽  
Yeast Cell Cycle ◽  
Interaction Map ◽  
Budding Yeast Cell Cycle
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