Literature DB >> 25645874

Quantitative and logic modelling of molecular and gene networks.

Nicolas Le Novère1.   

Abstract

Behaviours of complex biomolecular systems are often irreducible to the elementary properties of their individual components. Explanatory and predictive mathematical models are therefore useful for fully understanding and precisely engineering cellular functions. The development and analyses of these models require their adaptation to the problems that need to be solved and the type and amount of available genetic or molecular data. Quantitative and logic modelling are among the main methods currently used to model molecular and gene networks. Each approach comes with inherent advantages and weaknesses. Recent developments show that hybrid approaches will become essential for further progress in synthetic biology and in the development of virtual organisms.

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Year:  2015        PMID: 25645874      PMCID: PMC4604653          DOI: 10.1038/nrg3885

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  133 in total

1.  Integrating high-throughput and computational data elucidates bacterial networks.

Authors:  Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard O Palsson
Journal:  Nature       Date:  2004-05-06       Impact factor: 49.962

Review 2.  Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.

Authors:  Kouichi Takahashi; Satya Nanda Vel Arjunan; Masaru Tomita
Journal:  FEBS Lett       Date:  2005-03-21       Impact factor: 4.124

3.  Core transcriptional regulatory circuitry in human embryonic stem cells.

Authors:  Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

4.  High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells.

Authors:  Gang Chang; Shuai Gao; Xinfeng Hou; Zijian Xu; Yanfeng Liu; Lan Kang; Yu Tao; Wenqiang Liu; Bo Huang; Xiaochen Kou; Jiayu Chen; Lei An; Kai Miao; Keqian Di; Zhilong Wang; Kun Tan; Tao Cheng; Tao Cai; Shaorong Gao; Jianhui Tian
Journal:  Cell Res       Date:  2013-12-31       Impact factor: 25.617

5.  Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.

Authors:  C H Yuh; H Bolouri; E H Davidson
Journal:  Science       Date:  1998-03-20       Impact factor: 47.728

6.  Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops.

Authors:  Anatoly Kiyatkin; Edita Aksamitiene; Nick I Markevich; Nikolay M Borisov; Jan B Hoek; Boris N Kholodenko
Journal:  J Biol Chem       Date:  2006-05-09       Impact factor: 5.157

7.  A whole-cell computational model predicts phenotype from genotype.

Authors:  Jonathan R Karr; Jayodita C Sanghvi; Derek N Macklin; Miriam V Gutschow; Jared M Jacobs; Benjamin Bolival; Nacyra Assad-Garcia; John I Glass; Markus W Covert
Journal:  Cell       Date:  2012-07-20       Impact factor: 41.582

8.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

9.  Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

Authors:  Dagmar Waltemath; Richard Adams; Frank T Bergmann; Michael Hucka; Fedor Kolpakov; Andrew K Miller; Ion I Moraru; David Nickerson; Sven Sahle; Jacky L Snoep; Nicolas Le Novère
Journal:  BMC Syst Biol       Date:  2011-12-15

10.  A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

Authors:  Tomer Shlomi; Yariv Eisenberg; Roded Sharan; Eytan Ruppin
Journal:  Mol Syst Biol       Date:  2007-04-17       Impact factor: 11.429

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  131 in total

Review 1.  A Next Generation Multiscale View of Inborn Errors of Metabolism.

Authors:  Carmen A Argmann; Sander M Houten; Jun Zhu; Eric E Schadt
Journal:  Cell Metab       Date:  2015-12-17       Impact factor: 27.287

2.  Probe discovery: Disentangling gene networks.

Authors:  Finbarr Hayes
Journal:  Nat Chem Biol       Date:  2016-01       Impact factor: 15.040

Review 3.  Personalized Therapy of Hypertension: the Past and the Future.

Authors:  Paolo Manunta; Mara Ferrandi; Daniele Cusi; Patrizia Ferrari; Jan Staessen; Giuseppe Bianchi
Journal:  Curr Hypertens Rep       Date:  2016-03       Impact factor: 5.369

4.  High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

Authors:  Luciano Marcon; Xavier Diego; James Sharpe; Patrick Müller
Journal:  Elife       Date:  2016-04-08       Impact factor: 8.140

Review 5.  From the exposome to mechanistic understanding of chemical-induced adverse effects.

Authors:  Beate I Escher; Jörg Hackermüller; Tobias Polte; Stefan Scholz; Achim Aigner; Rolf Altenburger; Alexander Böhme; Stephanie K Bopp; Werner Brack; Wibke Busch; Marc Chadeau-Hyam; Adrian Covaci; Adolf Eisenträger; James J Galligan; Natalia Garcia-Reyero; Thomas Hartung; Michaela Hein; Gunda Herberth; Annika Jahnke; Jos Kleinjans; Nils Klüver; Martin Krauss; Marja Lamoree; Irina Lehmann; Till Luckenbach; Gary W Miller; Andrea Müller; David H Phillips; Thorsten Reemtsma; Ulrike Rolle-Kampczyk; Gerrit Schüürmann; Benno Schwikowski; Yu-Mei Tan; Saskia Trump; Susanne Walter-Rohde; John F Wambaugh
Journal:  Environ Int       Date:  2016-12-08       Impact factor: 9.621

Review 6.  Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

Authors:  Madalena Chaves; Hidde de Jong
Journal:  Methods Mol Biol       Date:  2021

7.  Representing dynamic biological networks with multi-scale probabilistic models.

Authors:  Alexander Groß; Barbara Kracher; Johann M Kraus; Silke D Kühlwein; Astrid S Pfister; Sebastian Wiese; Katrin Luckert; Oliver Pötz; Thomas Joos; Dries Van Daele; Luc De Raedt; Michael Kühl; Hans A Kestler
Journal:  Commun Biol       Date:  2019-01-17

8.  Parents' and Children's ADHD in a Family System.

Authors:  Kirby Deater-Deckard
Journal:  J Abnorm Child Psychol       Date:  2017-04

Review 9.  Connectivity and complex systems: learning from a multi-disciplinary perspective.

Authors:  Laura Turnbull; Marc-Thorsten Hütt; Andreas A Ioannides; Stuart Kininmonth; Ronald Poeppl; Klement Tockner; Louise J Bracken; Saskia Keesstra; Lichan Liu; Rens Masselink; Anthony J Parsons
Journal:  Appl Netw Sci       Date:  2018-06-18

10.  Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior.

Authors:  Dimitrios Voukantsis; Kenneth Kahn; Martin Hadley; Rowan Wilson; Francesca M Buffa
Journal:  Gigascience       Date:  2019-03-01       Impact factor: 6.524

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