Literature DB >> 23549147

A cell simulator platform: the cell collective.

T Helikar1, B Kowal, J A Rogers.   

Abstract

Diseases are often a result of multiple malfunctions in complex, nonlinear biological/biochemical networks. As such, these processes are far more complicated to understand because they tend to give rise to functions that are emergent in nature, i.e., higher-level (mal)functions that are more than the sum of their parts. Systems biology provides a new approach to understanding biological systems and diseases from a holistic perspective.

Entities:  

Mesh：

Year:  2013        PMID： 23549147      PMCID： PMC5242230          DOI： 10.1038/clpt.2013.41

Source DB:  PubMed          Journal:  Clin Pharmacol Ther        ISSN： 0009-9236            Impact factor:   6.875


  5 in total

1.  Emergent decision-making in biological signal transduction networks.

Authors:  Tomás Helikar; John Konvalina; Jack Heidel; Jim A Rogers
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-04       Impact factor: 11.205

2.  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

3.  Dynamics of influenza virus and human host interactions during infection and replication cycle.

Authors:  Alex Madrahimov; Tomáš Helikar; Bryan Kowal; Guoqing Lu; Jim Rogers
Journal:  Bull Math Biol       Date:  2012-10-19       Impact factor: 1.758

4.  The Cell Collective: toward an open and collaborative approach to systems biology.

Authors:  Tomáš Helikar; Bryan Kowal; Sean McClenathan; Mitchell Bruckner; Thaine Rowley; Alex Madrahimov; Ben Wicks; Manish Shrestha; Kahani Limbu; Jim A Rogers
Journal:  BMC Syst Biol       Date:  2012-08-07

5.  Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Authors:  Tomáš Helikar; Bryan Kowal; Alex Madrahimov; Manish Shrestha; Jay Pedersen; Kahani Limbu; Ishwor Thapa; Thaine Rowley; Rahul Satalkar; Naomi Kochi; John Konvalina; Jim A Rogers
Journal:  PLoS One       Date:  2012-10-17       Impact factor: 3.240
  5 in total
  13 in total

1.  Logical Reduction of Biological Networks to Their Most Determinative Components.

Authors:  Mihaela T Matache; Valentin Matache
Journal:  Bull Math Biol       Date:  2016-07-14       Impact factor: 1.758

2.  A practical guide to mechanistic systems modeling in biology using a logic-based approach.

Authors:  Anna Niarakis; Tomáš Helikar
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

3.  Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

Authors:  Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S Malik Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C Freeman; Paul Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; Aurélien Naldi; Eugenia Oshurko; Ioannis Xenarios; Sylvain Soliman; Claudine Chaouiya; Tomáš Helikar; Laurence Calzone
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

4.  RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.

Authors:  Bilal Shaikh; Gnaneswara Marupilla; Mike Wilson; Michael L Blinov; Ion I Moraru; Jonathan R Karr
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

5.  Integrating interactive computational modeling in biology curricula.

Authors:  Tomáš Helikar; Christine E Cutucache; Lauren M Dahlquist; Tyler A Herek; Joshua J Larson; Jim A Rogers
Journal:  PLoS Comput Biol       Date:  2015-03-19       Impact factor: 4.475

6.  Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions.

Authors:  Naomi Kochi; Tomáš Helikar; Laura Allen; Jim A Rogers; Zhenyuan Wang; Mihaela T Matache
Journal:  BMC Syst Biol       Date:  2014-09-05

Review 7.  Logical Modeling and Dynamical Analysis of Cellular Networks.

Authors:  Wassim Abou-Jaoudé; Pauline Traynard; Pedro T Monteiro; Julio Saez-Rodriguez; Tomáš Helikar; Denis Thieffry; Claudine Chaouiya
Journal:  Front Genet       Date:  2016-05-31       Impact factor: 4.599

8.  Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.

Authors:  Bhanwar Lal Puniya; Laura Allen; Colleen Hochfelder; Mahbubul Majumder; Tomáš Helikar
Journal:  Front Bioeng Biotechnol       Date:  2016-02-11

9.  A systems pharmacology model for inflammatory bowel disease.

Authors:  Violeta Balbas-Martinez; Leire Ruiz-Cerdá; Itziar Irurzun-Arana; Ignacio González-García; An Vermeulen; José David Gómez-Mantilla; Iñaki F Trocóniz
Journal:  PLoS One       Date:  2018-03-07       Impact factor: 3.240

10.  SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Authors:  Claudine Chaouiya; Duncan Bérenguier; Sarah M Keating; Aurélien Naldi; Martijn P van Iersel; Nicolas Rodriguez; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan Kowal; Benjamin Wicks; Emanuel Gonçalves; Julien Dorier; Michel Page; Pedro T Monteiro; Axel von Kamp; Ioannis Xenarios; Hidde de Jong; Michael Hucka; Steffen Klamt; Denis Thieffry; Nicolas Le Novère; Julio Saez-Rodriguez; Tomáš Helikar
Journal:  BMC Syst Biol       Date:  2013-12-10
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