Literature DB >> 21278724

New approaches to modeling complex biochemistry.

John A Bachman, Peter Sorger.   

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Year:  2011        PMID: 21278724      PMCID: PMC3100653          DOI: 10.1038/nmeth0211-130

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


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  7 in total

1.  Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.

Authors:  Michael W Sneddon; James R Faeder; Thierry Emonet
Journal:  Nat Methods       Date:  2010-12-26       Impact factor: 28.547

Review 2.  Rules for modeling signal-transduction systems.

Authors:  William S Hlavacek; James R Faeder; Michael L Blinov; Richard G Posner; Michael Hucka; Walter Fontana
Journal:  Sci STKE       Date:  2006-07-18

3.  Rule-based modeling of biochemical systems with BioNetGen.

Authors:  James R Faeder; Michael L Blinov; William S Hlavacek
Journal:  Methods Mol Biol       Date:  2009

4.  Internal coarse-graining of molecular systems.

Authors:  Jérôme Feret; Vincent Danos; Jean Krivine; Russ Harmer; Walter Fontana
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-03       Impact factor: 11.205

5.  Programming with models: modularity and abstraction provide powerful capabilities for systems biology.

Authors:  Aneil Mallavarapu; Matthew Thomson; Benjamin Ullian; Jeremy Gunawardena
Journal:  J R Soc Interface       Date:  2009-03-06       Impact factor: 4.118

6.  Domain-oriented reduction of rule-based network models.

Authors:  N M Borisov; A S Chistopolsky; J R Faeder; B N Kholodenko
Journal:  IET Syst Biol       Date:  2008-09       Impact factor: 1.615

7.  Exact model reduction of combinatorial reaction networks.

Authors:  Holger Conzelmann; Dirk Fey; Ernst D Gilles
Journal:  BMC Syst Biol       Date:  2008-08-28
  7 in total
  12 in total

Review 1.  Modeling for (physical) biologists: an introduction to the rule-based approach.

Authors:  Lily A Chylek; Leonard A Harris; James R Faeder; William S Hlavacek
Journal:  Phys Biol       Date:  2015-07-16       Impact factor: 2.583

Review 2.  Modeling cellular compartmentation in one-carbon metabolism.

Authors:  Marco Scotti; Lorenzo Stella; Emily J Shearer; Patrick J Stover
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-02-13

Review 3.  Biomarkers of Nutrition for Development-Folate Review.

Authors:  Lynn B Bailey; Patrick J Stover; Helene McNulty; Michael F Fenech; Jesse F Gregory; James L Mills; Christine M Pfeiffer; Zia Fazili; Mindy Zhang; Per M Ueland; Anne M Molloy; Marie A Caudill; Barry Shane; Robert J Berry; Regan L Bailey; Dorothy B Hausman; Ramkripa Raghavan; Daniel J Raiten
Journal:  J Nutr       Date:  2015-06-03       Impact factor: 4.798

Review 4.  Understanding immunology via engineering design: the role of mathematical prototyping.

Authors:  David J Klinke; Qing Wang
Journal:  Comput Math Methods Med       Date:  2012-09-03       Impact factor: 2.238

5.  CPT: Pharmacometrics and Systems Pharmacology.

Authors:  Piet H van der Graaf
Journal:  CPT Pharmacometrics Syst Pharmacol       Date:  2012-09-26

Review 6.  Consolidation and translation regulation.

Authors:  Shunit Gal-Ben-Ari; Justin W Kenney; Hadile Ounalla-Saad; Elham Taha; Orit David; David Levitan; Iness Gildish; Debabrata Panja; Balagopal Pai; Karin Wibrand; T Ian Simpson; Christopher G Proud; Clive R Bramham; J Douglas Armstrong; Kobi Rosenblum
Journal:  Learn Mem       Date:  2012-08-16       Impact factor: 2.460

7.  A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation.

Authors:  Stuart Aitken; Ross D Alexander; Jean D Beggs
Journal:  J R Soc Interface       Date:  2013-06-26       Impact factor: 4.118

8.  Systems modelling of NHEJ reveals the importance of redox regulation of Ku70/80 in the dynamics of dna damage foci.

Authors:  David Dolan; Glyn Nelson; Anze Zupanic; Graham Smith; Daryl Shanley
Journal:  PLoS One       Date:  2013-02-06       Impact factor: 3.240

9.  An evolutionary perspective on anti-tumor immunity.

Authors:  David J Klinke
Journal:  Front Oncol       Date:  2013-01-10       Impact factor: 6.244

10.  Programming biological models in Python using PySB.

Authors:  Carlos F Lopez; Jeremy L Muhlich; John A Bachman; Peter K Sorger
Journal:  Mol Syst Biol       Date:  2013       Impact factor: 11.429

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