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Items: 1 to 20 of 85

1.

Foundations of a query and simulation system for the modeling of biochemical and biological processes.

Antoniotti M, Park F, Policriti A, Ugel N, Mishra B.

Pac Symp Biocomput. 2003:116-27.

2.

Model building and model checking for biochemical processes.

Antoniotti M, Policriti A, Ugel N, Mishra B.

Cell Biochem Biophys. 2003;38(3):271-86.

PMID:
12794268
3.

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists.

Helikar T, Rogers JA.

BMC Syst Biol. 2009 Jun 6;3:58. doi: 10.1186/1752-0509-3-58.

4.

Guaranteed error bounds for structured complexity reduction of biochemical networks.

Prescott TP, Papachristodoulou A.

J Theor Biol. 2012 Jul 7;304:172-82. doi: 10.1016/j.jtbi.2012.04.002. Epub 2012 Apr 9.

PMID:
22554951
5.
7.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

Mishra B, Daruwala RS, Zhou Y, Ugel N, Policriti A, Antoniotti M, Paxia S, Rejali M, Rudra A, Cherepinsky V, Silver N, Casey W, Piazza C, Simeoni M, Barbano P, Spivak M, Feng J, Gill O, Venkatesh M, Cheng F, Sun B, Ioniata I, Anantharaman T, Hubbard EJ, Pnueli A, Harel D, Chandru V, Hariharan R, Wigler M, Park F, Lin SC, Lazebnik Y, Winkler F, Cantor CR, Carbone A, Gromov M.

OMICS. 2003 Fall;7(3):253-68.

PMID:
14583115
8.

Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

Zhang Q, Bhattacharya S, Andersen ME, Conolly RB.

J Toxicol Environ Health B Crit Rev. 2010 Feb;13(2-4):253-76. doi: 10.1080/10937404.2010.483943.

PMID:
20574901
9.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

Alves R, Vilaprinyo E, Hernádez-Bermejo B, Sorribas A.

Biotechnol Genet Eng Rev. 2008;25:1-40. Review.

PMID:
21412348
10.

Estimating parameters for generalized mass action models using constraint propagation.

Tucker W, Kutalik Z, Moulton V.

Math Biosci. 2007 Aug;208(2):607-20. Epub 2006 Dec 8.

PMID:
17306307
11.
12.
13.

Systems immunology: a survey of modeling formalisms, applications and simulation tools.

Narang V, Decraene J, Wong SY, Aiswarya BS, Wasem AR, Leong SR, Gouaillard A.

Immunol Res. 2012 Sep;53(1-3):251-65. doi: 10.1007/s12026-012-8305-7. Review.

PMID:
22528121
14.

Quantitative modeling of biochemical networks.

Hofestädt R, Thelen S.

In Silico Biol. 1998;1(1):39-53.

PMID:
11471241
15.

A moment closure method for stochastic reaction networks.

Lee CH, Kim KH, Kim P.

J Chem Phys. 2009 Apr 7;130(13):134107. doi: 10.1063/1.3103264.

PMID:
19355717
16.

Metabolic modeling: a tool of drug discovery in the post-genomic era.

Voit EO.

Drug Discov Today. 2002 Jun 1;7(11):621-8. Review.

PMID:
12047873
17.

Ordinary differential equations with applications in molecular biology.

Ilea M, Turnea M, Rotariu M.

Rev Med Chir Soc Med Nat Iasi. 2012 Jan-Mar;116(1):347-52.

PMID:
23077920
18.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

Egri-Nagy A, Nehaniv CL.

Biosystems. 2008 Oct-Nov;94(1-2):135-44. doi: 10.1016/j.biosystems.2008.05.019. Epub 2008 Jun 20.

PMID:
18611428
19.

Canonical modeling: review of concepts with emphasis on environmental health.

Voit EO.

Environ Health Perspect. 2000 Oct;108 Suppl 5:895-909. Review.

PMID:
11035999
20.

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41. doi: 10.1186/1752-0509-2-41.

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