Literature DB >> 15261526

Mathematical and computational techniques to deduce complex biochemical reaction mechanisms.

E J Crampin1, S Schnell, P E McSharry.   

Abstract

Time series data can now be routinely collected for biochemical reaction pathways, and recently, several methods have been proposed to infer reaction mechanisms for metabolic pathways and networks. In this paper we provide a survey of mathematical techniques for determining reaction mechanisms for time series data on the concentration or abundance of different reacting components, with little prior information about the pathways involved.

Mesh:

Year:  2004        PMID: 15261526     DOI: 10.1016/j.pbiomolbio.2004.04.002

Source DB:  PubMed          Journal:  Prog Biophys Mol Biol        ISSN: 0079-6107            Impact factor:   3.667


  35 in total

1.  Automated refinement and inference of analytical models for metabolic networks.

Authors:  Michael D Schmidt; Ravishankar R Vallabhajosyula; Jerry W Jenkins; Jonathan E Hood; Abhishek S Soni; John P Wikswo; Hod Lipson
Journal:  Phys Biol       Date:  2011-08-10       Impact factor: 2.583

2.  Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations.

Authors:  Michael Samoilov; Sergey Plyasunov; Adam P Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-08       Impact factor: 11.205

3.  Use and abuse of the quasi-steady-state approximation.

Authors:  E H Flach; S Schnell
Journal:  Syst Biol (Stevenage)       Date:  2006-07

4.  Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.

Authors:  N Yalamanchili; D E Zak; B A Ogunnaike; J S Schwaber; A Kriete; B N Kholodenko
Journal:  Syst Biol (Stevenage)       Date:  2006-07

5.  Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.

Authors:  Nader Pourmand; Stefano Caramuta; Andrea Villablanca; Silvia Mori; Miloslav Karhanek; Shan X Wang; Ronald W Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-27       Impact factor: 11.205

6.  Numerical Matrices Method for nonlinear system identification and description of dynamics of biochemical reaction networks.

Authors:  Alexey V Karnaukhov; Elena V Karnaukhova; James R Williamson
Journal:  Biophys J       Date:  2007-03-09       Impact factor: 4.033

Review 7.  Modelling reaction kinetics inside cells.

Authors:  Ramon Grima; Santiago Schnell
Journal:  Essays Biochem       Date:  2008       Impact factor: 8.000

8.  Algebraic methods for inferring biochemical networks: a maximum likelihood approach.

Authors:  Gheorghe Craciun; Casian Pantea; Grzegorz A Rempala
Journal:  Comput Biol Chem       Date:  2009-08-06       Impact factor: 2.877

9.  Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks.

Authors:  Martin T Swain; Johannes J Mandel; Werner Dubitzky
Journal:  BMC Bioinformatics       Date:  2010-09-14       Impact factor: 3.169

10.  Efficient, sparse biological network determination.

Authors:  Elias August; Antonis Papachristodoulou
Journal:  BMC Syst Biol       Date:  2009-02-23
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