Literature DB >> 12779446

On the deduction of chemical reaction pathways from measurements of time series of concentrations.

Michael Samoilov1, Adam Arkin, John Ross.   

Abstract

We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.

Year:  2001        PMID: 12779446     DOI: 10.1063/1.1336499

Source DB:  PubMed          Journal:  Chaos        ISSN: 1054-1500            Impact factor:   3.642


  20 in total

1.  Experimental test of a method for determining causal connectivities of species in reactions.

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2.  Dynamic metabolomic data analysis: a tutorial review.

Authors:  A K Smilde; J A Westerhuis; H C J Hoefsloot; S Bijlsma; C M Rubingh; D J Vis; R H Jellema; H Pijl; F Roelfsema; J van der Greef
Journal:  Metabolomics       Date:  2009-12-04       Impact factor: 4.290

3.  Untangling the wires: a strategy to trace functional interactions in signaling and gene networks.

Authors:  Boris N Kholodenko; Anatoly Kiyatkin; Frank J Bruggeman; Eduardo Sontag; Hans V Westerhoff; Jan B Hoek
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-19       Impact factor: 11.205

4.  Statistical Model for Biochemical Network Inference.

Authors:  Gheorghe Craciun; Jaejik Kim; Casian Pantea; Grzegorz A Rempala
Journal:  Commun Stat Simul Comput       Date:  2012-09-26       Impact factor: 1.118

5.  Inference of gene regulatory networks from genome-wide knockout fitness data.

Authors:  Liming Wang; Xiaodong Wang; Adam P Arkin; Michael S Samoilov
Journal:  Bioinformatics       Date:  2012-12-27       Impact factor: 6.937

6.  Inferring Gene Regulatory Networks Using the Improved Markov Blanket Discovery Algorithm.

Authors:  Wei Liu; Yi Jiang; Li Peng; Xingen Sun; Wenqing Gan; Qi Zhao; Huanrong Tang
Journal:  Interdiscip Sci       Date:  2021-09-08       Impact factor: 2.233

7.  Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction.

Authors:  Hiroyuki Kuwahara; Chris J Myers; Michael S Samoilov
Journal:  PLoS Comput Biol       Date:  2010-03-26       Impact factor: 4.475

Review 8.  Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Authors:  I-Chun Chou; Eberhard O Voit
Journal:  Math Biosci       Date:  2009-03-25       Impact factor: 2.144

9.  Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics.

Authors:  Paola Lecca; Daniele Morpurgo; Gianluca Fantaccini; Alessandro Casagrande; Corrado Priami
Journal:  BMC Syst Biol       Date:  2012-05-28

10.  Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering.

Authors:  Filippo Menolascina; Domenico Bellomo; Thomas Maiwald; Vitoantonio Bevilacqua; Caterina Ciminelli; Angelo Paradiso; Stefania Tommasi
Journal:  BMC Bioinformatics       Date:  2009-10-15       Impact factor: 3.169

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