Publications by Keng Cher Soh | EPFL Graph Search

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Keng Cher Soh, Meriç Ataman, Georgios Fengos, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

2018

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Keng Cher Soh, Noushin Hadadi, Jasmin Maria Hafner

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh

Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic ...

2017

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, Stefano Andreozzi

Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of om ...

Elsevier2016

Computational Studies on Cellular Bioenergetics

Keng Cher Soh

Genome-scale metabolic reconstructions have become indispensable tools for understanding and investigation of the metabolism of any organism in this post-genomic era. However, there are still knowledge gaps in our understanding of the metabolism of even th ...

EPFL2013

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, Anirikh Chakrabarti

Mathematical modeling is an essential tool for a comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possib ...

2013

DREAMS of metabolism

Vassily Hatzimanikatis, Keng Cher Soh

Metabolic networks have been studied for decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational app ...

Elsevier2010

Analysis of genome-scale metabolic model of mycobacterium tuberculosis for new combat strategies

Vassily Hatzimanikatis, John McKinney, Keng Cher Soh, Muhittin Emre Özdemir

2009