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Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Related publications (51)

Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis

Tuberculosis is an ancient human disease affecting millions of people every year. The common causative agent, Mycobacterium tuberculosis, is a peculiar pathogen that can persist in the host tissues for decades. Many of the key attributes of M. tuberculosis ...

EPFL2013

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

Vassily Hatzimanikatis, Ljubisa Miskovic, 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

Thermodynamics-based Significance Ranking of Candidates for Metabolomics

Vassily Hatzimanikatis

Integration of experimental measurements of intracellular metabolite concentrations in genome scale models restricts the thermodynamically feasible flux space and reduces uncertainty regarding the net outcome of by-directional reactions. By combining tFBA, ...

2013

Liver receptor homolog-1 is essential for pregnancy

Kristina Schoonjans

Successful pregnancy requires coordination of an array of signals and factors from multiple tissues. One such element, liver receptor homolog-1 (Lrh-1), is an orphan nuclear receptor that regulates metabolism and hormone synthesis(1). It is strongly expres ...

Nature Publishing Group2013

The genome of Dehalobacter restrictus - high gene redundancy for a restricted metabolism

Christof Holliger, Julien Maillard, Aamani Rupakula Boyanapalli, Hauke Smidt

Organohalide respiration (OHR) is a bacterial anaerobic respiratory metabolism dedicated to use halogenated compounds as terminal electron acceptors. OHR bacteria are strictly anaerobic microorganisms which use reductive dehalogenases (RdhA) as key enzymes ...

2012

A novel approach to find the missing links in genome-scale metabolic models: The BridgeIt mrthod

Vassily Hatzimanikatis, Keng Cher Soh, Marianne Seijo

Genome-scale metabolic reconstructions (GSMRs) are valuable resources in the analysis and understanding of cellular metabolism. They are based on genome sequence and annotation, and they are to develop bottom-up mathematical models of metabolic networks. T ...

2012

Metabolic control analysis of the central carbon pathway in optimally grown E. coli

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

The engineering of the metabolism requires the building of reliable kinetic models of the metabolic pathways through the integration of the information from heterogeneous data sources. Unfortunately, the quantitative knowledge about fluxes, mechanisms or k ...

2012

Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

Ana Jovicic

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression. The first miRNA was discovered less than 20 years ago in the context of studying Caenorabditis elegans development. The discovery of the second miR ...

EPFL2011

SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis

Ozgün Gökce, Heike Runne

Huntington's disease (HD), an incurable neurodegenerative disorder, has a complex pathogenesis including protein aggregation and the dysregulation of neuronal transcription and metabolism. Here, we demonstrate that inhibition of sirtuin 2 (SIRT2) achieves ...

National Academy of Sciences2010

Identification and characterization of proteins supporting dehalorespiration in Desulfitobacterium hafniense strain TCE1

Laure Prat

Respiration is a fundamental catalytic process in the aerobic and anaerobic energy metabolism of many prokaryotic and most eukaryotic organisms. The major difference between these organisms is that various organic and inorganic substrates can be used to do ...

EPFL2009

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