Publications by Meriç Ataman | EPFL Graph Search

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Natural soil is characterized as a complex habitat with patchy hydrated islands and spatially variable nutrients that is in a constant state of change due to wetting-drying dynamics. Soil microbial activity is often concentrated in sparsely distributed hot ...

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other t ...

Novel antimalarial therapies are urgently needed for the fight against drug-resistant para- sites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this co ...

The expanding generation of dynamic biological data requires approaches that integrate and analyze information from different types of cellular processes –metabolism, regulation, and signaling–, and ultimately increase our insights into the cell behavior u ...

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional ...

The present work is part of a series of papers aiming at a thorough understanding of the thermodynamics of metabolism over a broad range of external conditions. The focus here is on the systematic study of solvation/hydration of a variety of fluids via an ...

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network ...

Over the past few years, bio-succinic acid from renewable resources has gained increasing attention as a potential bio-derived platform chemical for the detergent/surfactant, ion chelator, food and pharmaceutical markets. Until now, much research was under ...

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

Metabolism is a network of biochemical reactions that converts carbon sources to cellu-lar fuels and building blocks. Metabolism of many organisms has been studied for many decades. These studies define metabolism as a very large and complex network. Stoic ...

Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the co ...

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chem ...

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annot ...

Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hen ...

Meriç Ataman

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Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Integration of Metabolic, Regulatory and Signaling Networks Towards Analysis of Perturbation and Dynamic Responses

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering

Constraint-based metabolic control analysis for rational strain engineering

Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

MEMOTE for standardized genome-scale metabolic model testing