Publications de Meriç Ataman | EPFL Graph Search

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

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Meriç Ataman, Anush Chiappino-Pepe, Homa Mohammadi Peyhani, Evangelia Vagena

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 ...

National Academy of Sciences2022

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

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 ...

2021

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

Vassily Hatzimanikatis, Meriç Ataman, Maria Masid Barcon

Altered metabolism is associated with many human diseases. Human genome-scale metabolic models (GEMs) were reconstructed within systems biology to study the biochemistry occurring in human cells. However, the complexity of these networks hinders a consiste ...

Nature Research2020

MEMOTE for standardized genome-scale metabolic model testing

Jens Nielsen, Vassily Hatzimanikatis, Cheng Zhang, Meriç Ataman, Georgios Fengos, Ali Kaafarani

NATURE PUBLISHING GROUP2020

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

Dani Or, Vassily Hatzimanikatis, Meriç Ataman

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 ...

2019

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri

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 ...

2019

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

Ljubisa Miskovic, Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman, Milenko Tokic

The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candi ...

2018

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

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

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

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 ...

Academic Press Inc Elsevier Science2017

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

Vassily Hatzimanikatis, Stepan Tymoshenko, Dominique Soldati-Favre, Meriç Ataman, Anush Chiappino-Pepe

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 ...

Public Library of Science2017

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

Vassily Hatzimanikatis, Meriç Ataman, Anush Chiappino-Pepe, Vikash Kumar Pandey

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 ...

2017

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

Vassily Hatzimanikatis, Meriç Ataman

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 ...

2017

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

Vassily Hatzimanikatis, Meriç Ataman, Daniel Federico Hernandez Gardiol, Georgios Fengos

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 ...

2017

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

Meriç Ataman

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 ...

EPFL2016

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

Konrad Hungerbühler, Vassily Hatzimanikatis, Meriç Ataman, Merten Morales

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 ...

Royal Soc Chemistry2016

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

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

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 ...

Royal Soc Chemistry2016

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

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 ...

Royal Soc Chemistry2015

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

Vassily Hatzimanikatis, Meriç Ataman

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 ...

Elsevier2015