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Vassily Hatzimanikatis

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Publications associées (123)

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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

Production of biofuels and biochemicals: in need of an ORACLE

Vassily Hatzimanikatis, Ljubisa Miskovic

The engineering of cells for the production of fuels and chemicals involves simultaneous optimization of multiple objectives, such as specific productivity, extended substrate range and improved tolerance – all under a great degree of uncertainty. The achi ...

Elsevier2010

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri

Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...

BMC2021

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Daniel Robert Weilandt, Pierre Guy Rémy Salvy, David Michael Moret

Kinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme levels through mechanistic relations, rendering them essential for understanding, predicting and optimizing the behaviour of living organisms. However, due to the la ...

NATURE PORTFOLIO2022

Linear Solvation-energy Relationships (lser) and Equation-of-state Thermodynamics: on the Extraction of Thermodynamic Information From the Lser Database

Vassily Hatzimanikatis

There is a remarkable wealth of thermodynamic information in freely accessible databases, the LSER database being a classical example. The LSER, or Abraham solvation parameter model, is a very successful predictive tool in a variety of applications in the ...

MDPI2023

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

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Vassily Hatzimanikatis, Jasmin Maria Hafner

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

Nature Research2021

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

Vassily Hatzimanikatis, Meriç Ataman, Noushin Hadadi

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

Statistical inference in ensemble modeling of cellular metabolism

Vassily Hatzimanikatis, Marc-Olivier Boldi, Tuure Eelis Hameri

Kinetic models of metabolism can be constructed to predict cellular regulation and devise metabolic engineering strategies, and various promising computational workflows have been developed in recent years for this. Due to the uncertainty in the kinetic pa ...

2019

Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks

Vassily Hatzimanikatis

Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the ...

Elsevier2010

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

Vassily Hatzimanikatis, Maria Masid Barcon

Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related ...

Nature Portfolio2022

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Anush Chiappino-Pepe, Homa Mohammadi Peyhani

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

2021

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

Vassily Hatzimanikatis, Noushin Hadadi, Adrian Shajkofci, Jasmin Maria Hafner, Aikaterini Zisaki

Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computationa ...

Amer Chemical Soc2016

Group contribution method for thermodynamic analysis of complex metabolic networks

Vassily Hatzimanikatis

Anew, to our knowledge, group contribution method based on the group contribution method of Mavrovouniotis is introduced for estimating the standard Gibbs free energy of formation (Delta(f)G'(degrees)) and reaction (Delta(r)G'(degrees)) in biochemical syst ...

2008

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Vassily Hatzimanikatis

Background: Bioremediation offers a promising pollution treatment method in the reduction and elimination of man-made compounds in the environment. Computational tools to predict novel biodegradation pathways for pollutants allow one to explore the capabil ...

BioMed Central2010

Thermodynamic Analysis of Biodegradation Pathways

Vassily Hatzimanikatis

Microorganisms provide a wealth of bio-degradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental da ...

2009

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" -Part 2

Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Michaël Roger Germain Moret, Bharath Narayanan, David Michael Moret

Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" by S. Choudhury et al. The code to use with these da ...

Zenodo2023

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

Thermodynamics-Based Metabolic Flux Analysis

Vassily Hatzimanikatis

A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use ...

2007

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vassily Hatzimanikatis, Vikash Kumar Pandey

Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndromes spanning a wide spectrum of diseases, from simple steatosis to the more complex nonalcoholic steatohepatitis. To identify the deregulation that occurs in metabolic processes at ...

2019