Vassily Hatzimanikatis

发表

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

Maria Masid, Meric Ataman, Vassily Hatzimanikatis, 2020, Nature Communications.

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

Vassily Hatzimanikatis, Tiziano Dallavilla, Laurence Abrami, 2016, PLoS Comput. Biol..

Session 8 - The Role of Chemical Engineers in Bioinformatics and Systems Biology World (Invited)

Babatunde A. Ogunnaike, Michael W. Deem, Ranjan Srivastava, 2004 .

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Stefano Andreozzi, 2012 .

Identification of steady-state genetic networks: linear vs. non-linear models, simulation-optimization based inference methods, missing genes and network architecture

Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis, 2006 .

Exploration of signaling cycles using dynamic optimization

Benoît Chachuat, Vassily Hatzimanikatis, Andrijana Radivojevic, 2010 .

A Novel Approach to Design of Metabolic Engineering Strategiesa

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, 2014 .

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

Vassily Hatzimanikatis, Meriç Ataman, Anush Chiappino-Pepe, 2017, PLoS Comput. Biol..

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Salvy, V. Hatzimanikatis, 2020, Nature Communications.

Uncertainty Reduction in Biochemical Kinetic Models: Enforcing Desired Model Properties

Ljubisa Miskovic, Vassily Hatzimanikatis, Michael Moret, 2019 .

Editorial: Metabolic modeling in biotechnology and medical research

Vassily Hatzimanikatis, Diethard Mattanovich, 2013, Biotechnology journal.

Modeling and control of intracellular processes

Vassily Hatzimanikatis, 2003, Proceedings of the 2003 American Control Conference, 2003..

How uncertainty in kinetic parameters affects metabolic control analysis of optimally grown E.coli

Ljubisa Miskovic, Vassily Hatzimanikatis, Georgios Fengos, 2016 .

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Vikash Pandey, Noushin Hadadi, 2019, PLoS Comput. Biol..

Context-specific cell signaling analysis using logic framework

Vassily Hatzimanikatis, Vikash Pandey, 2017 .

Exploring the diversity of complex metabolic networks

Chunhui Li, Linda J. Broadbelt, Christopher S. Henry, 2005, Bioinform..

MEMOTE for standardized genome-scale metabolic model testing

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2020, Nature Biotechnology.

The Origins of Time-Delay in Template Biopolymerization Processes

Vassily Hatzimanikatis, Mary Silber, Luis Mier-y-Teran-Romero, 2010, PLoS Comput. Biol..

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Ljubisa Miskovic, Vassily Hatzimanikatis, Michael Moret, 2019, PLoS Comput. Biol..

iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

Ljubisa Miskovic, Vassily Hatzimanikatis, Stefano Andreozzi, 2016, Metabolic engineering.

Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes

Ljubisa Miskovic, Vassily Hatzimanikatis, Michaël Roger Germain Moret, 2016 .

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

Vassily Hatzimanikatis, Thomas Pathier, Georgios Fengos, 2018, Bioinform..

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

Vassily Hatzimanikatis, Pierre Salvy, V. Hatzimanikatis, 2019, bioRxiv.

BIOT 329-Analysis of genome-scale metabolic model of mycobacterium tuberculosis for new combat strategies

Vassily Hatzimanikatis, Keng Cher Soh, M. Emre Oezdemir, 2009 .

Model Classification for Uncertainty Reduction in Biochemical Kinetic Models

Ljubisa Miskovic, Vassily Hatzimanikatis, Jonas Béal, 2018, bioRxiv.

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2018, bioRxiv.

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Meric Ataman, Vassily Hatzimanikatis, 2020, bioRxiv.

Exploring enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Ljubisa Miskovic, Vassily Hatzimanikatis, Stefano Andreozzi, 2015 .

Extracting networks from expression data

Vassily Hatzimanikatis, Eleftherios T. Papoutsakis, 2005 .

A model-based optimization framework for the inference on gene regulatory networks from DNA array data

Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis, 2004, Bioinform..

Analysis and synthesis of novel metabolic pathways

Elizabeth Brunk, Marilisa Neri, Vassily Hatzimanikatis, 2009 .

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

Linda J. Broadbelt, Vassily Hatzimanikatis, Stacey D. Finley, 2010, BMC Systems Biology.

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Jens Nielsen, Vassily Hatzimanikatis, Rasmus Agren, 2015, PLoS Comput. Biol..

The effects of model complexity and size on metabolic flux distribution and control. Case study in E. coli

Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri, 2019, bioRxiv.

A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data

Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis, 2007, BMC Bioinformatics.

Statistical inference in ensemble modeling of cellular metabolism

Vassily Hatzimanikatis, Tuure Hameri, Marc-Olivier Boldi, 2019, PLoS Comput. Biol..

BIOT 57-Network-based optimization of protein production

Vassily Hatzimanikatis, Jan Overney, Hermioni Zouridis, 2009 .

BIOT 375-Analysis and synthesis of novel metabolic pathways

Elizabeth Brunk, Marilisa Neri, Vassily Hatzimanikatis, 2009 .

Production of biofuels and biochemicals: in need of an ORACLE.

Ljubisa Miskovic, Vassily Hatzimanikatis, V. Hatzimanikatis, 2010, Trends in biotechnology.

The design of “Super E. coli” through automated reaction network generation and genome scale models

Vassily Hatzimanikatis, Keng Cher Soh, Noushin Hadadi, 2014 .

Bioinformatics, genomics, and the chemical engineer: a perspective

Vassily Hatzimanikatis, David Collins, Shawn Lawrence, 2000 .

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

Vassily Hatzimanikatis, Meriç Ataman, M. Ataman, 2017, PLoS Comput. Biol..

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

Vassily Hatzimanikatis, Georgios Fengos, Meriç Ataman, 2017, PLoS Comput. Biol..

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

Ljubisa Miskovic, Vassily Hatzimanikatis, Georgios Savoglidis, 2019, bioRxiv.

Set-membership Estimation, Analysis, and Experimental Design for Biological Systems

Rolf Findeisen, Vassily Hatzimanikatis, Fabian Theis, 2013 .

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

Vassily Hatzimanikatis, Julien Racle, Flora Picard, 2013, PLoS Comput. Biol..

Kinetic models in industrial biotechnology - Improving cell factory performance.

Marija Cvijovic, Mats Jirstrand, Vassily Hatzimanikatis, 2014, Metabolic engineering.

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

Vassily Hatzimanikatis, Meriç Ataman, Dani Or, 2019, PLoS Comput. Biol..

Large-scale dynamic models of metabolic networks

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, 2012 .

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases

Aggelos K. Katsaggelos, Sotirios A. Tsaftaris, Vassily Hatzimanikatis, 2006, 2006 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings.

Introduction to Metabolic Engineering Communications

Vassily Hatzimanikatis, Ryan T. Gill, 2014 .

Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh, 2012 .

Metabolic engineering under uncertainty. I: framework development.

Vassily Hatzimanikatis, Liqing Wang, V. Hatzimanikatis, 2006, Metabolic engineering.

Preface

Vassily Hatzimanikatis, Costas D. Maranas, V. Hatzimanikatis, 2005, Comput. Chem. Eng..

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

Konrad Hungerbühler, Stavros Papadokonstantakis, Vassily Hatzimanikatis, 2016 .

Engineering improved productivity of 1,4-butanediol in E. coli – a kinetic modeling approach

Ljubisa Miskovic, Vassily Hatzimanikatis, Stefano Andreozzi, 2014 .

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 Pandey, 2019, PLoS Comput. Biol..

Stochastic noise in translation

Vassily Hatzimanikatis, Julien Racle, Adam Jan Stefaniuk, 2011 .

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate–product pairs

Vassily Hatzimanikatis, Jasmin Hafner, V. Hatzimanikatis, 2020, bioRxiv.

Network-based optimization of protein production

Vassily Hatzimanikatis, Jan Overney, Hermioni Zouridis, 2009 .

Final Technical Report DE-FG02-02ER63457

Linda J. Broadbelt, Vassily Hatzimanikatis, 2009 .

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

Vassily Hatzimanikatis, Liliana Angeles-Martinez, V. Hatzimanikatis, 2021, PLoS Comput. Biol..

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

Vassily Hatzimanikatis, Georgios Fengos, Tuure Hameri, 2021, BMC Bioinformatics.

Bistability explains threshold phenomena in protein aggregation both in vitro and in vivo.

Theodore R Rieger, Vassily Hatzimanikatis, V. Hatzimanikatis, 2006, Biophysical journal.

Integrating computational methods to retrofit enzymes to synthetic pathways

Elizabeth Brunk, Ivano Tavernelli, Ursula Rothlisberger, 2012, Biotechnology and bioengineering.

Thermodynamic analysis of biodegradation pathways

Vassily Hatzimanikatis, Stacey D. Finley, Linda J Broadbelt, 2009, Biotechnology and bioengineering.

An algorithmic framework for genome-wide modeling and analysis of translation networks.

Vassily Hatzimanikatis, V. Hatzimanikatis, A. Mehra, 2006, Biophysical journal.

Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes.

Vassily Hatzimanikatis, Kelvin H. Lee, J. Bailey, 2002, Biotechnology and bioengineering.

Effects of codon distributions and tRNA competition on protein translation.

Vassily Hatzimanikatis, V. Hatzimanikatis, Hermioni Zouridis, 2008, Biophysical journal.

Insights into the relation between mrna and protein expression patterns: ii. Experimental observations in Escherichia coli 1

Vassily Hatzimanikatis, Leah B Shaw, Kelvin H Lee, 2003, Biotechnology and bioengineering.

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

Vassily Hatzimanikatis, V. Hatzimanikatis, Davide Merulla, 2013, Microbial biotechnology.

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

Vassily Hatzimanikatis, Keng Cher Soh, Noushin Hadadi, 2017, Biotechnology journal.

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

Vassily Hatzimanikatis, Oliver Hantschel, Georg E. Fantner, 2017, Nucleic acids research.

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Ljubisa Miskovic, Vassily Hatzimanikatis, Noushin Hadadi, 2019, Proceedings of the National Academy of Sciences.

Discovery of Novel Routes for the Production of Fuels and Chemicals

Linda J. Broadbelt, Christopher S. Henry, Vassily Hatzimanikatis, 2009 .

Insights into the relation between mRNA and protein expression patterns: I. theoretical considerations

Vassily Hatzimanikatis, Kelvin H Lee, Kelvin H. Lee, 2003, Biotechnology and bioengineering.

A computational framework for the design of optimal protein synthesis

Vassily Hatzimanikatis, Jan Overney, Julien Racle, 2012, Biotechnology and bioengineering.

Mathematical modeling of the eukaryotic heat-shock response: dynamics of the hsp70 promoter.

Theodore R Rieger, Vassily Hatzimanikatis, V. Hatzimanikatis, 2005, Biophysical journal.

A method for pulsed periodic optimization of chemical reaction systems

Vassily Hatzimanikatis, Gerasimos Lyberatos, Spyros A. Svoronos, 1993 .

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

Gregory Stephanopoulos, Vassily Hatzimanikatis, Noushin Hadadi, 2017, Metabolic engineering.

Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways.

Vassily Hatzimanikatis, Linda J Broadbelt, V. Hatzimanikatis, 2005, Journal of the American Chemical Society.

Constraining the flux space using thermodynamics and integration of metabolomics data.

Vassily Hatzimanikatis, Keng Cher Soh, Keng C. Soh, 2014, Methods in molecular biology.

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Lars M Blank, 2017, bioRxiv.

Computational discovery of biochemical routes to specialty chemicals

Linda J. Broadbelt, Christopher S. Henry, Vassily Hatzimanikatis, 2004 .

Computational framework for predictive biodegradation

Vassily Hatzimanikatis, Stacey D. Finley, Linda J Broadbelt, 2009, Biotechnology and bioengineering.

A computational framework for integration of lipidomics data into metabolic pathways.

Vassily Hatzimanikatis, Noushin Hadadi, V. Hatzimanikatis, 2014, Metabolic engineering.

Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks.

Vassily Hatzimanikatis, Daniel A Beard, Anne Kümmel, 2010, Biophysical journal.