Vassily Hatzimanikatis

According to our database, Vassily Hatzimanikatis authored at least 26 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2023

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models.

Daniel Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis

Bioinform., January, 2023

2022

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

Subham Choudhury, Michael Moret, Pierre Salvy, Daniel Weilandt, Vassily Hatzimanikatis, Ljubisa Miskovic

Nat. Mach. Intell., 2022

2021

The influence of the crowding assumptions in biofilm simulations.

Liliana Angeles-Martinez, Vassily Hatzimanikatis

PLoS Comput. Biol., 2021

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

Liliana Angeles-Martinez, Vassily Hatzimanikatis

PLoS Comput. Biol., 2021

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

Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis

BMC Bioinform., 2021

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

Jasmin Hafner, Vassily Hatzimanikatis

Bioinform., 2021

2019

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

Vikash Pandey, Noushin Hadadi, Vassily Hatzimanikatis

PLoS Comput. Biol., 2019

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.

Vikash Pandey, Vassily Hatzimanikatis

PLoS Comput. Biol., 2019

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties.

Ljubisa Miskovic, Jonas Béal, Michael Moret, Vassily Hatzimanikatis

PLoS Comput. Biol., 2019

Statistical inference in ensemble modeling of cellular metabolism.

Tuure Hameri, Marc-Olivier Boldi, Vassily Hatzimanikatis

PLoS Comput. Biol., 2019

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

Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or

PLoS Comput. Biol., 2019

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

Pierre Salvy, Georgios Fengos, Meriç Ataman, Thomas Pathier, Keng C. Soh, Vassily Hatzimanikatis

Bioinform., 2019

2017

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

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

PLoS Comput. Biol., 2017

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

Meriç Ataman, Vassily Hatzimanikatis

PLoS Comput. Biol., 2017

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

Meriç Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis

PLoS Comput. Biol., 2017

2016

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

Tiziano Dallavilla, Laurence Abrami, Patrick A. Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis, F. Gisou van der Goot

PLoS Comput. Biol., 2016

2015

Metabolic Needs and Capabilities of <i>Toxoplasma gondii </i> through Combined Computational and Experimental Analysis.

Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis

PLoS Comput. Biol., 2015

2013

A Genome-Scale Integration and Analysis of <i>Lactococcus lactis</i> Translation Data.

Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis

PLoS Comput. Biol., 2013

2010

The Origins of Time-Delay in Template Biopolymerization Processes.

Luis Mier-y-Teran-Romero, Mary Silber, Vassily Hatzimanikatis

PLoS Comput. Biol., 2010

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

Stacey D. Finley, Linda J. Broadbelt, Vassily Hatzimanikatis

BMC Syst. Biol., 2010

2007

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

Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis

BMC Bioinform., 2007

2006

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

Sotirios A. Tsaftaris, Vassily Hatzimanikatis, Aggelos K. Katsaggelos

Proceedings of the 2006 IEEE International Conference on Acoustics Speech and Signal Processing, 2006

2005

Preface.

Costas D. Maranas, Vassily Hatzimanikatis

Comput. Chem. Eng., 2005

Exploring the diversity of complex metabolic networks.

Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt

Bioinform., 2005

2004

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

Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis

Bioinform., 2004

2003

Modeling and control of intracellular processes.

Vassily Hatzimanikatis

Proceedings of the American Control Conference, 2003