Vassily Hatzimanikatis

27 papers C 1Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine.
PLoS Comput. Biol.
Evangelia Vayena, Lea Fuchs, Homa Mohammadi Peyhani, Konrad Lagoda, Bidong D. Nguyen, Wolf-Dietrich Hardt, Vassily Hatzimanikatis
2023 J jnl
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models.
Bioinform.
Daniel Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
2022 J jnl
Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks.
Nat. Mach. Intell.
Subham Choudhury, Michael Moret, Pierre Salvy, Daniel Weilandt, Vassily Hatzimanikatis, Ljubisa Miskovic
2021 J jnl
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs.
Bioinform.
Jasmin Hafner, Vassily Hatzimanikatis
2021 J jnl
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities.
PLoS Comput. Biol.
Liliana Angeles-Martinez, Vassily Hatzimanikatis
2021 J jnl
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli.
BMC Bioinform.
Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis
2021 J jnl
The influence of the crowding assumptions in biofilm simulations.
PLoS Comput. Biol.
Liliana Angeles-Martinez, Vassily Hatzimanikatis
2019 J jnl
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models.
PLoS Comput. Biol.
Vikash Pandey, Noushin Hadadi, Vassily Hatzimanikatis
2019 J jnl
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.
PLoS Comput. Biol.
Vikash Pandey, Vassily Hatzimanikatis
2019 J jnl
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH).
PLoS Comput. Biol.
Benedict Borer, Meriç Ataman, Vassily Hatzimanikatis, Dani Or
2019 J jnl
Statistical inference in ensemble modeling of cellular metabolism.
PLoS Comput. Biol.
Tuure Hameri, Marc-Olivier Boldi, Vassily Hatzimanikatis
2019 J jnl
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties.
PLoS Comput. Biol.
Ljubisa Miskovic, Jonas Béal, Michael Moret, Vassily Hatzimanikatis
2019 J jnl
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis.
Bioinform.
Pierre Salvy, Georgios Fengos, Meriç Ataman, Thomas Pathier, Keng C. Soh, Vassily Hatzimanikatis
2017 J jnl
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks.
PLoS Comput. Biol.
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis
2017 J jnl
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.
PLoS Comput. Biol.
Meriç Ataman, Vassily Hatzimanikatis
2017 J jnl
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.
PLoS Comput. Biol.
Meriç Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
2016 J jnl
Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.
PLoS Comput. Biol.
Tiziano Dallavilla, Laurence Abrami, Patrick A. Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis, F. Gisou van der Goot
2015 J jnl
Metabolic Needs and Capabilities of
PLoS Comput. Biol.
Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis
2013 J jnl
A Genome-Scale Integration and Analysis of
PLoS Comput. Biol.
Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis
2010 J jnl
In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene.
BMC Syst. Biol.
Stacey D. Finley, Linda J. Broadbelt, Vassily Hatzimanikatis
2010 J jnl
The Origins of Time-Delay in Template Biopolymerization Processes.
PLoS Comput. Biol.
Luis Mier-y-Teran-Romero, Mary Silber, Vassily Hatzimanikatis
2007 J jnl
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data.
BMC Bioinform.
Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis, Eleftherios T. Papoutsakis
2006 — conf
DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases.
ICASSP (2)
Sotirios A. Tsaftaris, Vassily Hatzimanikatis, Aggelos K. Katsaggelos
2005 J jnl
Exploring the diversity of complex metabolic networks.
Bioinform.
Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt
2005 J jnl
Preface.
Comput. Chem. Eng.
Costas D. Maranas, Vassily Hatzimanikatis
2004 J jnl
A model-based optimization framework for the inference on gene regulatory networks from DNA array data.
Bioinform.
Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis
2003 C conf
Modeling and control of intracellular processes.
ACC
Vassily Hatzimanikatis