Modeling and control of intracellular processes. - Vassily Hatzimanikatis (ACC, 2003)

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)

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)

Preface. - Costas D. Maranas; Vassily Hatzimanikatis (Comput. Chem. Eng., 2005)

DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases. - Sotirios A. Tsaftaris; Vassily Hatzimanikatis; Aggelos K. Katsaggelos (ICASSP (2), 2006)

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)

In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene. - Stacey D. Finley; Linda J. Broadbelt; Vassily Hatzimanikatis (BMC Syst. Biol., 2010)

The Origins of Time-Delay in Template Biopolymerization Processes. - Luis Mier-y-Teran-Romero; Mary Silber; Vassily Hatzimanikatis (PLoS Comput. Biol., 2010)

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data. - Julien Racle; Flora Picard; Laurence Girbal; Muriel Cocaign-Bousquet; Vassily Hatzimanikatis (PLoS Comput. Biol., 2013)

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. - Stepan Tymoshenko; Rebecca D. Oppenheim; Rasmus Agren; Jens Nielsen; Dominique Soldati-Favre; Vassily Hatzimanikatis (PLoS Comput. Biol., 2015)

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)

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)

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. - Meriç Ataman; Vassily Hatzimanikatis (PLoS Comput. Biol., 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)

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)

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)

Statistical inference in ensemble modeling of cellular metabolism. - Tuure Hameri; Marc-Olivier Boldi; 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)

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)

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)

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. - Jasmin Hafner; Vassily Hatzimanikatis (Bioinform., 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)

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities. - Liliana Angeles-Martinez; Vassily Hatzimanikatis (PLoS Comput. Biol., 2021)

The influence of the crowding assumptions in biofilm simulations. - Liliana Angeles-Martinez; Vassily Hatzimanikatis (PLoS Comput. Biol., 2021)

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)

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., 2023)

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine. - Evangelia Vayena; Lea Fuchs; Homa Mohammadi Peyhani; Konrad Lagoda; Bidong D. Nguyen; Wolf-Dietrich Hardt; Vassily Hatzimanikatis (PLoS Comput. Biol., 2025)