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Vassily Hatzimanikatis
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2020 – today
- 2023
- [j24]Daniel Weilandt, Pierre Salvy, Maria Masid
, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models. Bioinform. 39(1) (2023) - 2022
- [j23]Subham Choudhury, Michael Moret
Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks. Nat. Mach. Intell. 4(8): 710-719 (2022) - 2021
- [j22]Jasmin Hafner
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. Bioinform. 37(20): 3560-3568 (2021) - [j21]Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli. BMC Bioinform. 22(1): 134 (2021) - [j20]Liliana Angeles-Martinez, Vassily Hatzimanikatis
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities. PLoS Comput. Biol. 17(7) (2021) - [j19]Liliana Angeles-Martinez, Vassily Hatzimanikatis
The influence of the crowding assumptions in biofilm simulations. PLoS Comput. Biol. 17(7) (2021)
2010 – 2019
- 2019
- [j18]Pierre Salvy
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. Bioinform. 35(1): 167-169 (2019) - [j17]Vikash Pandey, Vassily Hatzimanikatis
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. 15(4) (2019) - [j16]Vikash Pandey, Noushin Hadadi
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. PLoS Comput. Biol. 15(5) (2019) - [j15]Benedict Borer
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH). PLoS Comput. Biol. 15(6) (2019) - [j14]Ljubisa Miskovic
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PLoS Comput. Biol. 15(8) (2019) - [j13]Tuure Hameri
Statistical inference in ensemble modeling of cellular metabolism. PLoS Comput. Biol. 15(12) (2019) - 2017
- [j12]Anush Chiappino-Pepe
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. PLoS Comput. Biol. 13(3) (2017) - [j11]Meriç Ataman
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS Comput. Biol. 13(7) (2017) - [j10]Meriç Ataman
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. PLoS Comput. Biol. 13(7) (2017) - 2016
- [j9]Tiziano Dallavilla
Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin. PLoS Comput. Biol. 12(2) (2016) - 2015
- [j8]Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PLoS Comput. Biol. 11(5) (2015) - 2013
- [j7]Julien Racle
A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data. PLoS Comput. Biol. 9(10) (2013) - 2010
- [j6]Stacey D. Finley
In silico feasibility of novel biodegradation pathways for 1, 2, 4-trichlorobenzene. BMC Syst. Biol. 4: 7 (2010) - [j5]Luis Mier-y-Teran-Romero, Mary Silber, Vassily Hatzimanikatis
The Origins of Time-Delay in Template Biopolymerization Processes. PLoS Comput. Biol. 6(4) (2010)
2000 – 2009
- 2007
- [j4]Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Vassily Hatzimanikatis
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinform. 8 (2007) - 2006
- [c2]Sotirios A. Tsaftaris, Vassily Hatzimanikatis, Aggelos K. Katsaggelos:
DNA Hybridization as a Similarity Criterion for Querying Digital Signals Stored in DNA Databases. ICASSP (2) 2006: 1084-1087 - 2005
- [j3]Vassily Hatzimanikatis
Exploring the diversity of complex metabolic networks. Bioinform. 21(8): 1603-1609 (2005) - [j2]Costas D. Maranas
Preface. Comput. Chem. Eng. 29(3): 405-406 (2005) - 2004
- [j1]Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis
A model-based optimization framework for the inference on gene regulatory networks from DNA array data. Bioinform. 20(17): 3221-3235 (2004) - 2003
- [c1]Vassily Hatzimanikatis:
Modeling and control of intracellular processes. ACC 2003: 2077-2078
Coauthor Index
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