Vassily Hatzimanikatis

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 47

Top Venues

Nature communications

PLoS computational biology

Bioinformatics (Oxford, England)

eLife

California Institute of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Education History

California Institute of Technology

United States

PHD :: Chemical Engineering

Publications

Marina Maurizio, Maria Masid, Kerry Woods, Reto Caldelari, John G Doench, Arunasalam Naguleswaran, Denis Joly, Martín González Fernández, Jonas Zemp, Mélanie Borteele, Vassily Hatzimanikatis, Volker T Heussler, Sven Rottenberg, Philipp Olias
Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites. Nature communications 15 (1) (2024)
Bharath Narayanan, Daniel Weilandt, Maria Masid, Ljubisa Miskovic, Vassily Hatzimanikatis
Rational strain design with minimal phenotype perturbation. Nature communications 15 (1) (2024)
Bharath Narayanan, Daniel Weilandt, Maria Masid, Ljubisa Miskovic, Vassily Hatzimanikatis
Rational strain design with minimal phenotype perturbation. Nature communications 15 (1) (2024)
Marina Maurizio, Maria Masid, Kerry Woods, Reto Caldelari, John G Doench, Arunasalam Naguleswaran, Denis Joly, Martín González Fernández, Jonas Zemp, Mélanie Borteele, Vassily Hatzimanikatis, Volker T Heussler, Sven Rottenberg, Philipp Olias
Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites. Nature communications 15 (1) (2024)
Bharath Narayanan, Daniel Weilandt, Maria Masid, Ljubisa Miskovic, Vassily Hatzimanikatis
Rational strain design with minimal phenotype perturbation. Nature communications 15 (1) (2024)
Marina Maurizio, Maria Masid, Kerry Woods, Reto Caldelari, John G Doench, Arunasalam Naguleswaran, Denis Joly, Martín González Fernández, Jonas Zemp, Mélanie Borteele, Vassily Hatzimanikatis, Volker T Heussler, Sven Rottenberg, Philipp Olias
Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites. Nature communications 15 (1) (2024)
Patrick A Sandoz, Robin A Denhardt-Eriksson, Laurence Abrami, Luciano Andrés Abriata, Gard Spreemann, Catherine Maclachlan, Sylvia Ho, Béatrice Kunz, Kathryn Hess, Graham William Knott, Francisco Sarmento Mesquita, Vassily Hatzimanikatis, F Gisou van der Goot
Dynamics of CLIMP-63 S-acylation control ER morphology. Nature communications 14 (1) (2023)
Patrick A Sandoz, Robin A Denhardt-Eriksson, Laurence Abrami, Luciano Andrés Abriata, Gard Spreemann, Catherine Maclachlan, Sylvia Ho, Béatrice Kunz, Kathryn Hess, Graham William Knott, Francisco Sarmento Mesquita, Vassily Hatzimanikatis, F Gisou van der Goot
Dynamics of CLIMP-63 S-acylation control ER morphology. Nature communications 14 (1) (2023)
Daniel R 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. Bioinformatics (Oxford, England) 39 (1) (2023)
Asli Sahin, Daniel R Weilandt, Vassily Hatzimanikatis
Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations. Nature communications 14 (1) (2023)
Daniel R 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. Bioinformatics (Oxford, England) 39 (1) (2023)
Patrick A Sandoz, Robin A Denhardt-Eriksson, Laurence Abrami, Luciano Andrés Abriata, Gard Spreemann, Catherine Maclachlan, Sylvia Ho, Béatrice Kunz, Kathryn Hess, Graham William Knott, Francisco Sarmento Mesquita, Vassily Hatzimanikatis, F Gisou van der Goot
Dynamics of CLIMP-63 S-acylation control ER morphology. Nature communications 14 (1) (2023)
Asli Sahin, Daniel R Weilandt, Vassily Hatzimanikatis
Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations. Nature communications 14 (1) (2023)
Patrick A Sandoz, Robin A Denhardt-Eriksson, Laurence Abrami, Luciano Andrés Abriata, Gard Spreemann, Catherine Maclachlan, Sylvia Ho, Béatrice Kunz, Kathryn Hess, Graham William Knott, Francisco Sarmento Mesquita, Vassily Hatzimanikatis, F Gisou van der Goot
Dynamics of CLIMP-63 S-acylation control ER morphology. Nature communications 14 (1) (2023)
Martin Schäfer, Alan R Pacheco, Rahel Künzler, Miriam Bortfeld-Miller, Christopher M Field, Evangelia Vayena, Vassily Hatzimanikatis, Julia A Vorholt
Metabolic interaction models recapitulate leaf microbiota ecology. Science (New York, N.Y.) 381 (6653) (2023)
Asli Sahin, Daniel R Weilandt, Vassily Hatzimanikatis
Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations. Nature communications 14 (1) (2023)
Asli Sahin, Daniel R Weilandt, Vassily Hatzimanikatis
Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations. Nature communications 14 (1) (2023)
Daniel R 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. Bioinformatics (Oxford, England) 39 (1) (2023)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Evangelia Vayena, Anush Chiappino-Pepe, Homa MohammadiPeyhani, Yannick Francioli, Noushin Hadadi, Meriç Ataman, Jasmin Hafner, Stavros Pavlou, Vassily Hatzimanikatis
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions. Proceedings of the National Academy of Sciences of the United States of America 119 (46) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Homa MohammadiPeyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. Nature communications 13 (1) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Subham Choudhury, Michael Moret, Pierre Salvy, Daniel Weilandt, Vassily Hatzimanikatis, Ljubisa Miskovic
Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks. Nature machine intelligence 4 (8) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charles E Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent J Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature communications 13 (1) (2022)
Liliana Angeles-Martinez, Vassily Hatzimanikatis
Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities. PLoS computational biology 17 (7) (2021)
Homa MohammadiPeyhani, Anush Chiappino-Pepe, Kiandokht Haddadi, Jasmin Hafner, Noushin Hadadi, Vassily Hatzimanikatis
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. eLife 10 (2021)
Jasmin Hafner, James Payne, Homa MohammadiPeyhani, Vassily Hatzimanikatis, Christina D Smolke
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. Nature communications 12 (1) (2021)
Liliana Angeles-Martinez, Vassily Hatzimanikatis
The influence of the crowding assumptions in biofilm simulations. PLoS computational biology 17 (7) (2021)
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 bioinformatics 22 (1) (2021)
Omid Oftadeh, Pierre Salvy, Maria Masid, Maxime Curvat, Ljubisa Miskovic, Vassily Hatzimanikatis
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics. Nature communications 12 (1) (2021)
Pierre Salvy, Vassily Hatzimanikatis
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nature communications 11 (1) (2020)
Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis
Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. ACS synthetic biology 9 (6) (2020)
Christian Lieven, Moritz Emanuel Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary A King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinglu, Gregory L Medlock, Jonathan M Monk, Jens B Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran Raosaheb Patil, Mark G Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
MEMOTE for standardized genome-scale metabolic model testing. Nature biotechnology 38 (3) (2020)
Maria Masid, Meriç Ataman, Vassily Hatzimanikatis
Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. Nature communications 11 (1) (2020)
Maria Masid, Meriç Ataman, Vassily Hatzimanikatis
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. Nature communications 11 (1) (2020)
Tuure Hameri, Marc-Olivier Boldi, Vassily Hatzimanikatis
Statistical inference in ensemble modeling of cellular metabolism. PLoS computational biology 15 (12) (2019)
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 computational biology 15 (4) (2019)
Ljubisa Miskovic, Jonas Béal, Michael Moret, Vassily Hatzimanikatis
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. PLoS computational biology 15 (8) (2019)
Vikash Pandey, Noushin Hadadi, Vassily Hatzimanikatis
Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. PLoS computational biology 15 (5) (2019)
Meric Ataman, Vassily Hatzimanikatis
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. PLoS computational biology 13 (7) (2017)
Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati, Vassily Hatzimanikatis
Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. PLoS computational biology 13 (3) (2017)
Meric Ataman, Daniel F Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS computational biology 13 (7) (2017)
Laurence Abrami, Tiziano Dallavilla, Patrick A Sandoz, Mustafa Demir, Béatrice Kunz, Georgios Savoglidis, Vassily Hatzimanikatis, F Gisou van der Goot
Identification and dynamics of the human ZDHHC16-ZDHHC6 palmitoylation cascade. eLife 6 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Vassily Hatzimanikatis