Vassily Hatzimanikatis

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Publications associées (124)

A NON-CD25-BINDING IL-2 VARIANT FOR THE EXPANSION OR ENGINEERING OF T CELLS THAT CONFER SUPERIOR TUMOR CONTROL

Vassily Hatzimanikatis, Maria Masid Barcon, Thomas Muller

Mary Ann Liebert, Inc2023

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

Vassily Hatzimanikatis, Maria Masid Barcon, Ming Yang

Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related ...

Nature Portfolio2022

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt, Pierre Guy Rémy Salvy

Kinetic models of metabolism relate metabolic fluxes, metabolite concentrations and enzyme levels through mechanistic relations, rendering them essential for understanding, predicting and optimizing the behaviour of living organisms. However, due to the la ...

NATURE PORTFOLIO2022

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Vassily Hatzimanikatis, Anastasia Sveshnikova

Synthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope ...

2022

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

Vassily Hatzimanikatis, Georgios Fengos, Maria Masid Barcon, Daniel Robert Weilandt, Zhaleh Hosseini, Pierre Guy Rémy Salvy

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

OXFORD UNIV PRESS2022

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Anastasia Sveshnikova, Victor Luc Etienne Viterbo

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line w ...

Zenodo2022

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Vassily Hatzimanikatis, Meriç Ataman, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Evangelia Vagena, Noushin Hadadi, Anush Chiappino-Pepe

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annot ...

National Academy of Sciences2022

Editorial Overview: Mathematical modeling: It's a matter of scale

Vassily Hatzimanikatis, Stacey Deleria Finley

ELSEVIER2021

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Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova

Zenodo2022