Vassily Hatzimanikatis

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Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

Iron is essential for most living organisms. In addition, its biogeochemical cycling influences important processes in the geosphere (e.g., the mobilization or immobilization of trace elements and contaminants). The reduction of Fe(III) to Fe(II) can be ca ...

A key player in the formation of endoplasmic reticulum sheets is CLIMP-63, but mechanistic details remained elusive. Here authors combined cellular experiments and mathematical modelling to show that S-acylation of CLIMP-63 regulates its function by mediat ...

Bimetallic Ru–Ni and Rh–Ni nanocatalysts coated with a phase transfer agent efficiently cleave aryl ether C–O linkages in water in the presence of hydrogen. For dimeric substrates with weaker C–O linkages, i.e. α-O-4 and β-O-4 bonds, low loadings of the pr ...

Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project ...

The central objective of this work is to revisit the development of the widely used Lewis acidity/basicity scales and seek possibilities for their eventual unification. The primary focus is on hydrogen bonding interactions which are dealt with the estimati ...

Dataset supporting the results presented in the paper entitled "Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production" by Narayanan, Jiang & Wang et al (https://doi.org/10.1016/j.ymben.2025.06.008). Dataset ...

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Escherichia coli-based bioreporters for arsenic detection are typically based on the natural feedback loop that controls ars operon transcription. Feedback loops are known to show a wide range linear response to the detriment of the overall amplification o ...

Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We ...

The synthesis of many important biochemicals involves complex molecules and numerous reactions. The design and optimization of whole-cell biocatalysts for the production of these molecules requires metabolic modeling to extract production pathways from bio ...

Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the co ...

Devising genetic interventions for desired cellular phenotypes remains challenging regarding time and resources. Kinetic models can accelerate this task by simulating metabolic responses to genetic perturbations. However, exhaustive design evaluations with ...

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...

Nontyphoidal Salmonella strains (NTS) are among the most common foodborne enteropathogens and constitute a major cause of global morbidity and mortality, imposing a substantial burden on global health. The increasing antibiotic resistance of NTS bacteria h ...

Designing putative metabolic pathways is of great interest in synthetic biology. Retrobiosynthesis is a discipline that involves the design, evaluation, and optimization of de novo biosynthetic pathways for the production of high-value compounds and drugs ...

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chem ...

This month: AI that learns patterns and facts, new protein-RNA and protein-protein relationships, engineering signaling and metabolism, and more variants of Cas9. ...

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 ...

Vassily Hatzimanikatis

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Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

Dynamics of CLIMP-63 S-acylation control ER morphology

Efficient cleavage of aryl ether C–O linkages by Rh–Ni and Ru–Ni nanoscale catalysts operating in water

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

On Lewis acidity/basicity and hydrogen bonding in the equation-of-state approach

Dataset - Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

Metabolic interaction models recapitulate leaf microbiota ecology

Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Rational strain design with minimal phenotype perturbation

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

Principles of Systems Biology, No. 11

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