Publication
Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways
Related publications (34)
Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information
Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...
WILEY-V C H VERLAG GMBH2023Modeling, analysis, and design of complex biological networks
Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...
EPFL2023Computational 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 LTD2022Data management and modelling of composite materials fatigue behavior
In this paper, we will present an update for the previously developed CCFatigue computational tool. This tool has been built around several analysis methods for fatigue life predictions of composite materials and includes modules that allow analysis over c ...
2021A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience
Daniel Keller, Andrii Stepaniuk
Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a ...
HUMANA PRESS INC2021redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast
Vassily Hatzimanikatis, Sofia Tsouka
Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...
OXFORD UNIV PRESS2020Towards Reliable Evaluation of Algorithms for Road Network Reconstruction from Aerial Images
Pascal Fua, Mateusz Kozinski, Leonardo Citraro
Existing connectivity-oriented performance measures rank road delineation algorithms inconsistently, which makes it difficult to decide which one is best for a given application. We show that these inconsistencies stem from design flaws that make the metri ...
2020Development of novel tools for imaging of metabolic fluxes in vivo
Bioluminescent imaging is a powerful technique that enables imaging in living organisms with high sensitivity, low background signal, low cost and without the need for radioactivity. The emitted photons are produced in the oxidation reaction of luciferin c ...
EPFL2020From Illich to Self-Tracking
Ivan Illich's research has accurately described the changing relationship between the experience of reading and the experience of the body. He sees the screen as a new tool for reading and begins to consider research hypotheses about this transformation. T ...
2020Modeling, predicting and mining metabolism at atom-level resolution
Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...
EPFL2020