Publication
Modeling, analysis, and design of complex biological networks
Related publications (74)
Computational study of transcription factor binding sites
Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the necessary information that the organism will ever need, from its development to a mature individual to environment specific resp ...
EPFL2020Modeling metabolic and signaling pathways in cancer cells
Cancer is a leading cause of death in the world, and the mechanisms that underlie this disease are still not completely understood. As cancer develops and progresses, cells undergo a diversity of mutations that sustain their rapid proliferation and the eva ...
EPFL2020redLips: 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 PRESS2020Methylation of arsenic by single-species and soil-derived microbial cultures
Arsenic (As) is simultaneously a ubiquitous and a toxic element. Arsenic is subject to bio-transformations catalyzed by microorganisms constituting the As biogeochemical cycle. The primordial Earth was devoid of oxygen, exposing life to the highly mobile a ...
EPFL2020Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Noushin Hadadi, Vikash Kumar Pandey, Anush Chiappino-Pepe, Merten Morales, Florence Mehl
Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation re ...
NATURE PUBLISHING GROUP2020Noninvasive rapid detection of metabolic adaptation in activated human T lymphocytes by hyperpolarized 13C magnetic resonance
Mor-Miri Mishkovsky, Arnaud Comment, Hikari Ananda Infinity Yoshihara, Nicolas Kunz, Emine Can
The metabolic shift induced in human CD4+ T lymphocytes by stimulation is characterized by an upregulation of glycolysis, leading to an augmentation in lactate production. This adaptation has already been highlighted with various techniques and reported in ...
2020Towards comprehensive and consistent kinetic models of metabolism under uncertainty
Metabolism is the sum of the chemical interactions occurring inside a cell that process nutrients into cellular constituents and energy. Research in the recent decades has enabled the characterization of metabolic reaction networks for multiple organisms. ...
EPFL2019RDHK Family, Regulators dedicated to Organohalide Respiration - Sequence Diversity and Functional Prediction
Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin
Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy from the use of organohalide molecules as terminal electron acceptors. Because most organohalides of anthropogenic origin are persistent pollutants, the study of ba ...
2019RDHK Family, Regulators dedicated to Organohalide Respiration - Sequence Diversity and Functional Prediction
Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin
Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy from the use of organohalide molecules as terminal electron acceptors. Because most organohalides of anthropogenic origin are persistent pollutants, the study of ba ...
2019Identifying microbial species by single-molecule DNA optical mapping and resampling statistics
Theo Lasser, Aleksandra Radenovic, Arno Pino Bouwens, Tomas Lukes, Adrien Charles-François Raymond Descloux, Kristin Stefanie Grussmayer, Jochem Deen
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to p ...
2019