Computational Framework for Predictive Biodegradation

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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 ...

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Author summary In nature, many organisms grow in crowded biofilms that protect against stressful conditions, making their control/eradication a challenge. Modeling these microbial systems is a valuable tool for studying the interactions among cells and exp ...

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive ad ...

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each ...

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

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 ...

New drugs are needed to assure effective therapies for previously untreated diseases, emerging diseases, and personalized medicine, but the process of drug development is complex, costly, and time-consuming. This is especially problematic considering that ...

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

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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 ...

Background: Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for impro ...

Energy transfer reactions occur in all areas of chemistry. One fundamental form of this is demonstrated by reactions in which an electronically excited atom transfers energy to a neutral, resulting in spontaneous ionisation, potentially combined with compl ...

Computational Framework for Predictive Biodegradation

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Modeling, analysis, and design of complex biological networks

Acetal-Stabilized Carbohydrates as Novel Platform Molecules for Renewable Polymer Production

Computational tools and resources for designing new pathways to small molecules

Sustainable polyesters via direct functionalization of lignocellulosic sugars

The influence of the crowding assumptions in biofilm simulations

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Constraint-based metabolic control analysis for rational strain engineering

New and improved methods for integrated models of metabolism and gene expression

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Modeling, predicting and mining metabolism at atom-level resolution

Algorithms and flowchart for the design of synthetic biochemical networks

Optimization methods and objective functions for analysis of metabolic network models

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Modeling metabolic and signaling pathways in cancer cells

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

The stereodynamics of ion forming reactions