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

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Building a Knowledge Graph of Chinese Kung Fu Masters From Heterogeneous Bilingual Data

Various endeavours into semantic web technologies and ontology engineering have been made within the organisation of cultural data, facilitating public access to digital assets. Although models for conceptualising objects have reached a certain level of ma ...

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Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows

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The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and implementations ...

NATURE PORTFOLIO2023

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

Stochastic derivative estimation for max-stable random fields

Erwan Fabrice Koch

We consider expected performances based on max-stable random fields and we are interested in their derivatives with respect to the spatial dependence parameters of those fields. Max-stable fields, such as the Brown-Resnick and Smith fields, are very popula ...

ELSEVIER2022

NAD(+) Precursors: A Questionable Redundancy

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The last decade has seen a strong proliferation of therapeutic strategies for the treatment of metabolic and age-related diseases based on increasing cellular NAD(+) bioavailability. Among them, the dietary supplementation with NAD(+) precursors-classicall ...

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Data and Workflow to: Three-dimensional buoyant hydraulic fracture growth: constant release from a point source (Möri and Lecampion, (2022))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fracture growth: constant release from a point source" by Möri and Lecampion, (2022 ...

2022

Learning of Continuous and Piecewise-Linear Functions With Hessian Total-Variation Regularization

Michaël Unser, Shayan Aziznejad, Joaquim Gonçalves Garcia Barreto Campos

We develop a novel 2D functional learning framework that employs a sparsity-promoting regularization based on second-order derivatives. Motivated by the nature of the regularizer, we restrict the search space to the span of piecewise-linear box splines shi ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2022

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

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Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system work ...

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An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Laure Marie Colette Leynaud-Kieffer Curran

Many challenges are faced in the conversion of biomass into advanced biofuels, one of which is finding the correct organism for the job. The filamentous fungus Aspergillus niger has been chosen as a biocatalyst for cellulose, hemicellulose, and lignin degr ...

EPFL2021

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

Vassily Hatzimanikatis, Jasmin Maria Hafner

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 ...

OXFORD UNIV PRESS2021

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Data and Workflow to: Three-dimensional buoyant hydraulic fracture growth: constant release from a point source (Möri and Lecampion, (2022))

Brice Tanguy Alphonse Lecampion, Andreas Möri

2022

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

Vassily Hatzimanikatis, Jasmin Maria Hafner

OXFORD UNIV PRESS2021

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Laure Marie Colette Leynaud-Kieffer Curran

EPFL2021