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

Orchestrating chromosome conformation capture analysis with Bioconductor

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

IMPROVED REGULARITY OF SECOND DERIVATIVES FOR SUBHARMONIC FUNCTIONS

Riccardo Tione, Xavier Fernandez-Real Girona

In this note, we prove that if a subharmonic function Delta u >= 0 has pure second derivatives partial derivative(ii)u that are signed measures, then their negative part (partial derivative(ii)u)- belongs to L-1 (in particular, it is not singular). We then ...

Amer Mathematical Soc2023

Data and Workflow to: Three-dimensional buoyant hydraulic fractures: finite volume release (Möri and Lecampion, (2023))

Andreas Möri, Brice Tanguy Alphonse Lecampion

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fractures: finite volume release" by Möri and Lecampion, (2023). ...

Zenodo2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

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 ...

EPFL2023

Reactivity of Bromine Radical with Dissolved Organic Matter Moieties and Monochloramine: Effect on Bromate Formation during Ozonation

Urs von Gunten, Sung Eun Lim

Bromine radical (Br center dot) has been hypothesized to be a key intermediate of bromate formation during ozonation. Once formed, Br center dot further reacts with ozone to eventually form bromate. However, this reaction competes with the reaction of Br c ...

AMER CHEMICAL SOC2023

TiCl3-Mediated Reductive Cyclization of Tetrasubstituted Alkenes and Enol Esters Bearing a 2-Nitrophenyl Substituent

Dina Boyarskaya

Indole is one of the most important heterocycles widely present in bioactive natural products, pharmaceuticals, agrochemicals and materials. Being easily accessible, the 2-nitrostyrenes are attractive starting materials for the indole synthesis and the Cad ...

EPFL2023

Synthesis and Applications of Ynimines and Enantioselective Total Synthesis of Artatrovirenol A

Rémi Hugo Lavernhe

The first chapter of this thesis describe the development of a general synthesis of ynimines, an under-exploited motif in organic chemistry. In the presence of an inexpensive copper catalyst and 2,2'-biquinoline, reaction of easily accessible O-acyloximes ...

EPFL2023

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

Lin Yuan, Yumeng Hou

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 ...

2023

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

Giovanni Pizzi, Antimo Marrazzo, Miki Bonacci, Junfeng Qiao, Andrea Ferretti

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

Carlos Canto Alvarez

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 ...

MDPI2022

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

Andreas Möri, Brice Tanguy Alphonse Lecampion

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, Joaquim Gonçalves Garcia Barreto Campos, Shayan Aziznejad

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

Daniel Keller

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 ...

2022

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