GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods

Publications associées (30)

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Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Cyril David Son-Tuyên Pulver, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Guido Van Mierlo, Judith Franziska Kribelbauer

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Media Coverage of 3D Visual Tools Used in Urban Participatory Planning

Jens Ingensand, Thibaud Nicolas Chassin

The opportunities provided by adopting digitally-generated visual tools in urban participatory planning are compelling. These visual tools can promote interactions between authorities and citizens and among citizens. However, the urban participatory practi ...

IGI GLOBAL2023

Numerical tools for burning plasmas

Jonathan Graves, Laurent Villard, Emmanuel Lanti, Baruch Rofman, Alberto Bottino, Ben McMillan, Xiao Wang, Emanuele Poli

The software stack under development within a European coordinated effort on tools for burning plasma modelling is presented. The project is organised as a Task (TSVV Task 10) under the new E-TASC initiative (Litaudon et al 2022 Plasma Phys. Control. Fusio ...

IOP Publishing Ltd2023

Understanding Revision Behavior in Adaptive Writing Support Systems for Education

Paola Mejia Domenzain, Luca Mouchel, Tanja Christina Käser Jacober, Thiemo Wambsganss

Revision behavior in adaptive writing support systems is an important and relatively new area of research that can improve the design and effectiveness of these tools, and promote students' self-regulated learning (SRL). Understanding how these tools are u ...

Zenodo2023

Digital Intervention for Collaborative and Human-Centered Activities in Design-Based Learning Scenarios

Denis Gillet, Isabelle Barbara Marie-Hélène Cardia

Training science and engineering students to become responsible citizens and professionals requires novel and creative pedagogical approaches, such as design thinking. This concept relies on processes and tools to develop creativity and problem-solving ski ...

IEEE2023

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Daniel Alexander Florez Orrego, Meire Ellen Gorete Ribeiro Domingos, Cédric Terrier, Michel Lopez

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

2023

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Marius Alexandru Botos Rogozsan

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Nature Portfolio2023

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ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Daniel Alexander Florez Orrego, Meire Ellen Gorete Ribeiro Domingos, Cédric Terrier, Michel Lopez

2023

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Marius Alexandru Botos Rogozsan

Nature Portfolio2023