Author

Claire Rioualen

InsermORCID 0000-0002-7684-8679Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Research Focus:software / tool· 3 Organism:E. coli· 2 Approach:experimental assay· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Jacques van HeldeniD· 2 shared Julio Collado‐VidesiD· 2 shared Víctor H. TierrafríaiD· 2 shared Carol Smith· 1 shared César Bonavides-MartíneziD· 1 shared Christiane BouchieriD· 1 shared Dimitri DesvillechabroliD· 1 shared Gabriele BaniulyteiD· 1 shared

Activity by Year

2017-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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2 shared papersBioinformatics

Jacques van HeldenORCID

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4 papers

Recent·Most cited

Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli

Patrick Lally, Laura Gómez-Romero, Víctor H. Tierrafría, Patricia Aquino, Claire Rioualen, Xiaoman Zhang, Sunyoung Kim, Gabriele Baniulyte, Jonathan Plitnick, Carol Smith, Mohan Babu, Julio Collado‐Vides, Joseph T. Wade, James E. Galagan

The paper maps DNA binding of 139 E. coli TFs using ChIP-Seq and trains BoltzNet, a neural network that predicts TF binding energy from DNA sequence, validated with biophysical experiments.

Nature Communications · May 7, 2025Peer-reviewedBioinformatics

A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types

Paloma Lara, Socorro Gama‐Castro, Heladia Salgado, Claire Rioualen, Víctor H. Tierrafría, Luis Muñiz-Rascado, César Bonavides-Martínez, Julio Collado‐Vides

The paper analyzes the sources of evidence for transcription factor regulatory interactions in E. coli K-12, classifies them into seven groups, and evaluates confidence levels of interactions using high-throughput data.

bioRxiv · Feb 25, 2023 · PreprintGenomics

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer

Sequanix provides a graphical interface for Snakemake workflows to make them more accessible to a broader audience.

Bioinformatics · Jan 18, 2018Peer-reviewedBioinformatics

SnakeChunks: modular blocks to build Snakemakeworkflows for reproducible NGS analyses

Claire Rioualen, Lucie Khamvongsa-Charbonnier, Jacques van Helden

SnakeChunks provides modular Snakemake rules for reproducible NGS analyses, demonstrated on RNA-seq and ChIP-seq data.

bioRxiv · Jul 19, 2017 · PreprintBioinformatics