Talk Author Index

TALK AUTHOR INDEX

Shortcuts: A B C D E F G H I J K L M N O P Q R S T U V W X Z

A
Ait El Hadj, Manel	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Allouch, Nina	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Andreeva, Antonina	The Pfam protein families database: embracing AI/ML
André, Catherine	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
André, Gwenaëlle	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Angel, Eric	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
Appé, Guillaume	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Assali, Ines	jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data
Audemard, Juliette	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Augé, Franck	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Azencott, Chloé Agathe	Variable selection in transcriptomics data using knockoffs in a classification framework
B
Baffo, Natacha	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Banon Garcia, Victor	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
Barbet, Pauline	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Bardet, Etienne	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
Baric, Marko	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Barillot, Emmanuel	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Barriot, Roland	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Barrot, Claire-Cécile	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic
Batantou Mabandza, Degrâce	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Bateman, Alex	The Pfam protein families database: embracing AI/ML
Batut, Bérénice	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Baudot, Anaïs	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Baum, Chloé	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Behdenna, Abdelkader	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Belda, Eugeni	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Belda, Eugeni	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Bellivier, Frank	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Belzeaux, Raoul	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Ben Hamida, Sana	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Benoist, Emile	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identiﬁes Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Benoit, Fantine	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Benoukraf, Touati	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
Bergk Pinto, Benoît	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Berland, Magali	OneNet—One network to rule them all: Consensus network inference from microbiome data
Berthelot, Camille	Natural selection acting on gene expression and regulation in mole-rats
Bessière, Chloé	Reindeer2: practical abundance index at scale
Besson, Aurore	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Bihouée, Audrey	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
Bileschi, Maxwell L	The Pfam protein families database: embracing AI/ML
Bittner, Lucie	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
Blum, Matthias	The Pfam protein families database: embracing AI/ML
Blum, Yuna	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Bolelli, Federico	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Bordron, Philippe	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
Bouri, Laurent	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Bouvier, Guillaume	Structural Space of Microproteins with Protein Language Models
Braikia, Houria	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Breurec, Sebastien	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Brière, Galadriel	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
C
Caceres-Delpiano, Javier	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
Cacheux, Lauriane	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Cadieu, Edouard	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Cadieu, Edouard	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Caetano, Tomas	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Campagne, Pascal	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Carpentier, Mathilde	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
Carrette, Camille	Gratools a tool for easy manipulation of GFA
Cartier, Julie	Variable selection in transcriptomics data using knockoffs in a classification framework
Cavalli, Florence	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Cazaux, Bastien	OReO: Optimizing Read Order for practical compression
Cazenave, Damien	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Champion, Camille	OneNet—One network to rule them all: Consensus network inference from microbiome data
Chapeaublanc, Elodie	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Chevaleyre, Yann	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Chica, Claudia	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Chuguransky, Sara Rocio	The Pfam protein families database: embracing AI/ML
Clementel, Damiano	The Pfam protein families database: embracing AI/ML
Cocco, Simona	SARS-CoV-2 viral evolution and antibody resilience
Cohen Boulakia, Sarah	Assessing bioinformatics software annotations : bio.tools case-study
Colajanni, Antonin	Metatranscriptomic classification in the study of microbial translocation
Colange, Maximilien	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Colwell, Lucy J	The Pfam protein families database: embracing AI/ML
Confais, Johann	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
Corre, Erwan	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Corre, Sébastien	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Cottret, Ludovic	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Couvin, David	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Creusot, Nicolas	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
D
Dallet, Romain	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Dameron, Olivier	Assessing bioinformatics software annotations : bio.tools case-study
Daunesse, Maëlle	Natural selection acting on gene expression and regulation in mole-rats
David, Ingrid	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
De Amorim, Camille	Searching for variable structural motifs in RNA graphs using simple descriptors
Degardins, Bastien	Vizitig: context-rich exploration of sequencing datasets
Delahaye-Duriez, Andrée	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder. Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic
Denecker, Thomas	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Denise, Alain	Searching for variable structural motifs in RNA graphs using simple descriptors
Derouin, Margot	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Derrien, Thomas	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Derrien, Thomas	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Dieuaide, Amanda	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Dillies, Marie-Agnès	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Dittami, Simon	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Diémé, Binta	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Dreo, Johann	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Droc, Gaetan	SynFlow: a Syri based interactive viewer
Dubreuil-Tranchant, Christine	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration Gratools a tool for easy manipulation of GFA
Dunne, Michael	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
Duprez, Estelle	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Duval, Charlotte	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Dyer, Matthew	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
E
Escande, Paul	jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data
Escudé, Christophe	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Essioux, Laurent	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Etain, Bruno	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Eveillard, Damien	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
F
Fagny, Maud	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Falentin, Hélène	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
Famechon, Alexandre	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Ferdinand, Séverine	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Fermanian, Adeline	Variable selection in transcriptomics data using knockoffs in a classification framework
Fertin, Guillaume	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identiﬁes Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Fichant, Gwennaele	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Fraboulet, Rose-Marie	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Frainay, Clément	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Fresnais, Louison	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Frioux, Clémence	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
G
Gaignard, Alban	Assessing bioinformatics software annotations : bio.tools case-study
Galibert, Marie-Dominique	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Gaspard-Boulinc, Lucie	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Gautheret, Daniel	Reindeer2: practical abundance index at scale
Gautreau, Guillaume	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Gaydukova, Ekaterina	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Girard, Mathilde	OReO: Optimizing Read Order for practical compression
Glaser, Philippe	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Gonay, Valentin	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
Gortana, Luca	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Got, Jeanne	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Goulet, Lindsay	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Goué, Nadia	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Grego, Tiago	The Pfam protein families database: embracing AI/ML
Grishin, Nick V	The Pfam protein families database: embracing AI/ML
Grüning, Björn	TBA
Gualdoni, Anakim	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Guerlais, Vincent	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Guglielmini, Julien	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Guichard, Anne	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Guschanski, Katerina	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
H
Haidamous, Anthony	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Halary, Sebastien	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Hamon-Giraud, Pauline	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Hergalant, Sébastien	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Herman, Simon	Structural Space of Microproteins with Protein Language Models
Hernandez Courbevoie, Yohan	Reindeer2: practical abundance index at scale
Hillion, Kenzo-Hugo	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Hiriart, Matéo	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Hitte, Christophe	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Hoffmann, Nicolaï	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Houel, Armel	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Hynninen, Johanna	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Hédan, Benoit	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
I
Ibrahim, El Chérif	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Isoviita, Veli-Matti	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
J
Jean, Géraldine	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identiﬁes Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Jensen, Axel	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Jourdan, Fabien	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Junier, Ivan	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
K
Kajava, Andrey	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
L
Lagoas, Johanna	Variable selection in transcriptomics data using knockoffs in a classification framework
Langenfeld, Florent	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
Lao, Julie	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Larmande, Pierre	Evaluating deep learning models for plant protein function prediction
Lavergne, Anne	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Lazaro Pinto, Beatriz	The Pfam protein families database: embracing AI/ML
Le, Quoc Khang	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
Le Bars, Victor	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Le Chatelier, Emmanuelle	OneNet—One network to rule them all: Consensus network inference from microbiome data
Le Chatelier, Emmanuelle	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Le Clanche, Ulysse	Assessing bioinformatics software annotations : bio.tools case-study
Le Corguillé, Gildas	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Le Cunff, Yann	Assessing bioinformatics software annotations : bio.tools case-study
Lefebvre, Marie	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Legeai, Fabrice	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Leloup, Julie	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Lemaitre, Claire	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Lespinet, Olivier	Structural Space of Microproteins with Protein Language Models
Limasset, Antoine	Reindeer2: practical abundance index at scale OReO: Optimizing Read Order for practical compression
Lin, Quy Xiao Xuan	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
Liotier, Marion	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Lisa, María-Natalia	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Llinares-López, Felipe	The Pfam protein families database: embracing AI/ML
Loire, Benjamin	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Lopes, Anne	Structural Space of Microproteins with Protein Language Models
Lorthiois, Matthias	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Lutz, Pierre-Eric	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
M
Maarala, Altti Ilari	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Maillet, Nicolas	AntiBody Sequence Database
Malesys, Simon	AntiBody Sequence Database
Marchet, Camille	Vizitig: context-rich exploration of sequencing datasets Reindeer2: practical abundance index at scale
Mareuil, Fabien	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Mariadassou, Mahendra	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data OneNet—One network to rule them all: Consensus network inference from microbiome data
Marie, Benjamin	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Marie-Claire, Cynthia	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Marin, Pierre	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Markov, Gabriel	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Marthe, Nina	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph Gratools a tool for easy manipulation of GFA
Marthey, Sylvain	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Mary-Huard, Tristan	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Massip, Florian	Variable selection in transcriptomics data using knockoffs in a classification framework
Mathé, Meije	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Medigue, Claudine	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Meng-Papaxanthos, Laetitia	The Pfam protein families database: embracing AI/ML
Messak, Imane	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Meunier, Léa	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Meyre, David	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Michau, Thomas-Sylvestre	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Mignon, Thomas	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Millot, Gaël	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Mohammed, Mourdas	Gratools a tool for easy manipulation of GFA
Mokhtari, Amazigh	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Momal, Raphaëlle	OneNet—One network to rule them all: Consensus network inference from microbiome data
Monlong, Jean	Integrating structural variants in genomic studies of rare and complex diseases with long-read sequencing and pangenomes
Mornico, Damien	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Mouffok, Mohamed	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Muller, Coralie	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Muranen, Taru	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Ménager, Hervé	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Mérot, Claire	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
N
N'Guyen, Lia	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Najm, Matthieu	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Nanema, Romaric K.	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Necsulea, Anamaria	Deciphering the genomic basis of convergent phenotypic evolution
Nerriere, Virginie	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Nguyen, Hoang Ha	Evaluating deep learning models for plant protein function prediction
Niarakis, Anna	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Nordor, Akpéli	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Néron, Bertrand	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
O
Oikkonen, Jaana	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Ortet, Philippe	Models for protein domain embedding
P
Papadopoulos, Christos	Structural Space of Microproteins with Protein Language Models
Paperman, Charles	Vizitig: context-rich exploration of sequencing datasets
Parey, Elise	Natural selection acting on gene expression and regulation in mole-rats
Paré, Louis	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
Paysan-Lafosse, Typhaine	The Pfam protein families database: embracing AI/ML
Perrière, Guy	Models for protein domain embedding
Pety, Solène	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
Philippe, Cathy	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Pichon, Julien	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Pietrosemoli, Natalia	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Pipoli, Vittorio	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Pita, Justin S.	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Plaza Oñate, Florian	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Ponger, Loïc	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Poplineau, Mathilde	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Postic, Guillaume	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
Pot, Matthieu	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Prifti, Edi	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Prifti, Edi	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Q
Quesneville, Hadi	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
Quetel, Isaure	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Quinquis, Benoît	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
R
Rau, Andrea	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
Ravel, Sebatien	Gratools a tool for easy manipulation of GFA
Redder, Peter	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Remy, Elisabeth	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Reynaud, Yann	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Rivals, Éric	Selection of test instances for string algorithms
Robert, Noé	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
Roginski, Paul	Structural Space of Microproteins with Protein Language Models
Rogniaux, Hélène	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identiﬁes Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Romano, Fabien	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic
Rousseau, Baptiste	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Rousseau, Coralie	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Rousseau, Jérémy	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
Roy, Gaspar	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Rukoz, Marta	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Ruppé, Etienne	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Rusakovich, Anastasia	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Réda, Clémence	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
S
Sabot, François	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph Gratools a tool for easy manipulation of GFA
Salazar, Gustavo	The Pfam protein families database: embracing AI/ML
Salson, Mikaël	Reindeer2: practical abundance index at scale
Sanchez-Villanueva, Jose-Antonio	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Sarah, Gautier	SynFlow: a Syri based interactive viewer
Saunier, Bertrand	AntiBody Sequence Database
Sauvestre, Clément	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
Schaeffer, R Dustin	The Pfam protein families database: embracing AI/ML
Schwikowski, Benno	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Schymanski, Emma	Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
Seiler, Julien	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Siegel, Anne	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Siguret, Cléa	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Silly, Louison	Models for protein domain embedding
Sola, Mathilde	OneNet—One network to rule them all: Consensus network inference from microbiome data
Sonnhammer, Erik	The Pfam protein families database: embracing AI/ML
Stosskopf, Thomas	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Summo, Marilyne	SynFlow: a Syri based interactive viewer
T
Tackx, Raphaël	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Tahi, Fariza	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
Temperville, Mélody	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Tessier, Dominique	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identiﬁes Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Thebault, Patricia	Metatranscriptomic classification in the study of microbial translocation
Thiebaut, Rodolphe	Metatranscriptomic classification in the study of microbial translocation
Thieffry, Denis	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy. MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
Thomas, François	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Tibiri, Ezechiel B.	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Tiendrebeogo, Fidèle	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Tirera, Sourakhata	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Toffano, Antoine	Evaluating deep learning models for plant protein function prediction
Torchet, Rachel	AntiBody Sequence Database
Tosatto, Silvio C E	The Pfam protein families database: embracing AI/ML
U
Uricaru, Raluca	Metatranscriptomic classification in the study of microbial translocation
V
Vandamme, Lea	OReO: Optimizing Read Order for practical compression
Varoquaux, Nelle	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
Vedy, Serge	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Vie, Jill-Jênn	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
Vigo, Elora	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Villar, Diego	Natural selection acting on gene expression and regulation in mole-rats
Villoutreix, Paul	jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data
Vu, Minh Ngoc	Evaluating deep learning models for plant protein function prediction
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Walter, Thomas	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Wan, Mariène	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
Weill, Solène	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Wolkenhauer, Olaf	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
Wood, Valerie	The Pfam protein families database: embracing AI/ML
X
Xue, Haoliang	Reindeer2: practical abundance index at scale
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Zagury, Jean-François	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
Zerrouk, Naouel	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Zucker, Jean-Daniel	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Zytnicki, Matthias	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph