JOBIM 2024: JOURNéES OUVERTES DE BIOLOGIE, INFORMATIQUE ET MATHéMATIQUES 2024

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Abdeddaïm, Saïd	Graph representation learning and semantic distribution: application to omic expression data
Alcraft, Rachel	Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis
Amblard, Elise	Constructing a robust framework to benchmark deconvolution algorithms
Andre, Caherine	“PhaseImpute” an NF-Core pipeline for genetic imputation
Andre, Catherine	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
André, Idriss	Graph representation learning and semantic distribution: application to omic expression data
Arndt, Peter	Modeling the mosaic structure of bacterial genomes to infer their evolutionary history
Asloudj, Yanis	scEVE: a scRNA-seq ensemble clustering algorithm that leverages the extrinsic variability to prevent over-clustering.
Aubin, Emilie	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Augé, Franck	Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis AttOmics: Attention-based architecture for diagnosis and prognosis from Omics data
Aury, Jean-Marc	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Azencott, Chloé-Agathe	Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm
B
Baaden, Marc	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Bailly-Bechet, Marc	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Balaramane, Delphine	MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole- genome datasets
Ballester, Benoit	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues
Bardet, Anaïs Flore	MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole- genome datasets
Baric, Marko	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Beaude, Aurélien	AttOmics: Attention-based architecture for diagnosis and prognosis from Omics data
Beaumont, Chloé	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Beauvoit, Bertrand	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Belda, Eugeni	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Belser, Caroline	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Bernard, Clement	RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Bernot, Gilles	Improving Snoussi constraints in the Thomas framework for Gene Networks
Bertrand, Vadim	Constructing a robust framework to benchmark deconvolution algorithms
Besson, Aurore	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Blum, Yuna	Constructing a robust framework to benchmark deconvolution algorithms
Bonath, Franziska	nf-core a community dedicated to best-practices Nextflow workflows
Bottini, Silvia	Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data
Bouarroudj, Lisa	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Boury, Théo	Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique
Bretaudeau, Anthony	Misconceptions about Galaxy debunked by the (French) Galaxy Community
Bricout, Raphaël	Can we Predict Evolution?
Brun, Christine	InteractORF, prediction of human sORF functions from an interactome study.
C
Cadieu, Edouard	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Calteau, Alexandra	MicroScope: 20 years of expertise in microbial genomics
Carillo, Petronia	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Carpentier, Mathilde	Origins and Functional Significance of Eukaryotic Protein Folds
Cassan, Cédric	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Castandet, Benoît	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Chaillou, Stéphane	Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Chavent, Matthieu	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Chiapello, Helene	Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Chomilier, Jacques	Origins and Functional Significance of Eukaryotic Protein Folds
Choteau, Sébastien	InteractORF, prediction of human sORF functions from an interactome study.
Chuffart, Florent	codabench, a web-plateform to organize scientific competitions
Coffion, Lucie	MicroScope: 20 years of expertise in microbial genomics
Colombié, Sophie	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Comet, Jean-Paul	Improving Snoussi constraints in the Thomas framework for Gene Networks
Coulpier, Fanny	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Cros, Jerome	Constructing a robust framework to benchmark deconvolution algorithms
D
Da Rocha, Martine	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Danchin, Etienne G.J.	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
De Langen, Pierre	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues
Delannoy, Etienne	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Delemotte, Lucie	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Dell'Aversana, Emilia	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Derrien, Thomas	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Despot-Slade, Evelin	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Dreo, Johann	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Dubois, Mathieu	MicroScope: 20 years of expertise in microbial genomics
Déjean, Sébastien	localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
E
Ebler, Jana	Pangenome graph construction from genome alignments with Minigraph-Cactus
Eizenga, Jordan	Pangenome graph construction from genome alignments with Minigraph-Cactus
El Baidouri, Moaine	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Espinosa-Carrasco, Jose	nf-core a community dedicated to best-practices Nextflow workflows
Ewels, Phil	nf-core a community dedicated to best-practices Nextflow workflows
F
Fellows Yates, James A	nf-core a community dedicated to best-practices Nextflow workflows
Flicek, Paul	Using data science to build a bridge from model systems to human disease
Fouteau, Stéphanie	MicroScope: 20 years of expertise in microbial genomics
François, Olivier	hdmax2, an R package to perform high dimension mediation analysis
Frioux, Clémence	Exploration of microbial ecosystems: from compositional patterns to metabolic models
G
Gabaldón, Toni	Tracing genomic adaptations in emerging fungal pathogens
Gabernet, Gisela	nf-core a community dedicated to best-practices Nextflow workflows
Gao, Yan	Pangenome graph construction from genome alignments with Minigraph-Cactus
Garcia, Maxime	nf-core a community dedicated to best-practices Nextflow workflows
Garcia, Steven	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Garrigue, Joseph	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Gautreau, Guillaume	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Gaydukova, Ekaterina	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Genin-Lajus, Aurélie	MicroScope: 20 years of expertise in microbial genomics
Genovesio, Auguste	Can we Predict Evolution?
Ghannay, Sahar	RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Gibon, Yves	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Gilbault, Elodie	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Goulet, Lindsay	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Grataloup, Guillaume	Improving Snoussi constraints in the Thomas framework for Gene Networks
Gueret, Elise	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues
Guichaoua, Gwenn	Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm
Guyon, Isabelle	codabench, a web-plateform to organize scientific competitions
H
Hakkaart, Christopher	nf-core a community dedicated to best-practices Nextflow workflows
Hall, Benjamin A.	Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis
Hammal, Fayrouz	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues
Hamraoui, Ali	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Hanczar, Blaise	AttOmics: Attention-based architecture for diagnosis and prognosis from Omics data
Hanssen, Friederike	nf-core a community dedicated to best-practices Nextflow workflows
Hassanaly-Goulamhoussen, Rahim	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Hedan, Benoit	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Hickey, Glenn	Pangenome graph construction from genome alignments with Minigraph-Cactus
Hilbert-Masson, Ghislaine	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Hitte, Christophe	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Hoffmann, Brice	Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm
Houel, Armel	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Howard, Rebecca J.	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Hörtenhuber, Matthias	nf-core a community dedicated to best-practices Nextflow workflows
J
Jumentier, Basile	hdmax2, an R package to perform high dimension mediation analysis
Junker, Romane	Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
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Karkar, Slim	Constructing a robust framework to benchmark deconvolution algorithms
Koutsovoulos, Georgios D	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Kozlowski, Djampa K	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
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Labadie, Karine	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Labory, Justine	Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data
Laine, Elodie	From sequences to fitness and motions, protein language models to the rescue?
Laudy, Claire	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Launay-Avon, Alexandra	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Le Bars, Victor	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Le Chatelier, Emmanuelle	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Le Crom, Stephane	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Le Nézet, Louis	“PhaseImpute” an NF-Core pipeline for genetic imputation
Lecointre, Guillaume	Origins and Functional Significance of Eukaryotic Protein Folds
Lemoine, Sophie	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Lepeule, Johanna	hdmax2, an R package to perform high dimension mediation analysis
Letournel, Anne-Catherine	codabench, a web-plateform to organize scientific competitions
Li, Heng	Pangenome graph construction from genome alignments with Minigraph-Cactus
Libouban, Romane	Misconceptions about Galaxy debunked by the (French) Galaxy Community
Liehrmann, Arnaud	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Lindahl, Erik	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Lindorff-Larsen, Kresten	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Llauro, Christel	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Lobentanzer, Sebastian	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Lorthiois, Matthias	Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility
Loudet, Olivier	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
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Marchall, Tobias	Pangenome graph construction from genome alignments with Minigraph-Cactus
Martin Pena, Luis	Constructing a robust framework to benchmark deconvolution algorithms
Massip, Florian	Modeling the mosaic structure of bacterial genomes to infer their evolutionary history
McCubbin, Tim	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Mercier, Eva	Misconceptions about Galaxy debunked by the (French) Galaxy Community
Mercier, Sabine	localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
Meštrović, Nevenka	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Miller, Edmund	nf-core a community dedicated to best-practices Nextflow workflows
Mir Pedrol, Júlia	nf-core a community dedicated to best-practices Nextflow workflows
Mirouze, Marie	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Mistou, Michel-Yves	Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Moing, Annick	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Monlong, Jean	Pangenome graph construction from genome alignments with Minigraph-Cactus
Mougin, Fleur	scEVE: a scRNA-seq ensemble clustering algorithm that leverages the extrinsic variability to prevent over-clustering.
Mourad, Raphael	Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences
Mouren, Jean-Christophe	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues
Médigue, Claudine	MicroScope: 20 years of expertise in microbial genomics
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Nakamura, Aurélie	hdmax2, an R package to perform high dimension mediation analysis
Niarakis, Anna	Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis
Nielsen, Lars Keld	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Njomgue-Fotso, Evariste	Benchmarking feature selection and feature extraction methods to improve the performances of machine-learning algorithms for patient classification using metabolomics biomedical data
Noel, Benjamin	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Novak, Adam M.	Pangenome graph construction from genome alignments with Minigraph-Cactus
O
Ollivier, Louis	Beyond Recombination: Exploring the Impact of Meiotic Frequency on Genome-wide Genetic Diversity
Onfroy, Audrey	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Oussaren, Mohamed	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
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Panaud, Olivier	When lianas and trees talk DNA: new insights into genetic exchanges in plants
Patel, Harshil	nf-core a community dedicated to best-practices Nextflow workflows
Paten, Benedict	Pangenome graph construction from genome alignments with Minigraph-Cactus
Perfus-Barbeoch, Laetitia	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Pierre, Philippe	InteractORF, prediction of human sORF functions from an interactome study.
Pinel, Philippe	Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm
Pittion, Florence	hdmax2, an R package to perform high dimension mediation analysis
Plaza Oñate, Florian	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Ponty, Yann	Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique
Postic, Guillaume	RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Poulain, Pierre	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Pouyet, Fanny	Beyond Recombination: Exploring the Impact of Meiotic Frequency on Genome-wide Genetic Diversity
Prifti, Edi	CroCoDeEL: accurate detection of cross-sample contamination in metagenomic data
Prigent, Sylvain	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Péré, Arthur	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
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Quignon, Pascale	“PhaseImpute” an NF-Core pipeline for genetic imputation
R
Rafiee Vahid, Milad	AttOmics: Attention-based architecture for diagnosis and prognosis from Omics data
Rancurel, Corinne	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Reinharz, Vladimir	Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique
Renaud, Christel	Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth- defence trade-off
Ribeiro-Dantas, Marcel	nf-core a community dedicated to best-practices Nextflow workflows
Richard, Magali	codabench, a web-plateform to organize scientific competitions hdmax2, an R package to perform high dimension mediation analysis Constructing a robust framework to benchmark deconvolution algorithms
Rigaill, Guillem	DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection
Robbe-Sermesant, Karine	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Robelin, David	localScore: an R package to highlight optimal and suboptimal segment in a sequence with associated p-values computation
Roche, David	MicroScope: 20 years of expertise in microbial genomics
Roest Crollius, Hugues	Can we Predict Evolution?
Romei, Martin	Origins and Functional Significance of Eukaryotic Protein Folds
Rouy, Zoé	MicroScope: 20 years of expertise in microbial genomics
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Schwikowski, Benno	Intégration reproductible d’informations de haut niveau dans des graphes de connaissances sémantiques avec OntoWeaver et BioCypher, applications en oncologie et en écologie
Senamaud-Beaufort, Catherine	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Sheinman, Michael	Modeling the mosaic structure of bacterial genomes to infer their evolutionary history
Slivak, Mathilde	InteractORF, prediction of human sORF functions from an interactome study.
Soualmia, Lina	Graph representation learning and semantic distribution: application to omic expression data
Spill, Yannick	MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole- genome datasets
Spinelli, Lionel	Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues InteractORF, prediction of human sORF functions from an interactome study.
Stam, Mark	MicroScope: 20 years of expertise in microbial genomics
Stoven, Véronique	Advancing Drug-Target Interactions Prediction: Leveraging a Large-Scale Dataset with a Rapid and Robust Chemogenomic Algorithm
Szczuka, Magdalena	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
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Tahi, Fariza	RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Thebault, Patricia	scEVE: a scRNA-seq ensemble clustering algorithm that leverages the extrinsic variability to prevent over-clustering.
Thomas-Chollier, Morgane	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
Tiemann, Johanna K. S.	MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Topilko, Piotr	A benchmark study of bioinformatics methods for single cell RNA-seq Nanopore long reads data
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Valence, Florence	Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Vallenet, David	MicroScope: 20 years of expertise in microbial genomics
Varoquaux, Nelle	Machine Learning Adventures in Biology: Overcoming Hurdles and Harvesting Biological Insights
Vergne, Nicolas	Graph representation learning and semantic distribution: application to omic expression data
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Weber, Michaël	MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole- genome datasets
Wincker, Patrick	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
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Zanzoni, Andreas	InteractORF, prediction of human sORF functions from an interactome study.
Zehraoui, Farida	AttOmics: Attention-based architecture for diagnosis and prognosis from Omics data
Zerrouk, Naouel	Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis
Zotta Mota, Ana Paula	Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

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