Publications HAL

2021/12 Scientific Reports – Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)

2021/12 Scientific Reports – MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach

2021/11 – Inferring cell cycle phases from a partially temporal network of protein interactions

2021/10 – An integrated analysis tool reveals intrinsic biases in gene set enrichment

2021/08 PLoS Computational Biology – A multi-objective genetic algorithm to find active modules in multiplex biological networks

2020/11 – A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

2019/12 – Population-based meta-heuristic for active modules identification

2019/09 Nature Methods – Assessment of network module identification across complex diseases

2019/05 Antimicrobial Agents and Chemotherapy – An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees

2018/07 Bioinformatics – Random walk with restart on multiplex and heterogeneous biological networks

2017/07 – Prediction of Disease-associated Genes by advanced Random Walk with Restart on Multiplex and Heterogeneous Biological Networks

2017/01 Journal of Discrete Algorithms – Designing optimal-and fast-on-average pattern matching algorithms

2016/04 BMC Biology – A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes

2015/01 G3 – Clone Mapper: An Online Suite of Tools for RNAi Experiments in Caenorhabditis elegans

2014/11 G3 – Clone Mapper: An Online Suite of Tools for RNAi Experiments in Caenorhabditis elegans

2014/01 Worm – ICeE an interface for C. elegans experiments

2013/01 BioSystems – Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters

2012/07 – Logical modelling of cellular decision processes with GINsim

2011/10 – ModClust: a Cytoscape plugin for modularity-based clustering of networks

2011/01 PLoS ONE – A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans

2009/12 Bioinformatics – SimCT: a generic tool to visualize ontology-based relationships for biological objects.

2009/06 – Dispersion sémantique dans des familles morpho-phonologiques : éléments théoriques et empiriques

2007/01 Journal of Discrete Algorithms – Local Similarity Between Quotiented Ordered Trees

2004/06 – Local Similarity Between Trees

2003/01 Theoretical Computer Science – R{NA} secondary structure comparison: exact analysis of the {Z}hang-{S}hasha tree edit algorithm