A5027579787- Evolution and Paleontology Studies
- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- Bioinformatics and Genomic Networks
- Genetic diversity and population structure
- semigroups and automata theory
- Gene Regulatory Network Analysis
- Morphological variations and asymmetry
- DNA and Biological Computing
- Gene expression and cancer classification
- Paleontology and Evolutionary Biology
- French Urban and Social Studies
- Paleontology and Stratigraphy of Fossils
- RNA and protein synthesis mechanisms
- Evolution and Genetic Dynamics
- Machine Learning in Bioinformatics
- Wildlife Ecology and Conservation
- Complex Network Analysis Techniques
- Tracheal and airway disorders
- Fractal and DNA sequence analysis
- Plant Diversity and Evolution
- Genome Rearrangement Algorithms
- Pleistocene-Era Hominins and Archaeology
- Nasal Surgery and Airway Studies
- Esophageal and GI Pathology
Centre National de la Recherche Scientifique
2015-2024
Université de Montpellier
2012-2024
Institut Polytechnique de Bordeaux
2015-2019
Centrale Marseille
2015-2019
Institut de Mathématiques de Marseille
1997-2018
Château Gombert
2016-2017
Aix-Marseille Université
2012-2016
SES (Luxembourg)
2016
Institut de Recherche Dupuy de Lôme
2001-2010
Institut de Neurobiologie de la Méditerranée
2008
Abstract Background In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss informationwhen parts alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. Results paper, HIV (Human Immunodeficiency Virus) SIV (Simian data used evaluate method. The...
Various biological networks can be constructed, each featuring gene/protein relationships of different meanings (e.g., protein interactions or gene co-expression). However, this diversity is classically not considered and the interaction categories are usually aggregated in a single network. The multiplex framework, where represented by network layers reflecting various nature interactions, expected to retain more information. Here we assessed aggregation, consensus multiplex-modularity...
Abstract Summary: GeneANOVA is an ANOVA-based software devoted to the analysis of gene expression data. Availability: freely available on request for non-commercial use. Contact: didier@genopole.cnrs.fr
Since the diversification process cannot be directly observed at human scale, it has to studied from information available, namely extant taxa and fossil record. In this sense, phylogenetic trees including both fossils are most complete representations of that one can get. Such reconstructed molecular morphological data, some extent. Among temporal such trees, ages by far precisely known (divergence times inferences calibrated mostly with fossils). We propose here a method compute likelihood...
Abstract Being given a phylogenetic tree of both extant and extinct taxa in which the fossil ages are only temporal information (namely, divergence times considered unknown), we provide method to compute exact probability distribution any time with regard speciation (cladogenesis), extinction, fossilization rates under Fossilized Birth–Death model. We use this new obtain for age Amniota (the synapsid/sauropsid or bird/mammal divergence), one most-frequently used dating constraints. Our...
In the last decade, Fossilized Birth-Death (FBD) process has yielded interesting clues about evolution of biodiversity through time. To facilitate such studies, we extend our method to compute probability density phylogenetic trees extant and extinct taxa in which only temporal information is provided by fossil ages (i.e. without divergence times) order deal with piecewise constant FBD process, known as "skyline FBD", allows rates change between pre-defined time intervals, well modelling...
Study of past biological crises is now a timely topic because we may be in the midst an anthropogenic mass extinction event. A skyline Fossilized Birth-Death (FBD) analysis dataset 21 varanopid taxa, ranging geological age from mid-Pennsylvanian to late Guadalupian, was undertaken assess impact putative events on Varanopidae. Our results suggest that this clade diversified Pennsylvanian but dwindled diversity Cisuralian. This reminiscent evolution biodiversity displayed by ophiacodontids,...
Abstract Phylogenetic comparative methods use random processes, such as the Brownian Motion, to model evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual motivated development complex models, often based Lévy processes. However, their statistical inference is computationally intensive and currently relies approximations, high-dimensional sampling, or numerical integration. We consider here Cauchy Process (CP), a particular pure-jump process in which trait...
Background As public microarray repositories are constantly growing, we facing the challenge of designing strategies to provide productive access available data. Methodology We used a modified version Markov clustering algorithm systematically extract clusters co-regulated genes from hundreds datasets stored in Gene Expression Omnibus database (n = 1,484). This approach led definition 18,250 transcriptional signatures (TS) that were tested for functional enrichment using DAVID knowledgebase....
Abstract Identification of modules in molecular networks is at the core many current analysis methods biomedical research. However, how well different approaches identify disease-relevant types gene and protein remains poorly understood. We launched “Disease Module DREAM Challenge”, an open competition to comprehensively assess module identification across diverse protein-protein interaction, signaling, co-expression, homology, cancer-gene networks. Predicted network were tested for...
<ns4:p>The identification of communities, or modules, is a common operation in the analysis large biological networks. The <ns4:italic>Disease Module Identification DREAM challenge</ns4:italic> established framework to evaluate clustering approaches biomedical context, by testing association communities with GWAS-derived trait and disease genes. We implemented here several extensions MolTi software that detects optimizing multiplex (and monoplex) network modularity. In particular, now runs...
A new compilation of the Old World fossil record Camelidae and a recent phylogenetic analysis allow assessment timing clade's diversification.Using implementation fossilized birth-death process, we show that divergence between Bactrian camel dromedary has peak probability density around 1 Ma probably occurred less than 2 million years ago.These dates are much younger molecular estimates, which place 4 8 ago.Calibration problems in dating seem to explain this difference.
<ns4:p>The identification of communities, or modules, is a common operation in the analysis large biological networks. The <ns4:italic>Disease Module Identification DREAM challenge</ns4:italic> established framework to evaluate clustering approaches biomedical context, by testing association communities with GWAS-derived trait and disease genes. We implemented here several extensions MolTi software that detects optimizing multiplex (and monoplex) network modularity. In particular, now runs...