A5052211659- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Microbial Community Ecology and Physiology
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Evolutionary Game Theory and Cooperation
- Fractal and DNA sequence analysis
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Photosynthetic Processes and Mechanisms
- Advanced Thermodynamics and Statistical Mechanics
- Mathematical and Theoretical Epidemiology and Ecology Models
- Fungal and yeast genetics research
- CRISPR and Genetic Engineering
- Digital Humanities and Scholarship
- Nonlinear Dynamics and Pattern Formation
- Wheat and Barley Genetics and Pathology
- Microbial Metabolic Engineering and Bioproduction
- Statistical Mechanics and Entropy
- Protein Structure and Dynamics
- Genomics and Chromatin Dynamics
- Quantum Mechanics and Applications
- Quantum chaos and dynamical systems
- Nuclear Structure and Function
- Machine Learning in Bioinformatics
Laboratoire de Biométrie et Biologie Evolutive
2015-2021
Université Claude Bernard Lyon 1
2015-2021
Centre National de la Recherche Scientifique
2015-2021
Cosmo Tech (France)
2018-2019
Stanford University
2012-2016
Rockford University
2013
Cosmote (Greece)
2013
National Centre of Scientific Research "Demokritos"
2007-2011
Molecular adaptation is typically assumed to proceed by sequential fixation of beneficial mutations. In diploids, this picture presupposes that for most adaptive mutations, the homozygotes have a higher fitness than heterozygotes. Here, we show contrary expectation, substantial proportion mutations should display heterozygote advantage. This feature in diploids emerges naturally from primary importance heterozygotes invasion new We formalize result framework Fisher's influential geometric...
Ciliates are unicellular eukaryotes with both a germline genome and somatic in the same cytoplasm. The macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from copy of micronucleus (MIC) at each sexual generation. In MIC Paramecium tetraurelia , genes interrupted by tens thousands unique intervening sequences called internal eliminated (IESs), which have to be precisely excised during development new MAC restore functional genes. To understand...
Abstract Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant fitness. Recently, we argued many adaptive might also be commonly overdominant Natural (directional) selection acting on should drive them into the population but then, instead of bringing fixation, maintain as balanced polymorphisms heterozygote advantage. If true, this would make evolution sexual differ drastically from haploids. The validity prediction has not yet been tested...
Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. cross-platform, perl/tcl-tk based, interactive front end designed break command line barrier introduce new user-friendly environment run simulations through Gromacs. Our GUI features novel workflow that guides each logical step of setup process, making it accessible both advanced novice users. This tool provides seamless Gromacs package, while...
Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well their colocalization with other genomic components. Here we investigate large-scale features Alu LINE1 spatial arrangement in human genome by studying size interrepeat distances. In most cases, have found power-law distributions extending several orders magnitude. We also correlations extent power law (linear region double-logarithmic scale) corresponding exponent (slope)...
Conserved, ultraconserved and other classes of constrained elements (collectively referred as CNEs here), identified by comparative genomics in a wide variety genomes, are non-randomly distributed across chromosomes. These defined using various degrees conservation between organisms several thresholds minimal length. We here investigate the chromosomal distribution studying statistical properties distances consecutive CNEs. find widespread power-law-like distributions, i.e. linearity double...
An understanding of the distribution natural patterns genetic variation is relevant to such fundamental biological fields as evolution and development. One recent approach has been focus on constraints that may arise a function network or pathway context in which genes are embedded. Despite theoretical expectations higher evolutionary constraint for encoding upstream versus downstream enzymes metabolic pathways, empirical results have varied. Here we combine two complementary models from...
Repeats or Transposable Elements (TEs) are highly repeated sequence stretches, present in virtually all eukaryotic genomes. We explore the distribution of representative TEs from major classes entire chromosomes across various organisms. employ two complementary approaches, scaling block entropy and box-counting. Both converge to conclusion that well-developed fractality is typical small genomes while large it appears sporadically some cases rudimentary. The human genome particularly prone...
Abstract Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and drug resistant pathogens. One approach to studying evolutionary predictability observe repeated, independent trajectories similar organisms under selection pressures in order empirically characterize this adaptive fitness landscape. As infeasible many natural systems, a number recent studies have attempted gain insight into landscape by testing plausibility different orders...
Abstract Ciliates are unicellular eukaryotes with both a germline genome and somatic in the same cytoplasm. The macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from copy of micronucleus (MIC) at each sexual generation. In MIC Paramecium tetraurelia , genes interrupted by tens thousands unique intervening sequences, called Internal Eliminated Sequences (IESs), that have to be precisely excised during development new MAC restore functional genes....
Predicting adaptive evolutionary trajectories is a primary goal of biology. One can differentiate between forward and backward predictability, where predictability measures the likelihood same trajectory occurring in independent evolutions particular path given knowledge starting final states. Recent studies have attempted to measure both using experimental evolution asexual haploid microorganisms. Similar experiments diploid organisms not been conducted. Here we simulate walks Fisher's...
ABSTRACT Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant fitness. Recently we argued many adaptive might also be commonly overdominant Natural (directional) selection acting on should drive them into the population but then, instead of bringing fixation, maintain as balanced polymorphisms heterozygote advantage. If true, this would make evolution sexual differ drastically from haploids. Unfortunately, validity prediction has not yet been...
The dynamics of complex systems far from their equilibrium state are currently not fully understood. Besides the theoretical interest for better understanding world around us this limitation has important practical implications to our ability model, understand and therefore manage control systems. In a first step non- improve model I implement cellular automaton gas mixing. simulate evolution towards starting macroscopic order as system evolves calculate Kolmogorov complexity, information...
Works of interactive fiction have been undergoing an expansive growth recently. However our understanding the laws and patterns governing their design, structure dynamics seem to be lagging behind. I here focus on sub-genre branching story books develop tools explore plot.