A5091754272- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- vaccines and immunoinformatics approaches
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- Biochemical and Structural Characterization
- RNA Research and Splicing
- Lipid metabolism and biosynthesis
- Microbial Natural Products and Biosynthesis
- Antibiotic Resistance in Bacteria
- Fungal and yeast genetics research
- Antibiotic Use and Resistance
- Machine Learning in Bioinformatics
- SARS-CoV-2 and COVID-19 Research
Laboratoire de Biologie Computationnelle et Quantitative
2021-2022
Centre National de la Recherche Scientifique
2021-2022
Institut de Biologie Paris-Seine
2021-2022
Sorbonne Université
2021-2022
Spanish National Cancer Research Centre
2015-2017
Significance During the COVID pandemic, new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerge and spread, some being of major concern due to their increased infectivity or capacity reduce vaccine efficiency. Anticipating mutations, which might give rise variants, would be great interest. We construct sequence models predicting how mutable SARS-CoV-2 positions are, using a single databases other coronaviruses. Predictions are tested against available mutagenesis...
The APPRIS database (http://appris-tools.org) uses protein structural and functional features information from cross-species conservation to annotate splice isoforms in protein-coding genes. selects a single isoform, the 'principal' as reference for each gene based on these annotations. A main isoform reflects biological reality most coding genes principal are best predictors of proteins isoforms. Here, we present updates database, new developments that include addition three species...
Alternative splicing of messenger RNA can generate a wide variety mature transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression alternative same not true alternatively spliced products. Large-scale mass spectroscopy experiments have identified at level, but conflicting results. Here we carried out rigorous analysis peptide from eight large-scale proteomics to assess scale that detectable by...
Significance Interacting proteins tend to coevolve through interdependent changes at the interaction interface. This phenomenon leads patterns of coordinated mutations that can be exploited systematically predict contacts between interacting in prokaryotes. We explore hypothesis coevolving protein interfaces are preferentially conserved long evolutionary periods. demonstrate residues prokaryotes identify interprotein particularly well corresponding structure their eukaryotic homologues....
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous proteins, to propose stochastic models experimental protein evolution. These predict quantitatively important features experimentally evolved libraries, like distributions position-specific mutational spectra. They also allow us efficiently simulate libraries a...
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis in most peptides is not well understood. Here, we provide biochemical bioinformatic evidence support role a unique class condensation domains dehydration (CmodAA). We also obtain crystal structure CmodAA domain, which part peptide synthetase AmbE antibiotic methoxyvinylglycine. Biochemical...
Abstract Protein-protein interactions are fundamental for the proper functioning of cell. As a result, protein interaction surfaces subject to strong evolutionary constraints. Recent developments have shown that residue co-evolution provides accurate predictions heterodimeric interfaces from sequence information. So far these approaches been limited analysis families prokaryotic complexes which large multiple alignments homologous sequences can be compiled. We explore hypothesis points...