A5089115213- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- Monoclonal and Polyclonal Antibodies Research
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- vaccines and immunoinformatics approaches
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- Marine Biology and Ecology Research
- Protist diversity and phylogeny
- CAR-T cell therapy research
- Mycobacterium research and diagnosis
- Immunodeficiency and Autoimmune Disorders
- Infectious Diseases and Mycology
- Data Quality and Management
- Parasitic Infections and Diagnostics
- Biomedical Text Mining and Ontologies
- Invertebrate Immune Response Mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Biomedical and Engineering Education
Station Biologique de Roscoff
2024
Sorbonne Université
2011-2023
Laboratoire de Biologie Computationnelle et Quantitative
2011-2023
Centre National de la Recherche Scientifique
2011-2023
Institut de Biologie Paris-Seine
2016-2018
Universidade Federal do Rio de Janeiro
2007-2015
Centro de Tecnologia Mineral
2011
Laboratório Nacional de Computação Científica
2008
Universidade do Porto
1991
The absorption of visible light in aquatic environments has led to the common assumption that organisms sense and adapt penetrative blue/green wavelengths but show little or no response more attenuated red/far-red wavelengths. Here, we two marine diatom species, Phaeodactylum tricornutum Thalassiosira pseudonana, possess a bona fide sensing phytochrome (DPH) uses biliverdin as chromophore displays accentuated red-shifted absorbance peaks compared with other characterized plant algal...
Biochemical and regulatory pathways have until recently been thought modelled within one cell type, organism species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing role symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires reconstruction at community level a given environment. In order to understand how environmental factors affect genetic material dynamics expression from...
Abstract B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian selection, generating a large BCR-antibody diversity. This process, known as affinity maturation, increases antibody affinity, forming specific lineage that includes the unmutated ancestor mutated variants. In lineage, cells with higher will clonal expansion, while those lower not proliferate probably be eliminated. Therefore, cellular (genotype) abundance provides valuable perspective on...
Abstract Motivation: Given a protein sequence and number of potential domains matching it, what are the domain content most likely architecture for sequence? This problem is fundamental importance in annotation, constituting one main steps all predictive annotation strategies. On other hand, when several conflict because overlapping boundaries, finding solution might become difficult. An accurate prediction multi-domain provides important information function prediction, comparative genomics...
An important problem in computational biology is the automatic detection of protein families (groups homologous sequences). Clustering sequences into at heart most comparative studies dealing with evolution, structure, and function. Many methods have been developed for this task, they perform reasonably well (over 0.88 F-measure) when grouping proteins high sequence identity. However, highly diverged performance these can be much lower, mainly because a common evolutionary origin not deduced...
Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences. However, when relevant signals become too weak to be identified by a global consensus, attempts for fail. Here we address the fundamental question of identification highly divergent proteins. By using high performance computing, demonstrate that limits state-of-the-art can bypassed. We design new strategy based on observation many structural and...
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and bridge the gap between education research. mimics setup of research projects takes advantage most popular tools cloud computing. Students are grouped teams 4–5 people have realize project from A Z answers challenging question biology. promotes "coopetition," as collaborate within across also competition with each other develop best final product. fosters...
Recombination systems are widely used as bioengineering tools, but their sites have to be highly similar a consensus sequence or each other. To develop recombination system free of these constraints, we turned toward attC from the bacterial integron system: single-stranded DNA hairpins specifically recombined by integrase. Here, present an algorithm that generates synthetic with conserved structural features and minimal sequence-level constraints. We demonstrate all generated functional,...
The nuclear proteome of Plasmodium falciparum results from the continual shuttle proteins between cell cytoplasm-nucleus and vice versa. Using shotgun proteomics tools, we explored mixed populations extracted infected erythrocytes. We combined GeLC-MS/MS 2D-LC-MS/MS with a peptide ion exclusion procedure in order to increase detection low abundant such as those involved gene expression. have identified 446 covering all expected protein families regulation. All structural ribosomal (40S 60S)...
Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches addressing this important problem. pHMM packages present relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises question whether structural alignments could impact performance pHMMs trained from proteins Twilight Zone, as often more accurate than sequence identifying motifs...
Abstract Background The Structural Descriptor Database (SDDB) is a web-based tool that predicts the function of proteins and functional site positions based on structural properties related protein families. alignments residues known set (defined as training set) are used to build special Hidden Markov Models (HMM) called HMM descriptors. SDDB uses previously calculated stored descriptors for predicting active sites, binding residues, function. database integrates biologically relevant data...
Abstract High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell (BCR) studies such as the antigen-driven evolution antibodies (soluble forms membrane-bound IG part BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in genes and affinity maturation. Exploring this essential immunity process could help elucidate generation...
Abstract As an innate property of life, the ability to reproduce is a key process for perpetuation organisms. Along evolution protist reproductive strategies, molecular machinery sexual recombination estimated have been inherited from last eukaryotic common ancestor (LECA). Nevertheless, unraveling cycles extant free-living lineages remains challenging, given enigmatic roles many uncultivated life stages. Among planktonic group Acantharia (Radiolaria), hypothetical cycle has proposed since...
Remote homology detection is a hard computational problem. Most approaches have trained models by using either full protein sequences or multiple sequence alignments (MSA), including all positions. However, when we deal with proteins in the "twilight zone" can observe that only some segments of (motifs) are conserved. We introduce novel logical representation allows us to represent physico-chemical properties sequences, conserved amino acid positions and MSA. From this, Inductive Logic...
2dSS is a web-server for visualising and comparing secondary structure predictions. It provides two main functionalities: 2D-alignment compare The “2D-alignment” has been designed to visualise conserved elements in multiple sequence alignment (MSA). From this we can study the content of homologous proteins (a protein family) highlight its structural patterns. “compare predictions” output several prediction tools, check their accuracy when compared with real extracted from 3D-structure....
The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of clonal lineages. A high number lineages in a population indicates highly diverse repertoire, while size distribution sequence diversity reflect antigen selective pressure. Identifying fundamental to many repertoire studies, including comparisons, tracking, statistical analysis. Several methods have been developed group sequences from high-throughput data. Current use clustering algorithms...
Corynebacterium pseudotuberculosis is a pathogenic bacterium with great veterinary and economic importance. It classified into two biovars: ovis, nitrate-negative, that causes lymphadenitis in small ruminants equi, nitrate-positive, causing ulcerative lymphangitis equines. With the explosive growth of available genomes several strains, pan-genome analysis has opened new opportunities for understanding dynamics evolution C. pseudotuberculosis. However, few pan-genomic studies have compared...
With the availability of complete genome sequences both human and non-human Plasmodium parasites, it is now possible to use comparative genomics look for orthology across species specific genes. This analyses could provide important clues development new strategies prevent treat malaria in humans, however, number functionally annotated proteins still low all species. In context genomes that are hard annotate because sequence divergence, such as Plasmodium, domain co-occurrence becomes...
Motivation The adaptive B-cell response is driven by the expansion, somatic hypermutation, and selection of clones. Their number, size sequence diversity are essential characteristics populations. Identifying clones in populations central to several repertoire studies such as statistical analysis, comparisons, clonal tracking. Several grouping methods have been developed group sequences from immune repertoires. Such principally evaluated on simulated benchmarks since experimental data...
The adaptive B cell response is driven by the expansion, somatic hypermutation, and selection of clones. A high number clones in a population indicates highly diverse repertoire, while clonal size distribution sequence diversity within can be related to antigen’s selective pressure. Identifying fundamental many repertoire studies, including comparisons, tracking statistical analysis. Several methods have been developed group sequences from high-throughput data. Current use clustering...
Motivation: Profile hidden Markov Models (pHMMs) are a popular and very useful tool in the detection of remote homologue protein families. Unfortunately, their performance is not always satisfactory when proteins 'twilight zone'. We present HMMER-STRUCT, model construction algorithm that tries to improve pHMM by using structural information while training pHMMs. As first step, HMMER-STRUCT constructs set Each constructed weighting each residue an aligned according specific property residue....
Protozoa parasites are responsible for several diseases in tropical countries, such as malaria, sleeping sickness, Chagas disease, leishmaniasis, amebiasis, and giardiasis, which together threaten millions of people around the world. In addition, most classic parasitic due to protozoa zoonotic. Understanding biology these organisms plays a relevant role combating diseases. Using homology inference comparative genomics, this study targeted 3 protozoan species from different Phyla:...