Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise

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Searched keyword : Phylogenetics

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Group : GIPhy - Embedded : PIßnet

| work as a research engineer in the ßioinƒormatics and ßiostatistics HUß of the |nstitut Pasteur. Holder of a PhD in bioinƒormatics, my main interest is on ƒast but robust phylogenetic inƒerence algorithms and methods ƒrom large genome-scaled datasets. |n consequence, | am oƒten involved in related bioinƒormatics projects, such as perƒorming de novo or ab initio genome assemblies, designing and processing core genome †yping schemes, building and analysing phylogenomics datasets, or implementing and distributing novel tools and methods.

AlgorithmicsClusteringGenome assemblyGenomicsGenotypingPhylogeneticsTaxonomyGenome analysisProgram developmentEvolutionSequence homology analysis

Projects (26)


After a PhD in Microbiology on bacterial toxin-antitoxin systems at the Free University of Brussels, I joined the Institut Pasteur for a 3 years postdoc in Eduardo Rocha’s lab. During this period, I performed comparative genomics and pylogenetic analysis on bacterial conjugation and type IV secretion systems. Then, I worked 2 years in Olivier Tenaillon’s team on the modelling and evolution of organismal complexity. I joined the HUB in 2015, and I am involved in phylogenetic and comparative genomics projects.

GenomicsPhylogeneticsSequence analysisGenome analysisGeneticsEvolutionPopulation genetics
Projects (12)

Frédéric LEMOINE

Group : DETACHED - Hub Core

After a Master degree in bioinformatics and biostatistics, I did a PhD in computer science / bioinformatics at University Paris-Sud (now in University Paris-Saclay), where I worked on integration and analysis of comparative genomics data. After a postdoc in Lausanne, Switzerland where I worked on small-RNA sequencing data, I joined GenoSplice where I was responsible for the development of bioinformatics projects related to next generation sequencing. I joined Institut Pasteur in Nov. 2015, to work in the Evolutionary Bioinformatics Unit and participate in the development of new tools and algorithms that are able to tackle efficiently the ever increasing amount of sequencing data.

AlgorithmicsData managementPhylogeneticsSequence analysisDatabaseGenome analysisProgram developmentScientific computingDatabases and ontologiesSequencingWorkflow and pipeline development

Projects (1)

Related projects (31)

Evolutionary relationships between giant viruses and eukaryotes

The phylogenetic position and status of “giant viruses”, formerly called NucleoCytoplasmic Large DNA viruses (NCLDV) or putative order Megavirales, are controversial. Many preliminary phylogenetic analyses have been published, but their presentations are usually highly biased by the prejudice of the authors concerning the nature of giant viruses. Our own preliminary analyses suggest that giant viruses are indeed ancient (they predate the last universal eukaryotic ancestor) and have possibly provided important functions to emerging eukaryotic cells (e.g. DNA topoisomerase activities). The number of giant virus genomes has recently dramatically increased, opening new opportunity to study their position in the “universal tree of life” and their evolutionary relationships with eukaryotes. The aim of the project is to perform an exhaustive phylogenetic analysis of all giant virus proteins with eukaryotic (archaeal/bacterial) homologues to (i) test the monophyly of giant viruses, (ii) determine their contribution to early eukaryotic evolution, iii) determine if some giant virus proteins can be useful to root the eukaryotic tree. We need the help of a bioinformatics colleague with good expertise in building phylogenetic trees from large data sets using different methods of tree construction and robustness evaluation. This work will be complemented by the systematic search for significant indels (insertion/deletion) in the alignments obtained by two members of the BMGE team (Patrick Forterre and Morgan Gaia).

Project status : Closed

Phylogenetic analysis of the Leishmania HSP70 protein family

Project status : Closed


Project status : Closed

Comparative genomic and phylogenetic analysis of Clostridium baratii strains

Project status : Closed

Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases

Microbial discovery remains a challenging task for which there are a lot of unmet medical and public health needs. Deep sequencing has profoundly modified this field, which can be summarized in two questions : i) which pathogens or association of pathogens are associated with diseases of unknown etiology and ii) among microbes infecting animal (including arthropod) reservoirs, which ones are able to infect large vertebrates, including humans. We are currently addressing these two questions and our current request comes with the willingness for Institut Pasteur to increase its contribution and visibility of this thematic, in particular in relation with hospitals and the Institut Pasteur International network (IPIN).  We expect to identify new microbes associated with human diseases, and this is expected to pave the way for basic research programs focusing on virulence mechanisms and host specificity, and will also lead to phylogenetic and epidemiological studies (frequency of host infection, mode of transmission etc...), as well as the development of improved diagnostic tests for human infections. Our objective is also to contribute to the efforts of Institut Pasteur in the field of infectious diseases, by building a pipeline, from sample to microbial identification, able to manage large cohorts of samples. This project is currently supported by the LABEX IBEID and the CITECH, and critically requires a bioIT support, justifying this application. Partners include different hospitals including Necker-Enfants malades University Hospital regarding patients with progressive disease, different IPIN laboratories, as well as INRA and CIRAD regarding animal/arthropod reservoirs.

Project status : In Progress

Genomic determinants for initiation and length of natural antisense transcripts in a compact eukaryotic genome and phylogenetic analysis of related Entamoeba species

Project status : Closed

Fusion proteins in mammals and yeasts

Membrane fusion is an essential process in all forms of life, and fusion proteins are responsible of catalysing this reaction by forcing the two membranes against each other by undergoing a fusogenic conformational change. Viral fusion proteins are the most well studied and are classified in three different groups: class-I, with a central trimeric alpha-helical coiled coil with the fusion peptide at the N-terminal end; class-II, which are folded as three beta-sheet rich domains with an internal fusion loop; and class-III, with a trimeric alpha-helical coiled coil with an internal fusion loop at the tip of a β-sheet rich domain. Despite their totally different structures, the proteins from the three classes use the same overall fusion mechanism. The syncytins, which are class-I fusion proteins captured from a retrovirus that integrated in the germ-line of a primitive mammal more than 25 millions years ago, are responsible for the development of the placenta. Recently, orthologs to the class-II viral fusion proteins have been found in eukaryotic organisms: the epithelial fusion factor (EFF) family in nematodes, responsible for skin formation, and HAP2-GCS1 proteins, responsible for gamete fusion for fertilization in green algae, higher plants, unicellular protozoa, cnidarians, hemichordates, and arthropods. The fact that HAP2 was identified in the main branches of the eukaryotic taxa with the exception fungi, suggest that they should also be present in these organisms. In particular, HAP2 was identified in some insects but not in all of them, and has not been detected in vertebrates. This project is aimed at the detection of amino acid sequences sequences compatible with class II fusion proteins among the membrane proteins present in vertebrates and yeast

Project status : Closed

Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa

Project status : Closed

Centrosome and basal body function in human parasites

Centrosomes are the main microtubule organizing center of eukaryotic cells with critical roles in cell division, polarity, signaling and structure. In most cells, one or both centrioles act as basal body (BB), nucleating microtubules to form cilia or flagella, sensory and motile organelles of vital importance for a wide range of biological functions. Notorious deadly diseases such as cancer, microcephaly and ciliopathies correlate with dysregulation in the number and/or structure of the centrosome/BB. Defects in centriolar proteins also impact cell division and flagellar function of parasitic protists. Notably, T. gondii can assemble flagella during its sexual cycle within the cat’s enteroepithelial tissue, a largely unattainable life stage in vitro. The state of the art of the field points at the centrosome and basal body of apicomplexan and trypanosomatid parasites as potentially rich sources of novel therapeutic targets to fight parasitic diseases. However, their molecular composition and the regulation of their biogenesis remain ill-described. Albeit a number of structural components appear to be conserved between parasitic protozoa and their vertebrate hosts, the absence of conserved homologs of regulatory components, suggests that their biogenesis is likely controlled by divergent triggers of unknown targets. Within the framework of a funded ACIP grant (076-2017), this team pursued the characterization of the centrosome composition in T. gondii, and explored the localization of newly identified principles in T. brucei. This proposal focuses on deciphering the role of the newly identified proteins in the biology of the centrosome in Toxoplasma gondii, as a model for the phylum apicomplexa, and to analyze the role of these conserved proteins in basal body biogenesis and function in Trypanosoma brucei. Based on our preliminary identification of novel centrosomal/basal body components and the powerful tools available in our model organisms, we now propose: 1. To analyze the phylogenetic distribution and functional domains of 20 novel proteins of T. gondii through bioinformatic approaches. 2. To assess the localization of these 20 proteins, and the function and cell cycle dynamics of those localized to the centrosome, in T. gondii. 3. To characterize the function of a protein complex linking the centrosome to nascent daughter cells in T. gondii. 4. To characterize the role of 3 novel T. brucei proteins homologs in basal body biology.

Project status : New

Comparative genomics analysis of cyclic-di-GMP metabolism across the Leptospira genus

Finely tuned sensory systems enable bacteria to sense and respond to fluctuating environments, coordinating adaptive changes in metabolic pathways and physiological outputs. For pathogenic Leptospira, signaling pathways allow a timely expression of virulence factors during the successive steps of infection of a mammal host. As the bacteria is excreted by its host, signaling pathways enable switching the expression towards factors promoting survival in the environment. A unifying theme across bacterial species is that biofilm formation coincides with the synthesis of the cellular signaling molecule bis-(3?-5?)-cyclic dimeric guanosine monophosphate (c-di-GMP) and this feature seems to be conserved in Leptospira. Our current work shows that the c-di-GMP regulation pathway is a major regulatory network involved in biofilm formation, virulence and motility in the pathogen Leptospira interrogans. Biofilm production and virulence expression is quite variable across the leptospira genus (highly virulent species, low virulent species and saprophytes species showing increase biofilm production). We would like to explore how the c-di-GMP metabolism, and the many genes associated with its synthesis, and degradation have evolved across the leptospira genus. We believe that understanding the evolutionary relationship of the c-di-GMP metabolism genes in the Leptospira genus would help us to understand the contribution of this second messenger to pathogenesis and biofilm formation in the Leptospira genus

Project status : In Progress

Neonatal acquisition of ESBL-PE in the community of a Low-Income Country

Severe bacterial infections are a leading cause of neonatal deaths, with low income countries (LICs) bearing the highest burden. In LICs, neonatal bacterial infections are mainly caused by Enterobacteriaceae. One important driver of unfavorable outcome in infections caused by these bacteria is multidrug resistance. Of particular concern, extended-spectrum beta-lactamase-producing enterobacteriaceae (ESBL-PE) are resistant to most penicillins and especially cephalosporins (3rd-4th generation). Enterobacteriaceae are known to colonize the digestive tract, which represents the first step for potential neonatal infections. The newborn is exposed at birth and during the first weeks of life to several possible sources of ESBL-PE acquisition, e.g. maternal, health-care facilities, and outside hospitals: parents, others relatives, food and environment. However, the routes of ESBL-PE acquisition in neonates are not well defined. Also, local environments and practices influence strongly the interactions of the infant with its environment. However, practices contributing to the transmission of ESBL-PE to neonates are not well characterized in LICs. The objectives of the project are: a better knowledge of the role of different routes of ESBL-PE transmissions to newborns in the community, and more specifically within a household, to understand local environments and practices that facilitate ESBL-PE transmission in Madagascar In Madagascar, 60 newborns and members of their households will be follow-up for one month. ESBL-PE will be characterized with last generation DNA sequencing methods. To integrate all these data globally, we will develop novel sophisticated analytical approaches combining mathematical modeling and statistics. Also, in-depth interviews will be conducted and mother-newborn pairs will be followed with a participants-observations methodology. Our study aims at identifying and quantifying the role of the different routes of transmission for newborns in the community. With a multidisciplinary approach, it should allow identifying the most acceptable interventions for local population to prevent ESBL-PE acquisition in newborns in Madagascar, where the burden of neonatal infection is huge. Partner : Institut Pasteur in Madagascar

Project status : Pending