Expertise

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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Related projects (21)

A reference panel of dengue vector genomes

Dengue prevention relies primarily on controlling populations of the main mosquito vector, Aedes aegypti, which is failing in many parts of the world because of the lack of sustained commitment of resources and ineffective implementation. Novel entomological approaches to dengue control are being developed that aim at replacing or suppressing mosquito vector populations. Insufficient genomic resources for Ae. aegypti, however, have until now impeded progress in both basic and applied research on this medically important mosquito species. The only available reference genome for Ae. aegypti is a draft that consists of over 4,800 unassembled fragments with incomplete annotation. Moreover, the inbred Ae. aegypti laboratory strain that was sequenced does not universally represent the considerable genetic and ecological diversity of the species worldwide. The large size of the genome and its high content in repeat-rich sequences of transposable elements was a major difficulty to assemble the Ae. aegypti genome sequence. In the present project, we aim to overcome this difficulty using a novel strategy for genome sequencing and assembly. The ultimate goal is to produce several, fully assembled, well-annotated, new Ae. aegypti reference genomes from epidemiologically relevant populations. The expected outcome is a genome reference panel including a catalog of species-wide genetic variation that will significantly improve genomic resources for Ae. aegypti research and help address a broad range of biological questions related to Ae. aegypti vectorial capacity and dengue virus transmission.



Project status : Closed

Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia

Extended spectrum β-lactamase (ESBL) genes encode resistance to penicillins and cephalosporins and can be horizontally transferred among Enterobacteriaceae. More than 60% of healthy humans living in southeast Asia are faecal carriers of ESBL-producing Enterobacteriaceae (ESBL-PE), compared to <10% in Western Europe, suggesting diverse exposure routes. In Cambodia, meat and fish consumption is high and food safety is poorly enforced. Thus, we hypothesized that meat and fish could be a source of exposure to ESBL-PE. From Sept-Nov 2016, we conducted a meat sampling study in Phnom Penh in collaboration with the BIRDY program (http://www.birdyprogram.org/), an ongoing study of neonatal health in low-income countries. We evaluated ESBL-PE contamination among pork, fish, and chicken from two markets and collected survey data from BIRDY mothers. We performed whole genome sequencing on 87 ESBL-producing E. coli recovered from meat and fish and from 91 BIRDY mothers who provided faecal swabs less than one year prior. Now, we will conduct a two-step exploratory analysis of these WGS data:

  • First, we will estimate the pairwise evolutionary distance between E. coli isolates, in order to infer a phylogenetic tree. We will use this tree to investigate such epidemiological questions as “Do E. coli sequences from women who reported eating poultry 3+ times/week cluster more closely with E. coli recovered from poultry samples, compared to women who reported never eating poultry?” This phylogenetic tree may be re-constructed using a finer resolution, as needed.
  • Second, we will annotate all E. coli genomes in order to identify genomic islands related to antibiotic resistance. We will subsequently use logistic regression to model associations between BIRDY mothers’ reported dietary patterns (i.e. exposure) and the presence or absence of these genomic islands among the ESBL-E. coli they were colonized with (i.e., outcome).



Project status : Closed

Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome



Project status : Closed

Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets

Despite the worldwide importance of malaria due to Plasmodium vivax, there is currently almost no data on the molecular responses of the Anopheles mosquito vectors to this parasite species. Understanding these responses will contribute to identify relevant strategies to interrupt the transmission of P. vivax by targeting the mosquito vector. Such approaches are urgently needed, as P. vivax is difficult to target on the long term in humans as a consequence of the hypnozoite stage that is responsible for relapses. This project will investigate the molecular response of Anopheles arabiensis, member of the Anopheles gambiae complex, to P. vivax from experimental infections performed in Madagascar where both mosquito and parasite are present. This is a unique situation that will capitalize on the strong knowledge and tools available for An. gambiae sensu lato. The response will be compared to the one triggered by P. falciparum, also present in Madagascar. From mosquitoes infected in a field setting, a transcriptomic (RNAseq) approach will be used to identify common and unique pathways to both parasite species. These analyses will further contribute to identify targets for interrupting transmission of each or both parasites simultaneously. However, a pilot study performed with the PF transcriptomics & epigenomics revealed that the current release of the An. arabiensis genome is poorly annotated. Therefore, to be able to make sens of the RNAseq analyses per se, a strong support from the C3BI Hub for bioinformatics and biostatistics is critical.



Project status : Closed

Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil

Burkholderia ambifaria bacteria are uiquituos microorganisms present in different environmental sources. Particularly these bacteria have been found to be frequently isolated from rhizospheric soils of a wide variety of plants. Burkholderia bacteria have been proved to be benificial to the plants by improving their growth trough different mechanisms. The B. ambifaria Q53 strain was isolated from the rizosphere of peanut (Arachis hypogaea L.). This leguminous plant is a very important crop in many countries around the world. The searching for clean environmental strategies to improve the productivity of the crops becomes an important issue of study for plant in general and peanut in particular. B. ambifaria Q53 strain has been tested in lab assays to have several mechanism of plant growth promotion including the increasing and availability of nutrients (phosphorus; nitrogen; ferrum) as well as the protection against fungus pathogenic agents. To achieve these mechanisms bacteria have to efficiently colonize the plant rizosphere. To do that bacteria communicate with each other by a mechanism dependent on the production and self detection of an autoinducer signal. In this way bacteria population is able to collectivelly regulate a subset of particular genes driving to global patterns of bacterial behaviour. Knowing and the genome sequence of this bacterium represents a key for studying and understanding the role of environmental burkholderias in the process of interaction with the plants.



Project status : Closed

Uncovering diversity and improving gene annotation of Leptospira sppo

Leptospirosis is an emerging zoonotic disease, with high prevalence in tropical regions. It affects both wild and domestic animals, as well as humans, and it is disseminated by asymptomatic carriers, such as rats and mice, that contaminate water with urine. Its etiological agents are some species of the genus Leptospira, member of the phylum Spirochaetes, which are able to colonize hosts through skin injuries or mucous membranes. Once inside the host, the bacteria is able to disseminate quickly through blood and replicate inside the kidneys, provoking renal failure, hemorrhages, liver damage, among other severe potential complications. High-throughput sequencing technologies have allowed to reconstruct the genomes of hundreds of Leptospira strains, enabling comparative analyses which in turn have accelerated the understanding of the its biology. However, leptospirosis is still classified as a neglected disease and many aspects of Leptospira pathogenesis remain unknown. This project aims to strengthen and establish new collaborations between members of the Réseau International des Instituts Pasteur (RIIP) (the Institut Pasteur, France, and the Institut Pasteur Montevideo, Uruguay), in the context of an ongoing, more extensive PTR project entitled “Global diversity, genomic epidemiology and pathogen evolution of Leptospira spp.” (coordinator: Mathieu Picardeau). In the context of this PTR project, we have proposed that a PhD student from Montevideo (Ignacio Ferrés) spend a couple of months in Paris to develop some specific project goals. This internship will be directed by Dr. Mathieu Picardeau and will be performed under the supervision of Dr. Amine Ghozlane at the C3BI. Specifically, the goals of the internship are: 1) to uncover hidden Leptospira's genome diversity by analyzing public environmental metagenomics databases; and 2) to improve functional annotation of Leptospira genomes by applying comparative molecular modeling techniques developed by Dr. Ghozlane and collaborators.



Project status : Closed