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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Searched keyword : Mosquito

Related people (2)

Etienne KORNOBIS

Group : PLATEFORM - Detached : Epigenetic regulation

After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.


Keywords
Data managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
Organisms
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
Projects (3)

Related projects (27)

Assessing the integrations of viral sequences into the genomes of Aedes albopictus and Aedes aegypti

Aedes albopictus is an important vector for transmitting arboviruses, such as Dengue, Chikungunya, West Nile or Zika viruses. Its worldwide distribution due to its high ability to adapt to variable environments makes this species a serious threat. This mosquito also better transmits Chikungunya than Dengue virus, and many studies are still trying to understand the deep relationships between these viruses and their vectors in order to develop new control strategies. Moreover, it is now well known that retroviruses partially integrate into host's genomes since it is mandatory for their replication cycle. Interestingly, Retroviridae are not the only viral family capable of host integration. Indeed, in the last decade, owing to new molecular technologies such as next-generation sequencing and bioinformatic tools, non-retroviral integrated RNA virus sequences (NIRVS) have been found into many animal genomes, including Aedes mosquitoes. This came as a surprise since RNA viruses do not have DNA intermediate in their replication cycle. However, little is known about these integrations and many questions remained unsolved. The aim of this project is to assess the production of NIRVS in persistently-infected cells from Ae. albopictus and Ae. aegypti. It is divided in several critical points : the first one is to know how fast the virus can integrate into the cell genome. The second one is to determine which part of the viral genome can integrate and finally, where can it integrate in the genome. This will allow us to understand the virus/host interaction and if NIRVS formation is a mechanism that vectors/hosts evolved as a general response to RNA viruses.



Project status : Closed

Characterization of the bacterial and fungal microbiota in Aedes aegypti natural breeding sites and larvae



Project status : Awaiting Publication

The resurgence of a neglected disease, Yellow fever: from jungle to urban environments

Yellow fever virus (YFV), a Flavivirus transmitted by mosquitoes causes a severe hemorrhagic fever in humans. Despite the availability of a safe and effective vaccine (17D), YFV is still a public health problem in tropical Africa and South America. In the Americas, the massive campaign of mosquito control during the first half of the 20th century led to the eradication of Aedes aegypti from most American countries, and as a consequence, urban outbreaks of YF were no longer observed. However, the relaxation of vector control led to the reinfestation of urban areas by Ae. aegypti and the subsequent establishment of the Asian tiger mosquito Aedes albopictus. In Brazil, while human cases are sporadically detected in the Amazonian basin where sylvatic YFV strains circulate between non-human primates and arboreal canopy-dwelling mosquitoes (Haemagogus sp.), they are increasingly reported outside the jungle moving towards the Atlantic coast, the most populated area. In the absence of routine immunization programs, YF may come back in the American towns as it was in the past. The causes leading to the current YF resurgence are multifactorial. From a mosquito vector viewpoint, changes in vector densities, distribution, vector competence or vector as a site of selection for epidemic YFV strains, can be regarded as critical factors. Our project aims to address the contribution of the invasive mosquito Ae. albopictus as a missing link to allow a selvatic YF strain (1D) to become adapted for a transmission in urban areas by the human-biting mosquito, Ae. aegypti. It will be done through three specific objectives: (i) identify Ae. albopictus-adaptive mutations after serial cycling of the selvatic YFV-1D on Brazilian Ae. albopictus mosquitoes, (ii) evaluate their potential to be transmitted to a vertebrate host, and (iii) deepen the transmission of the experimentally selected viruses by field-collected mosquito populations.



Project status : Closed

Assessing the integrations of viral sequences into the genomes of Aedes albopictus and Aedes aegypti

Aedes albopictus is an important vector for transmitting arboviruses, such as Dengue, Chikungunya, West Nile or Zika viruses. Its worldwide distribution due to its high ability to adapt to variable environments makes this species a serious threat. This mosquito also better transmits Chikungunya than Dengue virus, and many studies are still trying to understand the deep relationships between these viruses and their vectors in order to develop new control strategies. Moreover, it is now well known that retroviruses partially integrate into host's genomes since it is mandatory for their replication cycle. Interestingly, Retroviridae are not the only viral family capable of host integration. Indeed, in the last decade, owing to new molecular technologies such as next-generation sequencing and bioinformatic tools, non-retroviral integrated RNA virus sequences (NIRVS) have been found into many animal genomes, including Aedes mosquitoes. This came as a surprise since RNA viruses do not have DNA intermediate in their replication cycle. However, little is known about these integrations and many questions remained unsolved. The aim of this project is to assess the production of NIRVS in persistently-infected cells from Ae. albopictus and Ae. aegypti. It is divided in several critical points : the first one is to know how fast the virus can integrate into the cell genome. The second one is to determine which part of the viral genome can integrate and finally, where can it integrate in the genome. This will allow us to understand the virus/host interaction and if NIRVS formation is a mechanism that vectors/hosts evolved as a general response to RNA viruses.



Project status : Closed

An Aedes albopictus-driven epidemiological prediction for arboviral diseases outbreak in Europe



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