Genomics, Transcriptomics And Bioinformatics To Decipher Skin Homeostasis And Related Cutaneous Diseases

11 Jul 2023

Job Information

Organisation/Company

Institut Cochin

Department

Institut Cochin

Research Field

Biological sciences » Biology

Computer science » Database management

Researcher Profile

First Stage Researcher (R1)

Country

France

Application Deadline

20 Sep 2023 - 17:00 (Europe/Paris)

Type of Contract

Temporary

Job Status

Full-time

Offer Starting Date

1 Oct 2023

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Reference Number

110723ICIE bioinformaticien

Is the Job related to staff position within a Research Infrastructure?

Yes

Offer Description

Skin constitutes a vital barrier to protect internal organs from various external threats. The aim of our team is to study skin homeostasis and related disabling dermatoses for which there is an unmet medical need. Studies are conducted both in mice, humans and an alternative informative rodent model, the naked mole-rat. Our main research projects focus on:

- identifying new therapeutic strategies to treat delayed wound healing;

- exploring the physiopathology of follicular skin disorders using single cell sequencing;

- studying the emergence, the cellular and molecular heterogeneity and the dissemination of skin tumors.

For this latest project in particular, several clinical and experimental data indicate that dissemination of quiescent/stem cells may occur early in melanoma. Although sentinel lymph node biopsy may detect such events, it remains unable to predict the risks of metastatic dissemination. Since 60 to 70% of melanomas present BRAF or NRAS mutation, we set up a study to determine the prognostic value of the presence of mutated melanoma clones -detected by digital droplet PCR (ddPCR) - in the large healthy non invaded peritumoral tissue obtained routinely as part of the patients' management. The results of this study have the potential to open new tools in precision medicine and more specifically to evaluate the significance of clone detection and pave the way for adjuvant treatments even at some early steps.

Single cell analysis and ddPCR are powerful emerging technologies. However, manual analysis of the data is time consuming and algorithms for automated analysis of data are not yet fully developed.

The position involves the following direct tasks:

Develop and use mathematical models for statistical analysis and carry out dynamic simulations and pattern analysis for the different projects of the host team (with a priority on the melanoma dissemination project);

Plan appropriate protocols to set up the ongoing or future experiments in the lab that will need genomics, transcriptomics and thus bioinformatics analysis;

Create and maintain databases of genomic and transcriptomic information obtained in the lab;

Work in close collaboration with the Plate-forme de génomique de l'Institut Cochin.

The project involves the following collaborations:

Diana Passaro (Institut Cochin)

Olivier Lantz (Institut Curie)

Plate-forme de génomique de l'Institut Curie

Plate-forme de l'Institut Cochin

Unité de recherche Clinique (URC), Cochin

Requirements

Research Field

Biological sciences » Biology

Education Level

Master Degree or equivalent

Research Field

Computer science » Database management

Education Level

Master Degree or equivalent

Skills/Qualifications

We are thus looking for a highly motivated engineer in bioinformatics to join the laboratory of Cutaneous Biology led by Prof. Sélim Aractingi at Cochin Institute / INSERM U1016 in Paris, France. The candidate will be responsible for the analysis of the data obtained in the project aiming to understand melanoma clones' dissemination. In parallel, the successful candidate will participate in the bioinformatics analyses of other projects in the host laboratory that have generated bulk or single-cell RNAseq data (10x and SmartSeq3 protocol).

Desired skills: Previous work in bioinformatics with a background in the area of cellular biology. An experience in skin biology will be highly appreciated, but is not mandatory.

Required skills/qualifications:

Master degree

Good communication and presentation skills

Ability to work in a team

Excellent organization skills

Good communication skills in oral and written English

Languages

ENGLISH

Level

Good

Research Field

Biological sciences » Biology

Additional Information

Selection process

Applicants should send their CV, letter of motiviation and name of 2 references.

Envoyez votre CV, lettre de motivation et deux contacts de recommandations à :

Sélim Aractingi; email: [email protected]

Romain Fontaine; email: [email protected]

Bénédicte Oulès; email: [email protected]

Additional comments

Team « Cutaneous Biology » is part of the Institut Cochin located in the center of Paris, 22 rue Méchain – 75014 Paris, France.

Institut Cochin is one of the biggest biomedical French Research Center located in the center of Paris that provides a multidisciplinary scientific environment and very efficient core-facilities.

Visit our web : www. institutcochin.fr

FINANCIAL SUPPORT

Type: CDD Funding: URC-APHP

Début/Beginning: October 1st, 2023

Durée du contrat/Length of contract: 12 months

Structure employeur/organization INSERM

Work Location(s)

Number of offers available

1

Company/Institute

Institut Cochin

Country

France

State/Province

Ile de France

City

Paris

Postal Code

75014

Street

22, rue Méchain

Geofield

Where to apply

E-mail

[email protected]

Contact

State/Province

Ile de France

City

Paris

Website

https:// www. idf.inserm.fr/rubriques/l-inserm-en-ile-de-france/delegation- paris-5

Street

22, rue Méchain

Postal Code

75014

E-Mail

[email protected]

STATUS: EXPIRED