Open positions at CBIB

Bioinformatics PhD (Marie-Curie International Training Network)

Starting date: Oct 2019
Location: Bordeaux, France
Laboratory: Bordeaux Bioinformatics Center (CBiB) 
Address: CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex - ORGA 351 course of the Liberation, Building A12 33405 Talence Cedex

The project aims to develop bioinformatic computational methods for the analysis of HTS data in the context of plant virome studies. More precisely, the candidate will

1) Define and apply bioinformatic pipelines to detect viruses from HTS datasets in a computationally efficient manner.

2) Define rules and implement a method for the inter-sample contamination detection.

3) Design and develop new methods for homology free machine-learning specifically tailored for virome classification and for virome / microbiome interaction analysis;

4) Integrate the resulting pipeline within a user-friendly graphical system (such as Galaxy) providing a complete bioinformatics analysis workflow from raw sequencing reads.

SALARY

Remuneration is according to MSCA ITN rules. Stipend per month depends on the host country correction coefficient following the EC rules (Table 2 of the MSCA Work Programme 2018-2020, http://ec.europa.eu/research/participants/data/ref/h2020/wp/2018-2020/main/h2020-wp1820-msca_en.pdf,page 82). Net salary results from deducting all compulsory (employer /employee) social security contributions as well as direct taxes (e.g. income tax) from the gross amounts. 

In addition to the stipend, mobility allowance (600€ per month) will be paid as part of the salary or as other benefits depending on the organization. Family allowance*(500€ per month) will be paid as part of salary where the researcher has a family by the time of recruitment.

 

ELIGIBILITY CRITERIA

The Marie Curie Fellowships are directed at European organizations in need of developing new areas of competence. The Marie Curie funding is available for researchers that move, both within Europe and globally. The following criteria apply:

  • Nationals from any country may apply.
  • Mobility: at the time of the recruitment, the researcher must not have resided or carried out his/her main activity (work, studies, etc.), in the country of the chosen host institution (recruiting beneficiary) for more than 12 months in the 3 years immediately prior to the date of the recruitment.
  • Research category of Early Stage Researcher (ESR): researchers who, at the time of the recruitment, have not yet been awarded a doctorate degree and are in the first 4 years (full-time equivalent) of their research careers, including the research training period that would entitle them to a doctorate.

GENERAL EVALUATION CRITERIA

  • Educational background relevant for the chosen position (individual research project)
  • High proficiency in spoken and written English
  • Networking and communication skills (to be evaluated in the interview). 
  • Previous research experience, relevant to the chosen position is desirable. 
 

SELECTION PROCESS

Pre-selection: will be based on CV, experience, skills, motivation letter, and recommendation letters. 

Interviews: Short-listed candidates will be interviewed.

Start of contract: October 2019

 

HOW TO APPLY

Applicants should send full application consisting of:

  • Curriculum Vitae (Europass format recommended; Please specify your residence/work place in the last 3 years).
  • University transcripts (grades)
  • A motivation letter addressing his/her research interests in relationship to the selected individual research project.
  • Recommendation letters

CONTACTS:

Macha Nikolski - macha.nikolski@u-bordeaux.fr 

cc to Antonia Lorenzo - Antonia.LorenzoLopez@nib.si (indicating ref. “INEXTVIR call for ESRs” in the subject of the email)

 

Bioinformatics engineer

Duration: 12 months + extensible within the limits of the Sauvadet law
Starting date: April 2019
City: Bordeaux
Laboratory: Bordeaux Bioinformatics Center (CBiB) and ISM - Organic Synthesis and Natural Substances (ORGA)
Address: CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex - ORGA 351 course of the Liberation, Building A12 33405 Talence Cedex

 

CONTACTS :

Macha Nikolski - macha.nikolski@u-bordeaux.fr - 0557571247
Alexis Groppi - alexis.groppi@u-bordeaux.fr - 0557571218

 

Job description :

The Bordeaux Bioinformatics Center (https://www.cbib.u-bordeaux.fr) is a dynamic research and service team in the field of bioinformatics. We are looking for a bioinformatics engineer to join our team, first for a 12-month project (expandable within the limits of the Sauvadet law).

The objective of this project is to identify all the proteins targeted by different polyphenols in cell lysates or cells and to analyze the captured proteins by means of bioinformatic methods to determine their role in the metabolic and signalling pathways related to these diseases

You will work in a versatile and multidisciplinary bioinformatics team. You will work in strong interaction with the ISM laboratory (Orga group) that will generate the data for this project. You role entails the following tasks.

Missions :

Implementation of proteomic data analysis pipelines.
Bioinformatic and statistical processing of data.
Development of "omics" databases, analysis of metabolic pathways.
Methodological advice and assistance for data analysis.
Collaboration with biologists when preparing scientific papers or grant applications.
Technology watch + development + maintenance of workflows.

Required knowledge and skills:

Successful experience in bioinformatics (genomics, transcriptomics, metabolomics)
Experience in the development of data analysis pipelines
Knowledge of the most used statistical tools in bioinformatics

Operational knowledge of programming techniques:

Advanced programming in at least one language: Python, Perl, Java
Knowledge of the Unix / Linux / shell environment
Knowledge of expression analysis tools and networks such as GSEA

Essential Activities :

Implementation of standardized data processing pipelines
Development of new tools needed for data analysis and integration (pipelines, statistical tools, etc.)
Building of user interfaces that can be used by researchers for transfer, storage, quality control and data analysis
Taking part in the writing of specialized sections of articles
Assistance in setting up "omics" databases

Required Qualities :

Autonomous and rigorous, with a good organisational skills, comfortable to work on projects involving collaborators from several fields
Excellent interpersonal, listening and communication skills
Taste for teamwork and knowledge sharing
Initiative, curiosity, technical creativity
English proficiency

Training :

Applicants must have at least a BAC + 5, in Bioinformatics, Computer Science, Biostatistics or Applied Mathematics

Links:

Synthèse organique et substances naturelles (ORGA) : https://www.ism.u-bordeaux.fr/spip.php?article52

CBIB : https://cbib.u-bordeaux.fr/

 

Postdoc : Investigating the methylome of grape and oak under water stress

Durée : 12 mois + extensible de 18 mois
Date de début : début 2019
Ville : Bordeaux
Laboratoire : INRA et Centre de Bioinformatique de Bordeaux (CBiB
Adresse : INRA 71 Avenue Edouard Bourlaux, 33140 Villenave-d'Ornon  - CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex

 

CONTACTS :

Philippe Gallusci
Grégoire Le Provost
Macha Nikolski

 

 

Description du poste:

Global climate changes that includes several environmental constraints including drought, is a major concern that affects plant survival both in agro-systems and forest ecosystems. Indeed plants have evolved a wide range of mechanisms to cope with adverse environmental conditions that often lead to rapid and integrated reprogramming of gene expression patterns. Recent works have evidenced that epigenetic regulations, including DNA methylation, are essential to the responses of plants to environmental constraints, and may contribute to their long term adaptation to adverse conditions. In this context the METDRY project addresses the question of the potential involvement of genomic DNA methylation in the adaptation and responses to drought in woody perennial plants using grape and oak as representatives of cultivated plants and forest ecosystems respectively. It is based on the comparative analysis of methylomes, transcriptomes and small RNA populations in a drought sensitive and drought tolerant species in grapevine and oak and aims at identifying differentially methylated regions (DMRs) and gene expression profiles linked to long term adaptation to drought.

The main objectives of the project are:

1. To analyze the genome wide distribution of 5mC in a drought sensitive and tolerant species in oak and grapevine, and determine similarities and differences between these contrasted phenotypes in each genus.

2. To determine changes in DNA methylation landscape induced by drought in the sensitive and tolerant species in each genus.

3. To investigate if DNA methylation contributes in a similar way to the responses to drought stress and to long term adaptation to drought in plants from natural population (oak), and in plants that have been selected by breeders over several generation (grapevine).

4. To implement a robust bioinformatics data analysis pipeline for BS-seq data and integrative approaches including BS-Seq, RNA seq, and Small RNA seq data.


Applicants should be highly motivated and have a PhD with expertise in bioinfomatic and strong background in (epi)genomics . Knowledge in plant sciences is strongly recommended.

Qualifications: We seek a bright, highly motivated, and enthusiastic bioinformatician with a background in epigenomics or genomics and an interest for plant biology. Candidates with other backgrounds such as molecular biology, with a strong interest in bioinformatics, are also invited to apply. Experience with NGS technologies and pipeline development is required.  Applicants should have demonstrated abilities to work in a Linux environment and have experience in handling NGS data. Programming (Python, Perl, etc.) is required and knowledge of biostatistics is appreciated.  A high standard of spoken and written English is appreciated, as are good communication skills.  Ability to work autonomously, as well as part of a team, and to interact with scientist from different background including molecular biologist, plant physiologist and bioinformaticians is required. Applicants will have to share their time between three different laboratories.

Links:

UMR EGFV: https://www6.bordeaux-aquitaine.inra.fr/egfv/

CBIB: https://cbib.u-bordeaux.fr/

UMR BIOGECO: https://www6.bordeaux-aquitaine.inra.fr/biogeco

Gestionnaire d’infrastructures

Durée : 4 mois
Date de début : dès que possible
Ville : Bordeaux
Laboratoire : Centre de Bioinformatique de Bordeaux – (CBiB)
Adresse : 146 Rue Léo Saignat 33076 Bordeaux Cedex
 

CONTACTS :

Dr Alexis Groppi
Dr Macha Nikolski
 
Date de validité : 15/07/2018

Description du poste: 

Le Centre de Bioinformatique de Bordeaux (CBiB) est une équipe de service et de recherche dans le domaine de la bioinformatique (https://www.cbib.u-bordeaux.fr/). Nous recherchons actuellement un assistant ingénieur pour renforcer et développer l’informatique du centre.

Missions :

Le gestionnaire travaillera en étroite collaboration avec l’équipe actuelle (2 personnes à temps partiel en charge de l’informatique) pour mettre en place une nouvelle solution de sauvegarde des serveurs et participer à l’administration du système d’information.

Activités principales :

Mise en place d’une solution, basée sur des logiciels libres, de sauvegarde des serveurs.
La solution s’appuiera sur un espace de stockage existant (ZFS accessible via NFS).
Installation du serveur, des clients, tests, création de la documentation et des procédures.
Participation aux différentes activités du service :

  • mise à jour de la solution de supervision (actuellement sous Centreon)
  • migration des machines virtuelles (VMware vers KVM/Proxmox).
  • suivi des incidents, assistance utilisateur.

Connaissance opérationnelle des techniques de programmation :

Maîtrise de la programmation dans au moins un langage (Python, Perl, Java, C++)
Maitrise de Unix/Linux / shell
Connaissance souhaitée d’outils d'analyse d'expression et de networks tels que GSEA

Compétences souhaitées :
  • Connaissance approfondie des environnements GNU/Linux (CentOS côté serveurs),
  • Connaissance générale sur les infrastructures (LDAP, DNS, etc) et sur les réseaux (TCP/IP, LAN),
  • Connaissance générale sur la virtualisation,
  • Connaissance générale des procédures de sécurité informatique,
  • Anglais technique,
  • Gestion de projet (planification, suivi),
  • Transmission des informations et des compétences (communication, documentation),
  • Rigoureux, organisé.

Qualités requises :

Autonome et rigoureux, avec un sens de l'organisation qui permet de mener des projets impliquant des collaborateur venant de plusieurs disciplines
Excellentes qualités relationnelles, d'écoute et de communication
Goût pour le travail d'équipe et le partage des connaissances
Esprit d'initiative, curiosité, créativité technique
Maitrise de l'anglais

Formation requise :

BAC+2 minimum dans une filière informatique