Five young investigator positions open immediately at the Institute for Computational Biology (IBC) of Montpellier (France)

IBC will hire young investigators for each of the five work-packages, typically with a PhD plus some post-doc experience, a high level of publishing, strong communication abilities, and a taste for multidisciplinary research. Working full-time at IBC, these young researchers will play a key role in Institute life. Most of their time will be devoted to scientific projects. In addition, they are expected to actively participate in the coordination of workpackages, in the hosting of foreign researchers and in the organization of seminars and events (summer schools, conferences...). In exchange, these young researchers will benefit from an exceptional environment thanks to the presence of numerous leading international researchers, not to mention significant autonomy for their work. These positions are open for up to 4 years with a salary above the French post-doc standard.

Living at Montpellier: http://www.agropolis.org/english/guide/index.html

See details for each work-pakages :

WP1: HTS

WP1: Algorithms for High Throughput Sequencing

We are looking for an enthusiastic and motivated post-doctoral fellow with a background in computer science and algorithms to investigate theoretically, as well as to conceive and develop novel algorithms for analysing sequence data coming from High Throughput Sequencing technologies.

With their huge throughput and scope of applications, Next Generation Sequencing technologies are turning biology  into a data driven science. Many questions related to genome organisation and funtion can now be asked as computational questions and require large scale analysis on large volumes of sequence data. A key to scalability of used methods is to design sophisticated algorithms for processing this data and inferring biological knowledge. The IBC is a multidisciplinary institute with five collaborating axis of research, one of which is devoted to approaches for analysing sequencing data.

Overall topic: Practical algorithms and indexing data structures for NGS processing

For example, the following topics are of interest:
   - Designing methods for comparing sequences to a collection of similar genomes. Genomes from individual or populations from the same species usually differ by a limited number of positions. Hence, a succint representation of several of these genomes in a compact form in memory encode some reference and the differences from other genomes with respect to the reference one.
   - Novel approaches for large scale sequence assembly. Current genome assembly methods have strong limitations and are hindered by a varying  level of sequencing depth. To solve these limitations it is promising to develop approaches able to exploit variable size of overlaps between the input sequences, without loosing the effectiveness of de Bruijn graph based solutions.

The position is available as soon as possible. The official application have to be made on this site

** Background and requirements
   - Background keywords: computer science, text algorithms, combinatorial algorithms, indexing techniques, data compression
   - Required: advanced knowledge in algorithmics, software development in C/C++
   - Required: interested in life sciences, eager to work in a team and to collaborate with scientists from other disciplines
   - Knowledge of French  is not required
   - Desired: strong publication record, good communication skills in English.
   - Appreciated: experience  in High Performance Computing or in genomics analyses
   - Offered: good working environment, dynamic team, research budget, access to meso-computing server, opportunities of local and international collaborations with highly qualified life scientists, fantastic region and nice living quality.

Contacts:
Eric Rivals

This application is no longer available

WP2: Evolution

WP2: Evolutionary genomics
This project involves evolutionary analyses of large-scale genomic data, at the interface between phylogeny and population genetics. The candidate will develop research on some of the following topics: inference of very large phylogenies, reconciliation of gene/species trees at a genomic scale, detection of selection, inference of population divergence, dating and migration studies, simulation-based inference. Application domains will be quite open, with emphasis on virus evolution and plant genomes. We are seeking a candidate with a strong background in mathematical and computational evolutionary biology, with interest in applications and software development.

Contacts:
Jean-Michel Marin
François Rousset
Vincent Ranwez
Olivier Gascuel

This application is no longer available

WP3: Annotation

WP3: Pathogen proteome annotation
This project aims at the development and integration of bioinformatics tools for an interdisciplinary project dealing with structural and/or functional annotations of pathogen proteomes. We are seeking a high level computer scientist with strong experience in bioinformatics; knowledge in 3D protein structures and/or statistical learning would be a plus. The successful candidate will have good knowledge in one or several of the following topics: statistical learning, hidden Markov models, pattern matching, 3D and geometry algorithmics, protein domains, unstructured regions, tandem repeats, gene ontology

Contacts:
Laurent Bréhélin
Andrey Kajava

This application is no longer available

WP4: Imaging

WP4: 4D Image Analysis in Developmental Biology image2

A post-doctoral position for up to 4-years is available in Montpellier (France) to quantitatively explore genotype/phenotype relationships during animal embryo or plant meristem development.

The work will develop along two main threads:

Modelisation 3D

  1. quantitative exploration, annotation and handling of volumetric and segmented images obtained by confocal or light-sheet laser microscopy and
  2. development of a concept of 4D atlas, whereby cellular (e. g. geometry, mechanics) and molecular (e. g. gene expression) parameters can be projected onto 4D geometric models of developing cells or organs.

The recruited scientist will work in the Virtual Plants team at the new Institute of Computational Biology of Montpellier, supported by the French « Investments for the Future » National plan. The IBC brings together 15 experimental and computational research laboratories and one company developing innovative methods and software to analyze, integrate and contextualize large–scale biological data in health, agronomy and environment.
The IBC provides a stimulating intellectual environment through the invitation of foreign researchers, the organization of scientific events (conferences, schools, seminars), and the training of young researchers. Computational work will be carried out in tight collaboration with the biology teams generating the 3D images analyzed.

Project
The project will build on a powerful software pipeline, named MARS-ALT, to automatically segment and track cells in living tissues (Fernandez et al., Nature Methods, 7, 547–553).meristeme coupe The selected candidate will initially design and implement algorithms and models to quantify geometrical and mechanical parameters in volumetric or segmented images obtained by confocal or light-sheet fluorescent microscopy (Krzic et al., Nature methods 9, 730–3).
In a second phase, a concept of 4D atlas will be developed. Based on a series of developmental 4D time-lapse recordings, a template sequence that reflects the "average" development of these recordings will be constructed. This will involve the development of techniques to register 4D sequences of different individuals and to compute average sequences from the registered sequences. This template sequence will then be used to annotate shape development with geometric, genomic, physiological or biophysical data obtained from live microscopy (e.g. La Rota et al., The Plant cell 23, 4318–33 ). The 4D atlas will be interfaced to a sophisticated model organism database, NISEED (Tassy et al., Curr. Bio. 345–58; Tassy et al., Genome research 20, 1459–68). These tools will be applied to wild-type and mutant development, and to study the genetic determinants of variations in 3D morphologies within or between species.

Expected Skills / qualifications
meristemeCandidates will have a PhD in computer science, applied mathematics or in biology with a strong background in mathematics and quantitative modeling. Specific background in either pattern analysis, shape statistics, geometric modeling, 3D imaging or modeling in developmental science is expected. Additional knowledge in databases or new web technology will be appreciated. A good level of English and a strong publication record are required.

Contacts:
Christophe Godin, Inria Virtual Plants, UMR AGAP, Montpellier
Patrick Lemaire, CNRS, CRBM, Montpellier

This application is no longer available

WP5: Databases

WP5: Biological data and knowledge integration
This project aims at the design and implementation of a data management framework for plant genomics. Addressing the problem of data and knowledge integration at a large scale, with high numbers of distributed data sources and processes, is a major challenge.
The project plans to address this challenge by pursuing two complementary research directions:
(1) data integration using metadata and ontologies to merge data coming from different sources, with different formats and semantics.
(2) distributed workflow execution involving distributed processes and large amounts of heterogeneous data, with support of data provenance (lineage) to understand data results.

The basis for the project will be the BioSemantic and WebSmatch prototypes.

We are seeking a candidate with strong experience in distributed data management, in particular data integration, a good grasp on implementation aspects and interest for biology applications.

Key-words: data integration, (bio) ontologies, semantic web, semantic indexing, linked data, plant genomics data

Contacts:
Patrick Valduriez
Manuel Ruiz

This application is no longer available

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