Bioinformatics Job Openings

 

The CRG (Barcelona, www.crg.es) is opening NINE positions in bioinformatics, at the pre-doctoral and postdoctoral level. These positions are available within the Comparative Bioinformatics Laboratory (CBL) and the Bioinformatics and Genomics Group (BGG). The CBL focuses on the development of multiple comparison methods, is staffed with about 10 researchers and headed by Cedric Notredame. The BGG focuses on functional genomics and is a key partner of the ENCODE BioSapiens, and other international consortiums. The BGG is also part of the Spanish Institute of Bioinformatics; it is staffed with about 15 researchers and headed by Roderic Guigo who is also the program coordinator.

 

The CRG is one of the leading biological research institutes in Spain. The working language is English and the candidates are expected to be fluent. Practical knowledge of Catalan or Spanish is not required, but the candidates will be encouraged to acquire these languages through some of the free training courses provided by the CRG.

 

Contact: Please send CV + Letter + Name of potential referees to Romina Garrido (Romina.Garrido@crg.es) and quote the reference of the position you are applying for. Post-doctoral salaries start at 25-30 K€ but can be adapted according to experience.

 

Deadline: 30/01/09

Pointers: www.crg.es, www.tcoffee.org/Jobs

 

 

Post-Doc                     - Ref. CBL1

Systematic Benchmark of Bioinformatics Predictive Tools

This position will be shared between the CBL and the BGG. The Spanish Institute of Bioinformatics is currently setting up a large scale benchmarking effort for the monitoring of bioinformatics resources. The main duties of the candidate will be to centralize all existing resources on this topic, and make them available to the community, either as collection of links, packages corpuses of data or integrated tools. This work will be carried out in collaboration with our partners at the CNIO in Madrid, and other bioinformatics research groups in Europe. The position will also involve the development of new tools for the validation and benchmarking of short read assembly mapping and genome or transcriptome assemblers in general. The candidate will also be expected to help setting up web services associated with the benchmarking tools developed in the context of this project. The candidate should have a strong background in sequence analysis and computational biology with a practical knowledge of Perl, C, Java and R (or any languages with similar scopes).

Funding will be available for at least 3 years.

 

 

Post-Doc                     - Ref. CBL2

Comparative Genomics

The CBL lab is looking for a post-doc to contribute to the development of multiple genome comparison tools within the T-Coffee framework. T-Coffee is a multiple sequenced alignment program based on the consistency algorithm originally described by Notredame, Higgins and Heringa (JMB, 2000). Today, this algorithm forms the basis of the most accurate multiple sequence aligners. The goal of this project is to extend the scope of T-Coffee so that it becomes able to deal with genomic data. One of the aims is to make the package able to incorporate low level alignments (as produced by regular model based aligners) and higher level genomics alignments. Another aim of this project will be to integrate the comparison of genomic diversity (CNVs and SNPs) within the multiple comparison frameworks. We are also planning to use the framework thus develop to define new benchmarking methods and explore the effect of sequencing strategies on genomic data interpretation.

 

The successful candidate should have a strong background in sequence analysis and computational biology with a practical knowledge of Perl, C, Java and R (or any languages with similar scopes). The candidate will also be expected to help setting up web services associated with the benchmarking tools developed in the context of this project.

Funding will be available for at least 3 years.

 

 

Pre-Doc                      - Ref. CBL3

Comparative Genomics

A pre-doctoral position is also available within the context of the above-mentioned project. The successful candidate should have a master degree in genomics or bio-informatics, and a strong background in computational biology.

Funding will be available for at least 3 years.

 

Post-Doc                     - Ref. CBL4

Comparative genomics for farm animals (Quantomics)

The CBL and BGG are both part of the Quantomics project an EU-sponsored consortium aiming at analyzing the genomic variability within farm animals (Cattle, Pig, Chicken). The main task of the candidate will be to use available tools in order to design an integrated comparative genomics approach suitable for analyzing the variability in the considered species (cow, chicken, pig). The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for multiple genome comparison (lagan, pecan, TBA, Mauve…). The candidate should also be very skilled with scripting languages such as Perl and R and have an operational knowledge of the UNIX environment.

Funding will be available for at least 2 years.

 

Post-Doc                     - Ref. BGG1

Bioinformatics for the melon project (Melonomics)

 

The BGG is part of the Melonomics project, a project sponsored by Genoma España to sequence the melon genome. Sequencing will be performed using a combination of the traditional BAC based approach, and the new sequencing technologies (454 and solexa).

 The main task of the candidate will be to use available tools, as well as to develop appropriate tools for genome assembly and gene annotation. The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for genome assembly and gene finding and annotation. The candidate should also be very skilled with scripting languages. A background in Plant Genomics is a plus.

Funding will be available for at least 2 years

 

 

Post-Doc                     - Ref. BGG2

RNA reconstruction from data produced by High Throughput Sequencing technologies.

A postdoctoral position is available to develop and apply computational methods to reconstruct and characterize the RNA content of the cell from data produced by high throughput sequencing technologies. Focus will be in quantification of RNA, and in the discovery of novel splice forms, as well as in the understanding of the sequence determinants responsible for the splicing patterns characteristic of particular cell type or condition. The research project will be carried out in collaboration with the group of Juan Valcarcel, a leading expert in the regulation of splicing at the CRG. Familiarity with UNIX/LINUX operating systems, as well as good programming skills in C and scripting languages are necessary, as well as a good statistical and mathematical background.

 

Bioinformatician                    - Ref. BGP1

One bioinformatician is needed to manage the data generated by the next generation sequencing instruments at the CRG (currently one 454 and one solexa, plus, at least, another solexa, arriving in 2009).  The ideal candidate will be a computer scientist, or bioinformatician, with a phD relevant in the field and some additional experience.  We are looking for an individual with ample interests, since at the CRG, next generation sequencing technologies are used for a variety of purposes including ChipSeq, RNASeq, digital expression, de novo genome sequencing,  re-sequencing, detection of copy number variants, etc. The candidate should have a strong background in sequence analysis and computational biology with a practical knowledge of Perl, C, Java and R
(or any languages with similar scopes).



 

 

Database Administrator                       - Ref. DBA-0308

The Database Administrator (DBA) will be in charge of ensuring the proper maintenance of the public databases required for research purposes (e.g. PDB, GenBank, UniProt) and associated resources (e.g. ENSEMBL, ACEdb). He/she will also be responsible for setting up key databases for the institute (Genotyping, Genomic databases). The candidate should be familiar with MySQL, Oracle and be either a biologist or have experience in a biological research environment. The role will involve regular interactions with the various research groups to ensure that the main database needs are covered. The DBA will also design novel biological databases for internal and/or public usage and interact with the system administrator and the various groups to ensure a proper data storage policy. The ideal candidate will be an experienced DBA, familiar with the management of high throughput data and have a solid understanding of scripting (e.g. Perl, MySQL, php, Oracle).

 

 

Scientific Web Master                           - Ref. SWB-0308

The Scientific Web Master will be responsible for the scientific web services offered by the CRG to the scientific community. The CRG is a leader in the development and maintenance of several key scientific resources (geneid, T-Coffee, sgp, SelenoDB, U12db). The successful candidate will be responsible for designing a web framework in which all these projects can be made available to the community in a unified manner. His/her main task will be to design the framework needed for the development and the maintenance of the high impact web services produced by the various groups of the institute, and to organize the scientific content generated by the groups at the CRG.  He/she will work in collaboration with the system administrator and the DBA, ensuring that web services make an optimal usage of the database and computational facilities. The ideal candidate will be an experienced web master, with several years of experience in supporting bioinformatics web services and have a proven track record in utilizing computer-intensive services (e.g. Database search, phylogeny, prediction). The ideal applicant will also be familiar with HPC and have solid programming experience in JAVA, Perl, php, apache, cgi scripting, and Oracle portal.