The Functional Bioinformatics (FBI) group led by Dr. Michael Sammeth at the CNAG in Barcelona (http://fbi.sammeth.net) is looking for talented candidates who are highly motivated for cutting-edge research in functional genomics and transcriptomics, involving data produced by the latest Next-Generation Sequencing (NGS) technologies.
The FBI group investigates functional aspects of expressed genes, as by their mutual interaction and regulation, to advance in the understanding how the information encoded in a single genome can give rise to a plethora of different cell types that together form an organism.
To achieve these ambitious goals, we employ results of state-of-the-art sequencing experiments applied to the transcriptome (RNA-Seq) and from Chip-Seq assays, most of them carried out at the CNAG (http://www.cnag.eu).
With currently twelve state-of-the-art Illumina HiSeq sequencing machines, the CNAG centre is becoming one of the major high throughput Sequencing Centers in Europe, participating in several consortia of networked projects such as the International Cancer Genome Consortium, and EUfunded projects such as READNA, ESGI, GEUVADIS and BLUEPRINT.

Responsibilities
The successful candidate will be involved in different projects and collaborations, and explore various aspects of data yielded by deep sequencing in order to advance in our understanding about functionality of genomic elements. To this end, the candidate will primarily apply established pipelines to RNASeq and Chip-Seq datasets.
Depending on the candidate’s profile, the FBI also offers the possibility to participate actively in the development of computational approaches for analyzing NGS data, based on the programs Flux Capacitor / Simulator, and Astalavista we have developed.

Candidate profile:
We are looking for a post-doctorate research fellow and a technician with a PhD/Master’s Degree in Biology, Bioinformatics, or related fields.
The CNAG operates a powerful Unix cluster with currently ~1000 cores and 2 Petabyte of disk space; therefore, a profound knowledge of common Unix commands is an essential pre-requirement for the candidate to be eligible. Candidates are also expected to possess a background that provided them with a general knowledge about the biological concepts of gene expression.
The successful candidate will employ statistical frameworks (e.g., the “R” platform) and scripting to pursue comparisons of experimental data. The FBI group already developed pipelines for the low-level data processing, and we support candidates who are interested in extending and improving these computational tools implemented in Java and Groovy.
In addition to these technical skills, we especially encourage candidates with preliminary experiences in genomics, transcriptomics, and/or the analysis of high throughput sequencing data to apply.

Conditions:
We offer a 2-year contract is offered with prospective starting date in june/july or september 2012. Salary will be determined according to the academical degree and experience of the candidate.

Application procedure:
Interested candidates should send their CV to msammeth@pcb.ub.es

Candidate requirements:
PhD after 1 Jan 2009
Bioinformatics and statistical knowledge is mandatory.
R or MATLAB programming skills would be valuable.

For further information, please contact:
Agustín Lahoz (agustin.lahoz@uv.es), including a CV.
Death line: 30 May de 2012.

Perfil buscado:

Requisitos mínimos:
• Licenciado en bioinformática, ingeniería informática, biología molecular, genética o estudios relacionados.
• Experiencia en bioinformática.
• Capacidad de diseñar y desarrollar herramientas bioinformáticas
• Experiencia en programación (p.e. Python/Perl, C++, Java)
• Nivel medio/alto de ingles
Requisitos valorables:
• Experiencia en el análisis de datos de Next Generation Sequencing (NGS) y con bases de datos de información genómica
• Conocimiento de R y Bioconductor
• Conocimiento de varias tecnologías “omicas” además de NGS como por ejemplo qPCR de alto rendimiento, digital PCR, proteómica y/o experiencia de integración de diferentes tecnologías “omicas”
El personal se incorporaría inicialmente en el contexto de un proyecto de colaboración industrial entre el Centro Nacional de Biotecnología-CSIC e Integromics.

Contacto:
Hilmar Berger
hilmar.berger@integromics.com
Integromics S.L. , Tres Cantos, Madrid

General description:
The candidate will work in a multidisciplinary team involved in the development and application of biomedical text mining and natural language processing approaches. The overall aim of this work is to develop and apply text mining and natural language processing technologies to biomedical literature, covering aspects related to automatic text classification using machine learning methods, the detection of named entity mentions of biological interest from text and the extraction of relationships from the biomedical literature. A special focus will be given to certain topics such as cancer related literature.

Requirements:
-Applicants should have a solid formation in computational linguistics, Natural Language Processing, text mining or related areas.
-Ability to develop algorithms and software for natural language processing/text mining systems.
-Programming skills are required, in at least one of the following languages (Python, Perl, Java, C/C++, Ruby).
- Good English communication skills.
- Interest in the Biomedical field.
Expertise in the following points are a plus when applying for the position:
-Formation on topics related to statistics and machine learning.
-Development of online web applications.
-Previous experience with biomedical texts/domain.
-Ability to work in an interdisciplinary team.
-A publication record would be an advantage.
- Familiarity with NLP tasks such as named entity recognition, information extraction and information retrieval.

Background on our research group:
The Structural and Computational Biology Programme at CNIO, leaded by Dr. Alfonso Valencia integrates several research groups, including Computational Biology, Bioinformatics and text mining.
The computational facilities and infrastructure cover all the needs of the research in modern text mining and NLP, computational biology and provides excellent grounds for the  analysis of high-throughput genomic data. The research group contributed significantly to the biomedical text mining research over the past years, from initial work related to the analysis of protein families, microarray data and protein interactions to the development of online applications such as the iHOP server, PLAN2L or the BioCreative Metaserver. The group collaborates with experimental biomedicine labs to integrate NLP and text mining data with the results of bioinformatics data. It has been coorganizing community evaluation efforts in the BioNLP area, i.e. the BioCreative challenges.

Contact info:Requests for additional information or formal applications (including application letters, extensive CV) can be sent to Martin Krallinger (mkrallinger@cnio.es)

Read all the information here

Agustín Lahoz, PhD
Metabonomics and Chemometrics
Unit of Experimental Hepatology
Instituto de Investigación Sanitaria- Fundación Hospital La Fe
Semisótano. Escuela de Enfermería.
Avda./ Campanar, 21
46009 Valencia
Telf: 96 197 34 85
M: 618733341-Corp:485622
Fax: 96 349 44 16

Agustín Lahoz, PhD
Metabonomics and Chemometrics
Unit of Experimental Hepatology
Instituto de Investigación Sanitaria- Fundación Hospital La Fe
Semisótano. Escuela de Enfermería.
Avda./ Campanar, 21
46009 Valencia
Telf: 96 197 34 85
M: 618733341-Corp:485622
Fax: 96 349 44 16

The Institute of Systems and Synthetic Biology (iSSB) has an immediate postdoctoral opening in the field of computational protein design. The institute is part of Genopole, a consortium of leading research academic and private laboratories in genomics, post-genomics and related sciences. The job location is in Evry, 35 km south of Paris, 30 min by suburban train.

Job Description: The position awardee (1 year renewable) will be responsible for developing new computational methods and using existing retrosynthesis and reaction kinetics tools to design enzymes involved in a variety of processes including the production of exogenous chemicals (drugs, drug precursors and fine chemicals) and the toxicology of chemical mixtures.

Qualifications: The successful candidate will have a recent Ph.D. in biology, chemical/physical sciences, or computer and engineering sciences with a background in biology. Required qualifications include experience with bioinformatics or chemoinformatics demonstrated though publications, experience with machine learning, programming skills, strong collaborative skills and ability to work and communicate in a team environment.

We offer a competitive compensation package, which will be commensurate upon qualifications and experience. Applicants should send their CV, a cover letter, and the names of two eferences to Dr. Pablo Carbonell, to the following e-mail address: pablo.carbonell@issb.genopole.fr.