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Old 05-07-2014, 05:10 AM   #1
Marcos Ramos
Junior Member
Location: Portugal

Join Date: Oct 2013
Posts: 6
Default Bioinformatician – Cork Oak Genome Sequencing Project

Bioinformatician – Genosuber - Cork Oak Genome Sequencing Project

Are you interested in joining a challenging and exciting genome sequencing project and work in a warm sunny city in the south of Portugal? CEBAL (Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo) has available a postdoc position in the frame of Genosuber - Cork Oak Genome Sequencing Project (, ref ALENT-07-0224-FEDER-001754 funded by InAlentejo. The project involves several Portuguese research institutions and industry partners. The project goals are to sequence and annotate the cork oak genome, and unravel the molecular mechanisms controlling cork formation, using data generated with several high-throughput sequencing technologies.

Scientific Field
Life Sciences, Genetics, Bioinformatics

Description of the position
For this position we are looking for a highly motivated bioinformatician with experience in processing and analyzing high-throughput sequence data. The successful candidate will be involved in the assembly and annotation of the cork oak genome. Additionally, he/she will also participate in ongoing projects involving transcriptomics, epigenetics and genetic marker development, with the goal of determining the molecular mechanisms that control cork formation. Previous experience with de novo assembly and annotation of genomes and/or transcriptomes is extremely valuable. Expertise in the processing and analysis of Pacific Biosciences sequence data will be valued. Programming in Perl and/or Python, as well as experience with software for analysis of genomics and high-throughput sequence data, are essential. The successful candidate will be part of a multidisciplinary team, and will work closely with the project’s senior scientists and biologists.

• Process and analyze high-throughput sequence data, using custom scripts and publicly available software
• Apply state-of-the-art computational tools for the assembly and annotation of the cork oak genome
• Contribute to scientific projects aimed at deciphering the genetic mechanisms for cork formation
• Participate in the design and/or execution of experiments conceived to answer the project’s goals
• Maintain and document data analyses pipelines
• Play an active role in the development and maintenance of the infrastructure related to bioinformatics
• Keep updated knowledge about the latest developments in the bioinformatics field, contributing when necessary to improve the project’s hardware/software/analysis capabilities

• PhD degree in bioinformatics, genetics, computational biology or related field. Candidates without a PhD degree, but meeting the other requirements, can also apply.
• At least 1 year experience in the bioinformatics field
• Previous experience in analysis of high-throughput sequence datasets is essential; familiarity with genome assembly and annotation is highly desirable, as well as previous involvement in projects where transcriptomics and/or epigenetics approaches were used
• Strong programming skills in Perl and/or Python
• Excellent skills and demonstrated experience in UNIX/LINUX programming
• Strong problem solving skills
• Ability to provide information in a clear and concise way
• Strong interpersonal skills and ability to interact with project members in a team-oriented effort

Work place
The position will be based at CEBAL, in Beja, Portugal. The scientific coordination will be provided by Drs. Marcos Ramos (INIAV) and Sónia Gonçalves (CEBAL).

The position will be available for 17 months, with the possibility of extension, depending on funding availability.

The salary will consist of 32,000 euros per year. It can be increased for outstanding candidates, and will be adjusted for candidates without a PhD degree.

Selection criteria
The selection criteria will be the following:
• Expertise in bioinformatics (50%)
• Previous experience in genome assembly and annotation (30%)
• Publication record (20%)

Selection committee
The selection committee will consist of Dra. Sónia Gonçalves (CEBAL), as president, Dr. Marcos Ramos (INIAV) and Dr. Margarida Oliveira (ITQB), and Dr. Jose Matos (INIAV), as an alternative committee member.

Publication of the results
The results will be communicated to all candidates by e-mail.

Application procedure
The applications should be sent by email to:, and include a CV, motivation letter, copy of relevant diplomas and contact details of two references.
The application deadline is 30th May 2014.
The successful candidate can start the position as soon as possible.
For more information about this position please contact Dr. Marcos Ramos ( or Dr. Sónia Gonçalves (
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