Computational Biologist

Broad Institute
Job Location: 
Cambridge, MA
Job Description: 

The role of this researcher will be to contribute to the development and maintenance of the Trinity de novo transcriptome assembly software and related framework for reference-based and genomefree transcriptome studies. This requires developing and applying new and existing computational methods to facilitate transcriptome reconstruction and analysis, and being able to interpret results within the larger biological context.

The role involves direct interaction and collaborative development with co-workers in the laboratory of Aviv Regev, the Klarman Cell Observatory, other groups within the Broad Institute, and the growing Trinity user and development community. Responsibilities further include communication of results to the scientific community at Broad and externally through conference presentations, peer-reviewed publications, and project reports.

- Assist in the development and maintenance of Trinity and related RNA-Seq analysis tools and pipelines, including documentation, testing, and benchmarking.
- Devise new algorithms and software to tackle challenges in transcriptome reconstruction and analysis, coupled with publications in scientific journals.
- Lead or participate in workshops that provide training for transcript reconstruction and analysis using Trinity and related software tools.
- Present at scientific conferences, as appropriate.
- Support additional group research projects, as needed.

- Ph.D. degree in Computer Science, Engineering, Physics, Math, Bioinformatics, Biology or other relevant scientific discipline or equivalent experience required.
- Must have demonstrated experience designing computational methods and tools, including prior experience with algorithms relevant to computational biology. Skill and experience with probabilistic modeling and statistical analysis is strongly preferred.
- Have previously published articles relevant to computational biology or genomics.
- Familiarity with next-generation sequence data analysis tools, ideally for Illumina.
- Familiarity with a range of sequence alignment tools, ideally those used for RNA-Seq (Trinity, Tuxedo, etc.)
- Must have demonstrated proficiency with several of the following technologies: Unix, Perl, Python, Java, C++, R, and ideally have experience with relational databases (MySQL, SQLite) and web application development (Javascript, CSS).
- Basic understanding of molecular biology and next generation DNA sequencing
- Understanding of gene structure annotation and alternative splicing, and experience using genome browsers.
- Ability to work independently while making necessary connections with experts in various computational analysis groups
- Highly collaborative and works well with others.
- Self starter, highly motivated
- Extraordinary enthusiasm for computational molecular biology
- Excellent communication skills
- Excellent organization and time management skills

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