Computational Biologist

Broad Institute
Job Location: 
Cambridge, MA
Job Description: 

· 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.

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.


· Ph.D. degree in Computer Science, Engineering, Physics, Math, Bioinformatics, Biology, or another relevant field is 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
Salary Grade Info

Contact Information: 
About Our Organization: 

The Broad Institute brings together a diverse group of individuals from across its partner institutions — undergraduate and graduate students, postdoctoral fellows, professional scientists, administrative professionals, and academic faculty.

The culture and environment at the Broad is designed to encourage creativity and to engage all participants, regardless of role or seniority, in the mission of the Institute. Within this setting, researchers are empowered — both intellectually and technically — to confront even the most difficult biomedical challenges.

The Institute’s organization is unique among biomedical research institutions. It encompasses three types of organizational units: core member laboratories, programs and platforms. Scientists within these units work closely together — and with other collaborators around the world — to tackle critical problems in human biology and disease.