Positions

Multiple Postdoctoral Fellow and Software Developer positions

Description:

The Huttenhower lab in the Department of Biostatistics at the Harvard T.H. Chan School of Public Health (http://huttenhower.sph.harvard.edu) and Broad Institute is seeking multiple Postdoctoral Fellows and Software Developers for several recently funded positions. These fall under the broad umbrella of basic and population health research to understand molecular function in the microbiome as it affects human health, and specifically bioinformatic methods development and applications in the following areas:

  • Computational and biostatistical methods development for multi’omic molecular data integration and characterization in the human microbiome and other microbial communities. This includes extension of reference-based functional profiling methods such as HUMAnN2, strain profiling methods such as StrainPhlAn and PanPhlAn, and extensions to assembly-based methods for novel microbial gene variant discovery, prioritization, and automated function prediction.

  • Software development for the JDRF Microbiome Initiative Bioinformatics Center (http://jdrf-mibc.org), the Human Microbiome Project Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), the Human Microbiome Bioactives Resource (http://microbiome-bioactives.org), and the bioBakery (http://huttenhower.sph.harvard.edu/biobakery). This includes a combination of scientific software development in Python and R, and web application development using Django / Flask and HTML / CSS / Javascript.

  • Analyses of the gut microbiome in type 1 diabetes in the context of the Juvenile Diabetes Research Foundation (JDRF) and The Environmental Determinants of Diabetes in the Young (TEDDY) consortia. Data comprise over 12,000 longitudinal infant gut metagenomes and host genome sequencing with accompanying clinical, environmental, and lifestyle metadata, in addition to diverse metagenomic, amplicon, and host molecular profiling from collaborator groups in the JDRF Microbiome Initiative.

  • Strain and functional profiling of the gut microbiome in inflammatory arthritis, as the bioinformatics lead for the Inflammatory Arthritis Microbiome Consortium (IAMC). This research targets shotgun metagenomics for three primary populations: children with juvenile arthritis variants, cross-sectional rheumatoid arthritis and related phenotypes in adults, and longitudinal microbiome samples from newly diagnosed patients undergoing treatment. In addition to carrying out primary analyses on associated gut metagenome profiles, the Fellow will have the opportunity to collaborate with IAMC members investigating parallel gnotobiotic animal models, IgA-seq, and immune cell profiling.

At least one of these funded postdoctoral positions will be hired at a more senior research associate level, with additional mentoring, teaching, and research administration responsibilities (and corresponding additional leeway to direct and carry out research projects). All postdoctoral and software developer positions will have the opportunity to integrate with the group’s wet and dry laboratory facilities and researchers, who include bioinformaticians, microbiologists, translational researchers, statisticians, and computer scientists. The group overall works closely with the Harvard Chan School, the Broad Institute, the Dana-Farber Cancer Institute, and the broader Boston biomedical and life sciences communities, resulting in a rich environment for quantitative, computational, and laboratory collaborations.

Note that the group includes both wet and dry lab researchers, so both primarily computational (with biological experience) and primarily experimental (with quantitative experience) postdoctoral applicants are welcomed. Software developers should have demonstrable experience in a production software environment, but prior biological experience is not required; portfolios and/or code examples are appreciated. Please send application materials (CV and cover letter) to chuttenh@hsph.harvard.edu AND levesque@hsph.harvard.edu.

Qualifications:

For postdoctoral or research associate positions: Doctoral degree in Computer Science, Bioinformatics, Biostatistics, Quantitative Biology, or related field; experience and proficiency in Linux/Unix command line and research environments; working knowledge of Python and/or R, in addition to other scripting environments appropriate for scientific data management; basic familiarity with scientific software management and cloud computing environments; excellence in research, communication, and collaboration skills, as evidenced by publication record.

For software development positions: Bachelor’s, Master’s, or Doctoral degree in Computer Science or related field; experience in a professional software development environment, including good software engineering practices, software lifecycle management, documentation, revision control and change management, and testing; experience and proficiency in Linux/Unix, cluster, and cloud computing environments (particularly Slurm, LSF, and the Amazon EC2 and/or Google Clouds); prior biological or bioinformatic experience is not required but is beneficial.

Additional information:

Positions are based at either the Harvard T.H. Chan School of Public Health or at the Broad Institute, both of which offer outstanding benefits packages including vacation time, insurance, transportation, and work-life support:

https://www.hsph.harvard.edu/faculty-affairs/postdoctoral-research-fello... https://www.broadinstitute.org/benefits/benefits-working-broad

The Harvard and Broad Research Associate / Scientist career tracks are described at:

https://www.hsph.harvard.edu/faculty-affairs/annual-appointments/annual-... https://www.hsph.harvard.edu/faculty-affairs/research-scientist-appointm...