HPO-related job offers in the Robinson lab


Prof. Dr. Peter Robinson
 

The Robinson lab at the Jackson Laboratory (JAX) invites applications for
--
Software Engineer
-- Bioinformatician
-- Postdoctoral associate
-- Biocurator

...to join a highly interactive, supportive, and interdisciplinary group of faculty, staff scientists, postdoctoral fellows, and students and enjoy access to state-of-the-art equipment and facilities at the The
Jackson Laboratory for Genomic Medicine in Farmington, CT. Peter Robinson is one of three principal investigators (PIs) of the Monarch Initiative, an integrative data and analytic platform connecting phenotypes to genotypes across species and is a member of the the JAX Center for Precision Genetics, contributing bioinformatic resources to support research employing genetically well-defined laboratory mice. 

The Software Engineer will play an important role in advancing the mission of the Robinson lab, which focuses on developing algorithms, ontologies, and software to advance research and support medical practice. The Robinson lab leads the development of the Human Phenotype Ontology (HPO), which has become the international standard for computational phenotype analysis in Mendelian disease and other areas. The lab has recently spearheaded the development of the Medical Action Ontology (MAxO), which intends to provide a computational foundation for searching and analyzing treatments and other medical management with a focus on genetic disease. The lab develops software for phenotype (HPO) driven diagnostics including the Phenomizer and LIRICAL. We develop graph algorithms including the first use of random-walk analysis for disease gene prediction, which was cited over 1000 times (Walking the interactome...). We have developed machine-learning and statistical approaches towards predicting pathogenicity of variants in exome or genome sequencing, including Genomiser and SQUIRLS. We develop software for the analysis of genomic data including ChIP-seq, which applies a novel saturation-based algorithm and RNA-seq, which uses a hierarchical Bayesian network to simultaneously assess gene expression and alternative splicing. Our Exomiser software is widely used by projects such as the 100,000 Genomes project to assess diagnostic exome and genome data. Peter Robinson leads the machine learning subgroup of the National COVID Cohort Collaborative (N3C), and recent projects have included the application of machine learning to EHR data of COVID-19 patients.

Our lab strives to be a welcoming and supportive environment where people of all backgrounds have the opportunity to develop algorithms and software at the cutting edge of translational bioinformatics. Lab members typically focus on one or two areas of interest in fields such as ontologies, semantic algorithms, or machine learning. We provide extensive on-the-job training in algorithms and software engineering as needed for the projects. 

Expectations

As a rule, we have learned about algorithms during the projects and so we do not expect candidates to come to us with knowledge of the above mentioned topics, but we do expect a strong interest in ontologies or algorithms and a desire to create good software. The candidate would be expected to contribute to a diverse portfolio of research undertaken by the lab. The Robinson lab is very collaborative, taking a team science approach to many projects and participating in efforts such as the Global Alliance for Genomics and Health (GA4GH). We expect the candidate to participate in collaborations, which means concretely participating in virtual conferences and co-developing code using GitHub. Other duties include contributing to publications, submission of grants and funding applications, potential commercialization opportunities, as well as partnerships and collaborations with the community-wide efforts aimed at promoting open, integrated, and rigorous practices in research and scholarly communication. This position may be eligible for remote or remote/office flex work.

The Robinson lab develops software mainly in Java and Python but works with a range of other technologies such as SQL, JavaScript, C++, Rust, and R.

Please contact Peter with questions or go to the following links

Postdoc -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Postdoctoral-Associate---Bioinformatics_JR000362

 

 

Bioinformatician -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Bioinformatician-I-II-III_JR000396

 

 

Software Engineer – to be reposted shortly (please contact Peter).

 

Scientific Curator -

https://thejacksonlaboratory.wd1.myworkdayjobs.com/External_JAX/job/Farmington-Connecticut/Scientific-Curator_JR000398