Software Engineer, Scientific Information Retrieval Invitae
San Francisco, CA

Job Description

Invitae is a healthcare technology company that leverages genetic information to empower doctors and patients to make informed medical decisions. Our software engineers work on a variety of projects ranging from innovations in healthcare systems to taming the chaos of biology. We're constantly improving our tools and technologies to deliver the highest quality actionable information to doctors and patients.

About the Scientific Information Retrieval Team

Much of the information needed for interpreting our patients' genetic variants lies in unstructured and semi-structured data sources such as PubMed, ClinVar, and other clinical databases. The Scientific Information Retrieval Team builds NLP tools to centralize and integrate these data in order to scale variant interpretation.

What you will do:

* Design and build pipelines for text mining the biomedical literature using AWS technologies (AWS Batch, Lambda, S3, Dynamo)
* Design and build ETL pipelines for potentially noisy clinical data
* Data analytics to identify bottlenecks in literature search and propose and implement practical solutions

What you bring:

* MS/PhD or equivalent experience in computer science or bioinformatics
* Expert in Python
* Proficient with SQL and NoSQL databases (Postgres, MySQL, S3, Dynamo), ORMs (Django, SQLAlchemy), and IR systems (Solr, Elasticsearch)
* Proficient with Flask, Django, or other web framework
* Experience with PubMed or electronic medical record (EMR) data and with NLP tools (NLTK, spaCy, Apache CTakes, Pubtator)
* Knowledge of one or more biomedical databases and vocabularies (ClinVar, OMIM, Cancer Genome Atlas, COSMIC Catalogue of Somatic Mutations in Cancer, Human Phenotype Ontology, UMLS)
* Domain knowledge in clinical genetics or other related area is a big plus

At Invitae, we value diversity and provide equal employment opportunities (EEO) to all employees and applicants without regard to race, color, religion, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status. We will consider for employment qualified applicants with criminal histories in a manner consistent with the requirements of the San Francisco Fair Chance Ordinance.