BIOINFORMATICS PROGR 2 RP

Job Summary

Involves developing and utilizing computational tools and systems to analyze and interpret biological or other research data. Utilizes and develops algorithms, computational techniques, and standard statistical methodologies. Helps in the design of new experiments and leads the execution of building machine learning and statistical models. Implements end-user needs in database development, maintenance, searching, and integration. Maintains computational infrastructure and manages and tracks the flow of samples and information for large-scale studies. Provides bioinformatics and access to public and proprietary databases. Manages cloud and on-premises computational infrastructure and data.

Generic Scope

Professional who applies acquired job skills, policies, and procedures to complete substantive assignments / projects / tasks of moderate scope and complexity; exercises judgment within defined guidelines and practices to determine appropriate action.

Custom Scope

Our research efforts are at the intersection of cardiovascular disease and human genetics. Our clinical research efforts employ new techniques for deep phenotyping, such as deep learning. But these techniques rely on a solid foundation of classical bioinformatics. The Bioinformatics Programmer/Data Scientist will assist in managing, cleaning, and analyzing large scale medical data using a wide variety of analytic techniques, both in the cloud and with on-premises compute depending on data permissions. Experience with a cloud provider such as AWS, Microsoft Azure, or Google Cloud is a plus, and ability to learn how to manage cloud-based pipelines, and to perform cloud data management will be essential skills to develop and maintain.

Maintaining bioinformatic databases by obtaining and restructuring data, including both UCSF proprietary data and public data, and writing tools to streamline discovery and replication analyses using these databases will be core responsibilities. An important task will be writing and maintaining analytic pipelines in languages such as R, python, Go, Rust, shell, SQL, WDL, and/or other appropriate languages, and using tools such as Docker. Experience with databases or the ability to learn will be requisite.

Under the supervision of the PI, the Data Scientist will also be involved in data analysis, and will be comfortable with bioinformatic analyses including variant calling and annotation. There will be opportunities to employ cutting-edge methods and to develop new methods. The ability to learn and implement new techniques depending on the problem at hand will be an essential skill, thus requiring a strong foundation in computer programming.

This position will also include administrative duties and will have the opportunity to participate in—and to lead—authorship teams.

DEPARTMENT OVERVIEW

The Division of Cardiology is one of the largest clinical, research and training divisions of the Department of Medicine (DOM) at UCSF. Within the Division are nine sub-specialty sections for: Adult Congenital Heart Disease; Advanced Heart Failure, Transplant, and Pulmonary Hypertension; Cardiac Electrophysiology; Cardio-Oncology and Immunology; Critical Care Cardiology; Echocardiography and Cardiac Imaging; General Cardiology; Interventional Cardiology; and Prevention.

The Division runs several clinical practices in multiple sites, conducts basic and clinical research, and educates medical students, residents, clinical fellows and postdoctoral scholars through ACGME as well as non-ACGME training programs. In addition, the Division has significant and complex financial and administrative relationships with DOM and the UCSF Medical Center, as well as large patient care programs in the sections noted above, large clinical, Federal, and privately supported research programs and six faculty laboratories.

The Division has over 80 full-time faculty, and 39 clinical fellows. The Division currently expends over $22 million per year in pursuit of its clinical, research, training, and service missions. While the Division is primarily split between the Parnassus and Mission Bay campuses, fellows have rotations at the Zuckerberg San Francisco General Hospital (ZSFG) and the San Francisco Veterans Affairs Medical Center (SFVAMC).

The Pirruccello lab is also part of the Bakar Computational Health Sciences Institute and the Institute for Human Genetics at UCSF, and the Data Scientist will be part of the larger computational community and infrastructure.

ABOUT UCSF

The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10-campus UC system dedicated exclusively to the health sciences.