Bioinformatics Progr 2

Job Description
Clinical imaging and genetic data at scale are powerful tools for biological discovery and risk prediction. Carefully structured analyses and reproducible analytic pipelines accelerate ongoing efforts to gain clinically relevant insights.

Our research efforts are at the intersection of cardiovascular disease and human geneticsincluding both somatic and germline variation. 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 onpremises compute depending on data permissions. Experience with a cloud provider such as AWS or Google Cloud is a plus and ability to learn how to manage cloudbased pipelines and to perform cloud data management will be essential to learn. 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 cuttingedge 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 inand to leadauthorship teams.

The final salary and offer components are subject to additional approvals based on UC policy.

To see the salary range for this position (we recommend that you make a note of the job code and use that to look up): TCS NonAcademic Titles Search note: An offer will take into consideration the experience of the final candidate AND the current salary level of individuals working at UCSF in a similar role.

For roles covered by a bargaining unit agreement there will be specific rules about where a new hire would be placed on the range.

To learn more about the benefits of working at UCSF including total compensation please visit: degree in biological science computational / programming or related area and one or more years of relevant experience and / or equivalent experience / training

Working knowledge of bioinformatics methods and data structures

Working knowledge of biostatistics and basic statistical testing

Working knowledge of systems programming and databases

Working knowledge of application and data security concepts

Ability to effectively manage time and see assigned parts of projects through to completion on deadline

Basic consultation and communication skills

Demonstrated fluency and competency with statistical programming with the R programming language or the Python programming language

Experience with or a demonstrated ability to learn and implement data management and computational pipelines for management of largescale data

At least 6 months of experience in direct data management and analysis using medical and/or healthrelated data using the above tools

Ability to lead and maintain data pipelines for realtime data acquisition from clinical systems

Ability to multitask and work well with limited supervision

Working project management skills

Interpersonal skills in order to work with both technical and nontechnical personnel at various levels in the organization

Ability to communicate technical information in a clear and concise manner

Selfmotivated able to learn quickly meet deadlines and demonstrate problem solving skills

• MS or greater in a related science or an equivalent combination of education and experience
• PhD in a field relevant to biomedical research (bioinformatics biomedical engineering) or computer science (computer science machine learning artificial intelligence) or similar
• 12 months or more of demonstrated work experience using medical and/or healthrelated data or similar including developing pipelines for extracting transforming and loading data and data analysis

Equal Employment Opportunity
The University of California San Francisco is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race color religion sex sexual orientation gender identity national origin age protected veteran or disabled status or genetic information.

Department Description
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 subspecialty sections for: Adult Congenital Heart Disease; Advanced Heart Failure Transplant and Pulmonary Hypertension; Cardiac Electrophysiology; 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 nonACGME training programs. In addition the Division has significant and complex financial and administrative relationships with the Department of Medicine (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 74 fulltime faculty 13 nonfaculty academics 38 clinical fellows 8 postdoctoral research fellows and over 65 researThe 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 subspecialty sections for: Adult Congenital Heart Disease; Advanced Heart Failure Transplant and Pulmonary Hypertension; Cardiac Electrophysiology; 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 nonACGME training programs. In addition the Division has significant and complex financial and administrative relationships with the Department of Medicine (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 74 fulltime faculty 13 nonfaculty academics 38 clinical fellows 8 postdoctoral research fellows and over 65 research support and administrative staff and 12 staff centrally for fellowship support nonsponsored finance HR digital communications and faculty administrative support. 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 and the San Francisco Veterans Affairs Medical Center.

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 graduatelevel education in the life sciences and health professions and excellence in patient care. It is the only campus in the 10campus UC system dedicated exclusively to the health sciences. We bring together the worlds leading experts in nearly every area of health. We are home to five Nobel laureates who have advanced the understanding of cancer neurodegenerative diseases aging and stem cells.

Pride Values
UCSF is a diverse community made of people with many skills and talents. We seek candidates whose work experience or community service has prepared them to contribute to our commitment to professionalism respect integrity diversity and excellence also known as our PRIDE values.

In addition to our PRIDE values UCSF is committed to equity both in how we deliver care as well as our workforce. We are committed to building a broadly diverse community nurturing a culture that is welcoming and supportive and engaging diverse ideas for the provision of culturally competent education discovery and patient care. Additional information about UCSF is available at

Join us to find a rewarding career contributing to improving healthcare worldwide.