Data Scientist

University of California San Francisco; San Francisco (CA); On-site; USD 80,000 - 110,000; Full time

Job summary

Join a leading university dedicated to health worldwide as a Bioinformatics Programmer/Data Scientist. This role involves managing and analyzing large-scale medical data, employing cutting-edge techniques in bioinformatics and deep learning. You'll write and maintain analytic pipelines, work with cloud-based data management, and collaborate with a diverse team of experts. The position offers opportunities for professional growth and the chance to contribute to meaningful research in cardiovascular disease and human genetics. If you are passionate about data science and its application in healthcare, this is the perfect opportunity for you.

Qualifications

• 1+ years of experience in data management and analysis using medical data.
• Fluency in R or Python for statistical programming.
• Ability to lead and maintain data pipelines.

Responsibilities

• Manage, clean, and analyze large scale medical data.
• Write and maintain analytic pipelines in R, Python, or other languages.
• Participate in data analysis and bioinformatic analyses.

Skills

Bioinformatics methods

Data management

Statistical programming (R, Python)

Systems programming

Biostatistics

Communication skills

Education

Bachelor's degree in biological science or related area

MS or greater in a related science

PhD in bioinformatics or computer science

Tools

AWS

Google Cloud

Docker

SQL

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 genetics—including 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 on-premises 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 cloud-based 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 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.

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

Please 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.

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 sub-specialty 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 non-ACGME 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 full-time faculty, 13 non-faculty academics, 38 clinical fellows, 8 post-doctoral 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 sub-specialty 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 non-ACGME 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 full-time faculty, 13 non-faculty academics, 38 clinical fellows, 8 post-doctoral research fellows, and over 65 research support and administrative staff, and 12 staff centrally for fellowship support, non-sponsored 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.

Required Qualifications

• Bachelor's 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 large-scale data
• At least 6 months of experience in direct data management and analysis using medical and/or health-related data using the above tools
• Ability to lead and maintain data pipelines for real-time data acquisition from clinical systems
• Ability to multi-task and work well with limited supervision
• Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization
• Ability to communicate technical information in a clear and concise manner
• Self-motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills

Preferred Qualifications

• 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 health-related data, or similar, including developing pipelines for extracting, transforming, and loading data, and data analysis

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. We bring together the world’s 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 diversity.ucsf.edu

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

The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law.

Organization

Campus

Job Code and Payroll Title

009402 BIOINFORMATICS PROGR 2

Job Category

Clinical Systems / IT Professionals, Research and Scientific

Bargaining Unit

99 - Policy-Covered (No Bargaining Unit)

Employee Class

Percentage

100%

Location

Campus

Mission Bay (SF)

Work Style

Fully On-Site

Shift

Days

8 Hours

Monday-Friday 8:00am-5:00pm

Data Scientist | University of California San Francisco