Bioinformatics Programmer

Job Description Job Summary

The Division of HIV, Infectious Diseases and Global Medicine at Zuckerberg San Francisco General Hospital (ZSFG) is an internationally recognized global leader in HIV clinical care, research and education and has grown to encompass a network of specialty clinics, multiple research and clinical trials, an infectious diseases/HIV education program, an international research program in East Africa and a vibrant community forum for clinicians and researchers.

Dr. Lee’s research group (https://sulggileelab.ucsf.edu/), housed within the division, focuses on clinical and translational research, and in particular, observational cohort and clinical trial studies that focus on infectious diseases, such as HIV and SARS-CoV-2. The Bioinformatics Programmer 3 will work closely with the Principal Investigator and Study Investigators in running the computational aspects of Dr. Lee’s research group. They will have the unique opportunity to work directly with project directors and research collaborators to help design and implement data analysis methods to analyze a wide range of multidisciplinary projects.

These include host genome wide (e.g., whole genome sequencing, GWAS microarray), single cell sequencing (e.g., 10X scRNA/VDJ/ATAC/antibody), pathogen-specific assays (e.g., HIV reservoir quantification by droplet digital PCR methods, HIV-host integration PCR assays) and applying advanced statistical modeling approaches to these data (e.g., linear and nonlienar mixed effects modeling, causal inference modeling). The incumbent will lead and help design complex analyses applying novel computational methods and managing the research group’s server space (e.g., UCSF Wynton HPC cluster), assist in overseeing and mentoring trainees (e.g., postdoctoral fellows, graduate students), and be a major part of bringing the analysis projects to completion.

The candidate should have a strong background in mathematics, biostatistics, statistical genetics, and bioinformatics. They should have strong interpersonal and communication skills to be able to interact with an interdisciplinary collaborators (clinical and laboratory-based). The candate should use skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms and systems; identifies and resolves a wide range of issues / software bugs.

They should also demonstrate good judgment in selecting methods and techniques for obtaining solutions and operates independently as a leader and team member.

The Division of HIV, Infectious Diseases and Global Medicine at the University of California, San Francisco (UCSF) is an internationally recognized global leader in clinical care, research, and education. With its home-base located at Zuckerberg San Francisco General Hospital and Trauma Center (ZSFG), the Division has been ranked as the top facility in the country for AIDS care since 1983. The Division’s work is featured frequently in the media, and it is often visited by numerous international, national, state, and local dignitaries and delegations.

The Division consists of approximately 38 faculty members, 14 fellows/postdoctoral scholars and 170 academic and staff employees. It is the largest Division of the Department of Medicine (DOM) at ZSFG, with a total expenditure budget of approximately $52 million dollars.

Required Qualifications:

• Thorough knowledge of bioinformatics methods, applications programming, web development and data structures.
• Advanced knowledge of HPC / data science / CI
• Advanced skills, and 2-3 years demonstrated experience in the area of bioinformatics, computer science, mathematics,…