Bioinformatics Programmer 3

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 ( 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 genomewide (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.

ABOUT DIVISION OF HIV, INFECTIOUS DISEASES AND GLOBAL MEDICINE

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.

Responsibilities

Qualifications

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, bioinformatics, computational biology, physics, and/or statistical genetics, and associated with one or more of the following: HPC hardware and software power and performance analysis and research, design, modification, Implementation and deployment of HPC or data science or CI applications and tools.
• Thorough knowledge of bioinformatics programming design, modification and implementation.
• Understanding of relational databases, web interfaces, and operating systems.
• Strong project management skills. Proven ability to successfully work on multiple concurrent projects.
• Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization.
• Ability to communicate technical information in a clear and concise manner.
• Demononstrated ability to interface with management on a regular basis.
• Self motivated, and able to work independently or as part of a team. Able to learn quickly and effciently, able to meet deadlines and complete projects in a timely manner, and prioritize multiple projects to ensure the completion of essential tasks by deadlines and demonstrate problem solving skills.
• Strong demonstrated ability to deliver high quality work with attention to detail and the ability to meet strict deadlines
• Thorough knowledge of web, application and data security concepts and methods.
• Demonstrated broad experience in one or more of the following: optimizing, benchmarking, HPC performance and power modeling, analyzing hardware, software, and applications for HPC / data / CI
• Expertise in working with genomic, transcriptomic, and/or immunologic (flow cytometry) data and relevant analytic tools (e.g., PLINK, SKAT, R Seurat package, FlowJo)
• Experience in advanced single cell sequencing and genomewide association data analyses
• 3 or more years of directly relevant programming experience
• Demonstrated experience and ability to collaborate effectively with all levels of staff; technical, students, faculty and administrators
• Solid technical understanding and proficiency with programming languages (e.g., R, Python, Perl, Matlab, C/C++) and SQL
• Ease with handling large datasets (e.g., >1 terabyte) and working within Linux-based cloud computing clusters.

Preferred Qualifications:

• PhD degree in Bioinformatics/ Systems Biology/ Math/ Statistics/ Computer / Computational / Data Science, or Domain Sciences with computer / computational / data specialization or equivalent experience. Strong preference for those with experience in advanced single cell sequencing and genomewide association data analyses – especially in the area of translational infectious diseases research.
• Thorough knowledge of modern biology and applicable field of research.
• Prior laboratory-based experience and/or training in the areas of biology, immunology, or genetics and experience conducting research involving molecular biology, immunology, and genetic sequencing techniques – especially related to HIV translational research.
• Humanitarian-minded
• Previous experience working with clinical datasets, especially related to HIV, COVID-19, and other infectious diseases
• Demonstrated ability to contribute research and technical content to grant proposals and manuscript submissions

Education, Licenses and Certifications:

• Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training.
• Master’s degree in Bioinformatics/ Systems Biology/ Math/ Statistics/ Computer / Computational / Data Science, or Domain Sciences with computer / computational / data specialization or equivalent experience.
• 3 or more years of directly relevant programming experience

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 here.

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

Equal Employment Opportunity

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.

Salary Information

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

Your placement within the salary range is dependent on a number of factors including your work experience and internal equity within this position classification at UCSF. For positions that are represented by a labor union, placement within the salary range will be guided by the rules in the collective bargaining agreement.

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