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 (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 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.

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of time

Essential Function (Yes/No)

Key Responsibilities

50 Y Applies complex bioinformatics concepts to design, develop, modify, debug, and evaluate software programs, systems, and web tools.

Plans, designs, develops, modifies, debugs, deploys and evaluates complex HPC software and/or hardware, data science or computational science, continuous integration (CI) research software and technologies, or combination thereof for the direct application to genomic and immunologic datasets. These data include genomewide data that includes over 700,000 genetic variants from >1000 people with HIV, single cell transcriptomic data that includes over 30,000 genes from thousands of individual immune cells, and other high-dimensional genomic and immunologic datasets.

15 Y Conducts bioinformatics programming and testing of new algorithms that interact with other related databases.

Develops, implements, and executes complex analytical software and hardware research and development plans. This includes researching and identifying novel analytical and bioinformatics methods to be applied to datasets. Performs complex high performance computing (HPC), computational and bioinformatics modeling, performance and integration testing for direct application to genomic and immunologic HIV datasets.

15 Y Analyzes existing programs or works to formulate logic for new systems, devises logic procedures, flowcharts, data analysis, codes and tests / debugs programs.

Analyzes existing software, scientific codes, data science / analytics codes / algorithms, and HPC related hardware or works to formulate logic for new complex systems and devises complex algorithms for these studies. Performs complex analysis and tests / debugs complex software and hardware.

10 Y Develops, implements, and maintains web interfaces to share and display bioinformatics analysis and content with collaborators and other users.

Develops, implements, and maintains changes to operational systems and databases with collaborators and other users. Performs performance and integration testing, and builds user interfaces for a variety of internal and external constituents. Leads the maintenance of dataservers.

Applies complex programming and mathematical modeling practices while working with domain scientists and overseeing trainees to analyze datasets generated from human clinical trials, epidemiologic observational cohorts (e.g., cardiovascular disease and HIV biospecimen datasets) to perform these responsibilities and adopts, learns, and applies domain science knowledge to these studies.

Document scripts, bioinformatics pipelines, usage modes, capabilities, characteristics and performance of research codes. Document research HPC systems (hardware and software) and CI tools / software. Publishes and presents, based on research and development work, results about CI tools, HPC systems, data science techniques and tools, performance and algorithm enhancement in research venues to attract usage from domain science communities, or to promote latest technologies within the genomics and immunology data science community.

5 Y Recommends and implements changes in development, maintenance and sets system standards for analysis algorithms, tools, and infrastructure.

Leads and meaningfully participates in HPC / data science / CI research proposals and final manuscript reporting of research findings in collaboration with other researchers and Principal Investigator (PI) s from Dr. Lee’s research group and collaborating organizations.This includes presentation at major conferences for dissemination of findings.

5 Y Performs complex data modeling, performance and integration testing, and builds user interfaces for a variety of internal and external constituents.

Understands and applies complex research and development practices, community standards and department policies and procedures relating to work assignments. Interacts with senior level internal personnel. May serve as technical lead for a research and development project of moderate scope. Has the ability to negotiate research and development project plans with interested collaborators, stakeholders and users as applicable.

100%

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