Bioinformatics Programmer 3

University of California, San Francisco•San Francisco, CA

About The Position

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. Dr. Lee’s research group focuses on clinical and translational research, including observational cohort and clinical trial studies on infectious diseases like HIV and SARS-CoV-2. The Bioinformatics Programmer 3 will support the computational aspects of this research group, working with project directors and collaborators to design and implement data analysis methods for multidisciplinary projects. These projects involve analyzing host genomewide data (whole genome sequencing, GWAS microarray), single cell sequencing (10X scRNA/VDJ/ATAC/antibody), pathogen-specific assays (HIV reservoir quantification, HIV-host integration PCR), and applying advanced statistical modeling (linear and nonlinear mixed effects modeling, causal inference modeling). The role involves leading and designing complex analyses, managing research group server space (UCSF Wynton HPC cluster), and mentoring trainees. A strong background in mathematics, biostatistics, statistical genetics, and bioinformatics is required, along with excellent interpersonal and communication skills for interdisciplinary collaboration. The candidate will function as an experienced bioinformatics programming professional, identifying and resolving software issues, and operating independently. ABOUT DIVISION OF HIV, INFECTIOUS DISEASES AND GLOBAL MEDICINE: The Division of HIV, Infectious Diseases and Global Medicine at UCSF is a global leader in clinical care, research, and education, based at ZSFG. It is the top-ranked facility for AIDS care in the country and comprises approximately 38 faculty, 14 fellows/postdoctoral scholars, and 170 academic and staff employees. It is the largest Division in the Department of Medicine (DOM) at ZSFG, with a budget of approximately $52 million.

Requirements

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.
Demonstrated 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 efficiently, 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.
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

Nice To Haves

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

Responsibilities

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.
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.
Researches and identifies 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.
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.
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.
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.
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.