The Department of Medicine is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego and employs 500+ full-time salaried faculty members and 150+ academic appointees. Staff personnel include 800+ staff in 9 bargaining units, students, and volunteers. There are over 250 clinical faculties practicing at multiple sites and hospitals.

Under general supervision of the PI, the incumbent will perform programming and/or assist in design and analysis of systems to decipher the role of genetic variation on human traits. Projects will focus on investigation of structurally complex regions of the genome associated with human diseases using a variety of techniques including graph-based genome representations. The incumbent will be responsible for maintaining computational pipelines for processing, analyzing, and visualizing large volumes of whole genome sequence data and analysis of large biobanks. Pipelines will consist of open source as well as custom software. The incumbent will also develop and maintain web applications and assist in packaging custom software as open source tools. Finally, the incumbent will occasionally be required to coordinate with an international team of scientists to develop data acquisition, analysis, and visualization strategies.

Uses skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms; identifies and resolves a wide range of issues / software bugs. Demonstrates good judgment in selecting methods and techniques for obtaining solutions. Operates independently.

• Seven years of related experience, education/training, OR a Bachelor's degree in related area plus three years of related experience/training.

• Thorough knowledge of bioinformatics methods, applications programming, web development and data structures.

• Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization. Demonstrated interpersonal, written and verbal communication skills and ability to interact effectively and tactfully withindividuals and groups, both within and outside the university.

• Demonstrated experience using Github or a related platform for code maintenance and collaboration.

• Thorough knowledge of bioinformatics programming design, modification and implementation. Demonstrated programming skills in C/C++, Python, R with the ability to work comfortably in a Linux environment.

• Understanding of relational databases, web interfaces, and operating systems.

• Strong project management skills.

• Thorough knowledge of modern biology and applicable field of research.

• Ability to communicate technical information in a clear and concise manner.

• Ability to interface with management on a regular basis.

• Self motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills.

• Thorough knowledge of web, application and data security concepts and methods. Demonstrated understanding of network computer operating system configurations, and experience with managingcross platform network communications and protocols, computer systems analysis and debugging methods, and current techniques for troubleshooting applications and system problems, including general knowledge of data structures, memory management, file systems, and database management techniques.

• Demonstrated ability to maintain high level of confidentiality in handling files and data and clear understanding of the Universities data privacy and acceptable use policies and procedures.

• Demonstrated ability to work comfortably in cloud computing environments, such as Amazon Web Resources.

• Demonstrated experience in virtual machines and designing and creating web applications in HTML, CSS, and Javascript.

• Demonstrated experience with HPC, including job submission and resource management.

• Understanding of whole genome sequencing using various technologies (e.g. short and long reads).

• Employment is subject to a criminal background check.