The Division of Infectious Diseases in the Department of Medicine was established in 1969 and since then has grown to have 40+ faculty members. Our research space is located in several buildings on and off campus including the Clinical Teaching Facility, the Antiviral Research Center in Hillcrest, the Stein Clinical Research Building, the Moores Cancer Center, the Biomedical Research Facility, the San Diego VA Medical Center, the Cellular and Molecular Medicine East Building, and the George Palade Laboratories for Cellular and Molecular Medicine. Major international collaborations in Mozambique, Mexico, India, South Africa and Peru play important roles in the Division's expansion of its international programs.

The division continues to grow and expand with the development of our international medicine program, as well the ongoing studies and interests of our faculty.

Under general direction, the Senior Research Associate will make significant innovative contributions in research focused on viral pandemics. In this capacity, the incumbent will use their extensive knowledge of virology, immunology, molecular biology and next generation sequencing.

This position requires an individual who is able to design, implement and execute experiments and groups of experiments related to major research projects without specific day-to-day direction. The individual is required to execute laboratory phases of major research projects over a considerable period to time. The successful candidate will be expected to contribute to the formulation of innovative approaches and the development of novel assays to further our understanding of the population genetics of HIV. Assays include assessing the development of drug resistance, viral latency and persistence in the face of ongoing therapy through sequence analysis and quantitative analysis of viral and cellular transcriptional patterns. Experience with specific "Unique Integration Site (UIS) Sequencing" of HIV is a plus. Requirements include several years of experience in the use of high-density immuno-profiling platform to study immune responses of pandemic viruses and the interpretation of data accumulated. Several years' experience in both academic and biotechnology (industry) research and a demonstration of intellectual productivity through prior authorship or co-authorship in significant scientific publications is strongly desired.

Duties will include designing, executing, and providing key insights into the design and implementation of methods to study UIS for HIV in the human genome, conceiving research hypotheses and analyzing sequencing data, reporting experimental findings, as well as analyzing the results and completing complete written reports.

• Advanced theoretical knowledge of infectious diseases, specifically, understanding of HIV infection, including dynamics in vivo, clinical sequelae and assays.

• Demonstrated familiarity with next-generation sequencing (NGS) methods, data formats and data analysis, as well as understanding of quantitative bio-assay methods, including digital PCR.

• Demonstrated familiarity with statistical analysis of digital PCR data, real-time PCR data or similar quantitative bio-assay data.

• Demonstrated ability to work successfully both independently and in a team setting.

• Demonstrated data processing experience including data entry procedures and quality assurance processes.

• Demonstrated experience in management of a staff involving complex projects or studies.

• Demonstrated ability to obtain and respond to sensitive and personal health information in a professional manner.

• Thorough knowledge of applicable compliance requirements related to the use of human subjects in research.

• Demonstrated organizational ability in handling multiple tasks with time sensitivity.

• Excellent communication skills. Ability to facilitate in written and verbal communication with clinical researchers, laboratory technicians, statisticians, bioinformatics experts and administrative personnel.

• Demonstrated experience with preparation of abstracts and manuscripts, and public-speaking in a wide variety of forums.

• Proven ability to utilize a computer for tasks such as word processing and statistics. Specific knowledge of Word, Excel, Access, Power Point, SPSS, SAS, and Velos.

• Familiarity with HIV research methods and ability to critically read published studies related to HIV translational research

• Demonstrated ability to communicate effectively to participants and encourage continued involvement and participant retention. Demonstrated ability to work with diverse groups, employing cultural sensitivity and a high level of professionalism.

• Ability to identify trends in study participation and to develop strategies to maximize retention.

• Broad familiarity with quantitative analysis of biological data.

• Experience with statistical analysis of digital PCR data, real-time PCR data or similar quantitative bio-assay data, especially experience with Bayesian statistical analysis involving missing or censored data.

• Experience with NGS data analysis using existing pipelines, especially familiarity with NGS data pipeline development.

• Master's degree or Doctoral degree in a related field.

• Employment is subject to a criminal background check.

• Willingness to work with pathogenic viruses, hazardous materials. Ability to operate and maintain laboratory equipment. Appropriate handling of the above items under well-defined laboratory practices is required.

• Willing to work occasional evenings and weekends as required.