Bioinformatics Postdoc - Systems Immunology of Infectious Diseases

The Peters Lab at the La Jolla Institute for Immunology (LJI) is looking for a bioinformatics postdoc to join our efforts in profiling immune system responses to a variety of infectious agents, such as M. tuberculosis and B. Pertussis, as well as various cancers. Qualified applicants will have the opportunity to collaborate with our interdisciplinary team of experimental and computational scientists working towards understanding, preventing, and curing immune-related diseases by accurately translating immunological questions into a computable form. We are looking to fill a postdoctoral position with experience in the analysis of sequencing data and immunology.

Projects: Areas of research may include the following:

• TB: Around 2 billion individuals are infected with Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Despite the relative low lifetime risk of latently infected individuals developing the active disease, it has been estimated that 80% of new cases of TB are due to reactivation of latent disease. In hoping to meet the World Health Organizations goals of TB eradication, our aim is to develop an efficient diagnostic test that can predict which individuals are likely to progress to active TB.
• Pertussis: In the mid-1990s, concerns over vaccine-related side effects prompted the replacement of the whole-cell Pertussis (wP) vaccine in favor of a safer acellular Pertussis (aP) vaccine. Recently, there has been a worldwide reemergence of Pertussis (whooping cough) despite widespread vaccination. Our approach is to compare individuals born before 1995 and vaccinated in infancy with wP, with individuals born in 1996 or later and vaccinated with aP in infancy. We hope to identify the cascade of immune events following Pertussis booster vaccination, and to identify correlates of long-lasting vaccine-induced immunity.
• IEDB: The Immune Epitope Database and Analysis Resource (IEDB), a freely available online resource supported by NIAID, was founded in 2003. The IEDB contains vast data on B and T cell epitopes for humans, non-human primates, rodents, and other animal species from infectious diseases, allergens, autoimmune diseases, and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.
• Cancer: We have multiple cancer bioinformatics projects that may be of interest, including the Cancer Epitope Database and Analysis Resource (CEDAR), which is a new resource funded by the NCI as of 2021. The successful candidate may be involved in our ongoing effort to develop cancer-specific computational tools to aid in the identification of T cell epitopes specific to tumors. They will work with data from our network of clinical and experimental collaborators, as well as data from public resources to develop improved algorithms.

Qualifications & Requirements: (Note that there is also the possibility to create custom positions for applicants that do not match the specifics here but have outstanding skills in two or more of the areas below).

• The ideal candidate will have extensive skills/knowledge in at least 2 of the following areas:

1. Experimental data analysis—RNA-Seq, flow/mass cytometry, single cell analysis
2. Immunology—adaptive immunity and epitope recognition
3. Data analysis techniques—statistics, data visualization, machine learning
4. Software development—programming in Python preferred, or proficiency in other programming languages (Unix Shell, version control)
5. Knowledge representation—database systems, RDF/OWL, OBO ontologies

• Have the ability to independently drive projects
• Hold a PhD or MD degree, OR must have gathered expert level skills through multi-year hands-on work in the area.

To Apply: Please submit a CV & Cover Letter and indicate one or more potential matches to the specific projects from above. Responsibilities and pay will depend on the candidate’s skills/qualifications. Applications without a cover letter will NOT be reviewed.

Appointment: Appointment term is typically 2-5 years, with opportunity to move into more senior roles.

Start Date: Start date is flexible for the ideal candidate until position is filled.

About LJI: In 2017 and in 2019, LJI was ranked as one of the best places to work in San Diego by the San Diego Business Journal. LJI is located in the Science Research Park on the campus of UC San Diego, with easy access to the San Diego life sciences community and the La Jolla area has to offer. Full-time employment at LJI includes a competitive salary, medical/dental/vision benefits, paid vacation/sick leave, and contributions to a (403b) retirement plan.

LJI provides Equal Employment Opportunity (EEO) to all employees and applicants for employment, and prohibits discrimination and harassment of any type, regardless of race, color, religion, age, sex, national origin, marital status, disability status, genetics, medical conditions, protected veteran status, sexual orientation, gender identity or expression, reproductive health decisions, or pregnancy, or any other condition protected by state and local laws. This applies to all terms and conditions of employment, including recruitment, hiring, placing, training, promotion, compensation, benefits, transfers, educational assistance, terminations, layoffs, recalls, transfers, leaves of absences, and social and recreational programs.

With over 30 different countries represented, diversity is respected and celebrated at LJI. We are committed to ensuring a safe and compassionate environment that is equal, just, and fair. Science and discovery benefit from a diversity of talents, a diversity of approaches, and a diversity of perspectives. The La Jolla Institute’s Diversity, Equity, and Inclusion Initiative is designed to help us identify areas at the Institute that need improvement so we can together create an environment that is inclusive, provides equal opportunities, and opens doors that propel our research for human health.

La Jolla Institute is committed to compensation that is externally competitive and internally equitable. We validate this commitment by conducting regular market analyses to remain competitive with organizations of similar size in the nonprofit, independent research sector. Compensation decisions consider a variety of factors including experience, education, unique skill sets, organizational need, and internal equity.