Sr Bioinformatics Scientist - Immunology and Neoantigen Discovery

About City of Hope

City of Hope is an independent biomedical research and treatment organization for cancer, diabetes, and other life-threatening diseases.

Founded in 1913, City of Hope is a leader in bone marrow transplantation and immunotherapy such as CAR T cell therapy. City of Hope’s translational research and personalized treatment protocols advance care throughout the world. Human synthetic insulin, monoclonal antibodies and numerous breakthrough cancer drugs are based on technology developed at the institution.  AccessHope™, a subsidiary launched in 2019 serves employers and their health care partners by providing access to City of Hope’s specialized cancer expertise.

A National Cancer Institute-designated comprehensive cancer center and a founding member of the National Comprehensive Cancer Network, City of Hope is ranked among the nation’s “Best Hospitals” in cancer by U.S. News & World Report and received Magnet Recognition from the American Nurses Credentialing Center. Its main campus is located near Los Angeles, with additional locations throughout Southern California and in Arizona.

City of Hope’s commitment to Diversity, Equity, and Inclusion

We believe diversity, equity and inclusion is key in serving our mission to provide compassionate patient care, drive innovative discovery, and advance vital education focused on eliminating cancer and diabetes in all our communities.  Our commitment to Diversity, Equity and Inclusion ensures we bring the full range of skills, perspectives, cultural backgrounds, and experiences to our work -- and that our teams align with the people we serve to build trust and understanding.  We are dedicated to fostering a community that embraces diversity - in ideas, backgrounds, and perspectives; this is reflected in our work and represented in our people.

Position Summary

As a City of Hope Bioinformatician, the position will partner with investigators and collaborators in the Diamond Laboratory to leverage high-dimensional data to drive scientific discoveries. Needed is an Informatics Specialist with extensive knowledge of antigen processing and epitope selection to assist in the implementation and analysis of neoantigen characterization, nucleotide sequence analysis, somatic variant detection, HLA haplotyping, epitope prediction, peptide processing, therapeutic application, etc. The Neoantigen Specialist will be responsible for consultation on neoantigen experiments, development of prediction pipelines, implementation of exploratory and predictive analyses, visualization of data, and the communication and presentation of results.

The position will also support the analyses and management of research laboratory data. Performs specialized analyses of nucleotide sequences, sequence variants, and genomes. Makes original and significant contributions to research publications, presentations, and grant proposals. Designs and manages the implementation of laboratory databases and informatics systems. Defines requirements for, reviews, recommends, and manages the acquisition of vendor supplied software and informatics systems.

Essential Functions:

·         Support the design, collection, and analysis of neoantigen data at City of Hope. Interact with third-party consultants who may provide prioritization of sequence variants for experimental and clinical use.

·         Performs data analyses for neoantigen discovery research.  Analyses involve complex statistical and other mathematical techniques, and computer simulations using available software packages or novel custom software. Interact with team members involved in preclinical work and clinicians when designing vaccines for therapeutic application.

·         Prepares textual descriptions, figures and presentation slides for the presentation and publication of results. Presents results internally and for potential third-party investors.

·         Identify and integrate disparate data sources, both internal and external, including raw or unstructured data from medical researchers or clinicians, and publicly available databases.  

·         Work with large datasets from different neoantigen pipelines, determine discovery significance, and create data visualizations. Assist team members in vaccine design for therapeutic use in cancer patients.

·         Enhances professional growth and development by reviewing current literature and by participation in educational programs, workshops, conferences, and in-service meetings. Communicate results to technical and non-technical audiences along with internal and external stakeholders. 

·         Collaborate with researchers and clinicians to identify high-impact opportunities for neoantigen research and publications.    

Basic education, experience and skills required for consideration:

·         PhD in a scientific or computer science/computation biology with a strong background in immunology and neoantigen discovery. 

·         5 years of experience analyzing and managing research data and working with research software and informatics/bioinformatics systems and solutions. Demonstrated experience preparing clear written reports and verbal presentations. Demonstrated experience in one or more high level programming languages.

·         Experience with bioinformatic workflow including somatic variant detection, HLA typing, peptide processing, peptide-MHC prediction, expression analysis, etc.

·         Experience with standard bioinformatics tools

·         Experience working with advanced bioinformatics concepts (e.g., graph alignment, genotyping of complex haplotypes, etc.)

·         Experience creating and managing immunogenomics pipelines

·         Software development in R and/or Python

·         Experience with publicly available bioinformatics databases (e,g., TCGA, Uk Bio Bank, DBGAP, etc.)

·         Knowledge of software development best practices (e.g., version control, unit testing, regression testing), and experience with an agile software development methodology

·         Knowledge of best practices in data analysis and scientific computing (e.g., literate programming, reproducible research)

·         Experience with working in a cloud environment

·         Experience with using and managing data in clinically regulated environments.

·         Effectively communicate technical information to both technical and non-technical collaborators: identify core challenges in complex situations, explain tradeoffs, and incorporate feedback to make decisions using code reviews, docs, wikis, meetings, etc.

Additional Information:

As a condition of employment, City of Hope requires staff to comply with all state and federal vaccination mandates.

The estimated pay scale represents the typical [salary/hourly] range City of Hope reasonably expects to pay for this position, with offers determined based on several factors which may include, but not be limited to, the candidate’s experience, expertise, skills, education, job scope, training, internal equity, geography/market, etc.  This pay scale is subject to change from time to time.

City of Hope is committed to creating a diverse environment and is proud to be an equal opportunity employer.  All qualified applicants will receive consideration for employment without regard to race, religion, color, national origin, sex, sexual orientation, gender identity, age, status as a protected veteran, or status as a qualified individual with disability.