Temporary Bioinformatics Specialist

Job Summary

There is an immediate opening for a Bioinformatics Specialist in the Bioinformatics Core Facility at the La Jolla Institute for Immunology (LJI). This is a service-oriented position that generally involves partnering with a postdoc to assist labs with their data analysis needs. A large part of the work involves the analysis of next-generation sequencing datasets (mostly bulk and single-cell RNA-Seq) by leveraging analysis pipelines and tailoring each analysis to the needs of the project. The candidate should be able to quickly get up-to-speed on current projects and the resources available at LJI and should be comfortable handling projects with minimal supervision.

Although the primary responsibilities relate to NGS data, there will be numerous opportunities to work with various other data types as well. The candidate should have excellent oral and written communication skills, be comfortable with dealing with a variety of data types, be familiar with standard bioinformatics practices and databases, and have a solid understanding of statistics for biology.

There are also opportunities to contribute to the Institute’s catalog of analysis pipelines and scripts by fixing bugs, adding features, or creating completely new workflows. The successful candidate will be able to thrive in a fast-paced (but friendly!) environment, understand priorities, complete tasks with minimal oversight in a timely manner, and communicate effectively with non-bioinformatics staff. If the interest and abilities are demonstrated, the candidate will have the opportunity to contribute to academic publications at LJI.

This is an excellent opportunity to gain experience working with large-scale, next-generation sequencing datasets and directly contribute to projects aiming to improve human health.

Supervisory Responsibilities

• None

Skills, Abilities, and Conditions of Employment

• This position requires the candidate to be on-site every Wednesday, with the option to work from home on other weekdays. LJI follows a 9-5 weekday work schedule and candidates are expected to be available via Slack, email, and phone during those hours.
• This is a 1 year contract position, with an opportunity for longer-term employment.
• Experience with next-generation sequencing datasets and tools, in particular bulk RNA-Seq and single-cell RNA-Seq GEX/CITE/VDJ
• e.g., 10X CellRanger, Seurat, Monocle, FastQC, MultiQC, DESeq, GSEA, pathway analysis, etc.
• Familiarity with standard bioinformatics practices and databases
• Programming experience in at least two of the following languages: Python, R, Perl, Bash, C, C++
• Ability to consistently meet deadlines

Education and Experience

• Master's degree in Bioinformatics or related field with demonstrated programming and data analysis experience. Exceptionally experienced candidates with Bachelor’s degrees will also be considered.
• 3+ years experience working with NGS datasets (in a production setting preferred)

Highly desired skills and knowledge:

• Basic understanding of immunology
• Experience using a job submission system (e.g., Slurm, Torque, etc.) on a HPC
• Experience building or running pipelines/workflows with a workflow management system (e.g., Nextflow, Snakemake, etc.)
• Experience with spatial transcriptomics data analysis
• Familiarity with programming best practices (e.g., revision control, testing, etc.)
• Understanding of containerization and experience with Docker and/or Singularity

Physical Requirements

• While performing the duties of this job, the noise level in the work environment is usually quiet
• Ability to sit or stand for extended periods, often 6-8 hours per day, primarily at a desk in front of a computer screen.
• Fine motor skills to operate a keyboard, mouse, and other standard office equipment.
• Repetitive motions, such as typing, and mousing are frequent.
• Good vision to read computer screens and printed documents.
• Ability to use close vision, adjust focus, and engage in tasks that require prolonged visual concentration.
• Ability to hear and understand spoken communications during meetings, whether in person, Zoom, or over the phone.
• Clear ability to hear and follow conversations and instructions accurately.
• Occasionally will need to move about the office or workstation to interact with colleagues, or attend meetings.
• Ability to reach, stoop, and bend as necessary
• Occasionally will need lift or move objects weighing up to 15 pounds, such as laptops, documents, or small office equipment.

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.