Bioinformatics Analyst II

Job location is at 10010 N Torrey Pines Rd, La Jolla, CA 92037

The Kaech Lab studies the role T cells, and other immune cells play in viral infections and cancer, with a focus on T cell and macrophage function, metabolism and differentiation. We study the pathways involved in T cell exhaustion and tissue-residence memory as well as neuro-immune interactions in tumors and in the central nervous system.

The Bioinformatics Analyst (BA) position will work closely with the PI and other members of the lab to analyze single cell RNA & ATAC-seq datasets, single-cell spatial datasets, metabolomics and other multiomics data generated in the lab. The BA will be responsible for executing and maintaining current analysis pipelines, building new analysis pipelines, and integrating new genomics tools when appropriate. The BA will also work closely with members in collaborations for integrated analysis and interpret multiple –omics datasets as well as assist in non-pipeline bioinformatics applications. The BA will also work with scientists to visualize their data and develop high quality figures for papers when appropriate. The BA would work on multiple projects simultaneously and would result in authorship on papers. The BA will oversee the maintenance, organization and long-term storage of sequencing and omics raw and processed data.

Who We Are

The Salk Institute is an internationally renowned research institution that values diversity, equity, and inclusion. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces diverse perspectives and unique life experiences, fostering innovation, and a sense of belonging. Together, we strive to improve the wellbeing of humanity through groundbreaking research.

Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Salk's vibrant community comprises a diverse and talented group of individuals, each playing a crucial role in driving our mission forward. From visionary leaders to dedicated administrators and brilliant faculty members, the Institute is united by a shared passion for scientific exploration and innovation.

What Your Key Responsibilities Will Be

• Work independently to develop advanced computational and statistical methods for big-data analysis.
• Must be familiar with many different algorithms and software tools to generate data analysis pipelines and execute analysis in a timely manner.
• Work independently to create and implement machine learning algorithms for identifying patterns and signatures relevant to biological datasets.
• Work independently or with limited supervision on informatics research projects under direction from senior core staff or with research collaborators.
• Work with Institute researchers and contribute to scientific discovery by implementing, optimizing and executing computational approaches for DNA methylation analysis, mapping, genome sequence analysis, transcriptome analysis, and data visualization.
• Use published and available pipelines, scripts, and tools to prepare and process large datasets.
• Work in a high-performance computing environment.
• Keep informed of new developments and technical advances in the bioinformatics, image processing, visualization, genomics and biological fields related to current projects.
• Research, implement, test, and present on new tools and pipelines for high-throughput data analysis.
• Independent design and coding of analysis pipelines and cutting-edge bioinformatics analysis algorithms.
• Participate in the design, coding, and presentation of novel analysis tools for cutting-edge bioinformatics analysis.
• Present advanced analysis results, tools, and pipelines at group meetings and contribute to publications in scientific journals.
• Contribute and assist with project inception, experimental design, analysis and manuscript presentation.
• Work on the preparation of data for, manuscripts, publications, grant applications, posters and other presentations.
• Present results verbally and with visual aids in one-on-one meetings, group meetings, or conferences.
• Maintain lab notebook, online code-share repositories such as GitHub, GitLab, BitBucket, etc including experimental design, time, methods, materials and results.
• Help maintain scripts, software, tools, and pipelines used in the lab.
• Help ensure that lab servers and hardware are operating properly and report all possible problems.
• Help users of lab software and servers to troubleshoot potential problems.
• Liaise with IT department and manufacturers with regard to hardware maintenance.
• Back-up data in the lab server on a regular basis.
• Performs other related duties as assigned

Supervisory Responsibilities:

• This job has no supervisory responsibilities.

What we Require 

• BS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, or related discipline or equivalent relevant experience.
• Minimum of 4+ years of professional experience in a scientific role in a relevant field (graduate studies included).
• Hands-on work experience in single cell analyses and integration, harmonization of data sets, statistics, and machine learning.
• Willingness to understand and interpret the data analysis and have a high level of scientific rigor.
• Must be fluent in coding.
• Relevant experience and proficiency in Python programming; fluency in at least 2 common programming languages (Bash, AWK, or R); next-generation sequencing technologies and assays; and high-performance computing (e.g., SGE environment)
• Excellent communication and organizational skills of data files, analyses, and generation of plots and graphs for figures for manuscripts and grants.
• Outstanding time management and able to work on tight deadlines.

Preferred: 

• MS or PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline.
• Minimum of 3 years of relevant bioinformatics experience with a Master’s degree. If PhD, experience acquired through PhD program may be considered in lieu of professional experience.
• Minimum of 1 year of analysis experience on omics datasets and/or single cell datasets
• Minimum of 2 years of analysis experience with NGS / High-throughput sequencing data analysis.

What We Can Offer

The expected pay range for this position is $67,500 to $88,750 per annum. Salk Institute provides pay ranges representing its good faith estimate of what the institute reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.

Benefits

Salk Institute offers competitive benefits, including medical, dental, vision, retirement, paid time off, tuition reimbursement, patient advocacy services, and transit/parking program.

Salk Values

The Salk Community, both scientists and administrators, worked together to define values that we believe support Salk’s pursuit of excellence. To be truly the best scientific institution requires not only incredible discoveries, but a common understanding of how we should work together to enable those discoveries.

The acronym “I CARE” provides a simple way to remember each of the values and reminds each of us of the importance of what we do each day.

Equal Employment Opportunity Statement

The Salk Institute for Biological Studies is an Equal Opportunity Employer and is committed to providing equal access to opportunities for students, employees, applicants for employment and other visitors. Salk has also adopted and maintains a policy to encourage professional and respectful workplace behavior and prevent discriminatory and harassing conduct in our workplace.

Accordingly, the Institute prohibits harassment and discrimination in employment on the basis of, and considers all qualified applicants for employment without regard to, actual or perceived race, color, religion, religious creed (including religious dress and grooming practices), national origin, ancestry, citizenship, physical or mental disability, medical condition (including cancer and genetic characteristics), genetic information, marital status, age, sex (including pregnancy, childbirth, breastfeeding, or related medical conditions), gender, gender identity, gender expression, sexual orientation, veteran and/or military status (disabled veteran, veteran of the Vietnam era, other covered veteran status), political affiliation, and any other status protected by state or federal law.