The Harnessing Plants Initiative (HPI) is developing crop and wetland plants that will store more carbon, longer, to reduce atmospheric CO₂ and mitigate climate change. Within HPI, there are two tracks: CO₂ Removal on a Planetary Scale (CRoPs) and Coastal Plant Restoration (CPR).

The CRoPS track is developing crop plants that sequester more carbon via extensive root systems containing recalcitrant carbon polymers to fight climate change. A major component of this research is to conduct genetic and genomic analyses for understanding relevant traits and translation from model organisms to target crops. Many of the CRoPS projects depend on genomics data, including gene expression analysis and genome building/annotation.

The Bioinformatics Analyst I will work on several genomics research projects, most notably with next-generation sequencing datasets, independently and/or under the supervision of senior analyst(s) and PI leadership. The analyst will contribute directly to research in the CRoPS track, specifically through implementing, optimizing and executing computational approaches for genome sequence analysis, transcriptome analysis, and data visualization using data from RNA-seq, DAP-seq, etc.

DUTIES AND RESPONSIBILITIES:

Bioinformatics analysis (55%)

• Assist CroPS researchers and contribute to scientific discovery by analyzing genomics/next-generation sequencing data, including, but not limited to: RNA-Seq, DAP-seq, ChIP-Seq, single-cell RNA-Seq and other emerging methods.
• Work independently or with limited supervision on informatics research projects under direction from senior analyst(s), PI, or with research collaborators.
• Use published pipelines, scripts, and tools to prepare and process large datasets.
• Work in a high-performance computing environment.
• Keep abreast of new scientific advances in bioinformatics, genomics, next-generation sequencing, and biological fields related to current projects. Research, implement, test, and present on new tools and pipelines for high-throughput data analysis. Participate in the design and coding of novel analytical tools, pipelines and cutting-edge bioinformatics analysis algorithms. Present advanced analysis results, tools, and pipelines at group meetings under the supervision of senior project personnel.

Research design (25%)

• Present results verbally and with visual aids in one-on-one meetings, group meetings, or conferences. Assist with the preparation of data for manuscripts, publications, grant applications, posters and other presentations. Document data and analysis, including code, to facilitate data-sharing and enable reproducibility. Contribute and assist with project inception, experimental design, analysis and manuscript presentation.

Training and support (10%)

• With the guidance from senior analyst(s), provide basic assistance and training to researchers on how to analyze and interpret next-generation sequencing data. Help educate and advise researchers on the pros and cons of available NGS assays, analysis tools, and approaches in one-on-one training sessions or larger group workshops. Ensure users are aware of the limitations of analyses and approaches to help ensure high standard of scientific research.

Maintenance and management (10%)

• Help maintain project data and computational resources such as scripts, software, websites, tools, and pipelines and provide the team with instructions for their use. Help project members troubleshoot potential problems with bioinformatics analyses, software and servers.

EDUCATION

Required:

• BS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline.

Preferred:

• MS or PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline.

SKILLS AND ABILITIES

Required:

• 0 – 3 years’ related experience.
• Strong presentation and communication skills.
• Proven organizational and time management skills to successfully set priorities, meet established deadlines and recognize new problems with constantly changing priorities and frequent interruptions.
• Strong verbal and written communication skills needed to interact professionally and effectively in the work environment. Ability to read, comprehend, and discuss research materials. Proven ability to write, edit and proofread research results. Skilled at explaining difficult concepts and training users and students.
• Ability to interact diplomatically and professionally with all levels of Institute staff and external contacts.
• Ability to identify, download, install, troubleshoot and assess new analysis tools.

Preferred:

• A minimum of 6 months experience with analysis of large omics datasets
• A minimum of one year experience programming (Python, shell, R, or other scripting language) 
• Background in statistics
• Background in molecular biology, biochemistry, or general familiarity with wet-lab assays.
• Theoretical and practical knowledge of biological sciences (particularly genetic and molecular biology).
• Experience using a high-performance Linux-based computing environment
• Experience visualizing data and analysis results
• Experience implementing machine learning analyses
• Experience analyzing large amounts of sequencing data
• Experience with Standard business office equipment and commonly used software and tools, such as Microsoft Office
• Demonstrated ability to contribute to experimental design and assist with the analysis and interpretation of results.
• Familiarity with next-generation sequencing technologies and assays.
• Familiarity with online databases for published sequencing data
• Familiarity with online tools and databases for plant genomics analysis such as Arabidopsis.org, BAR, and Phytozome
• Familiarity with algorithms used in bioinformatics analysis such as sequence alignment and clustering

The expected pay range for this position is $56,000 to $72,750 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.

SPECIAL CONDITIONS OF EMPLOYMENT

• Must be willing to work an adjusted schedule to support research needs.
• Must be willing to work in an animal-related research environment.
• Successful completion of the Institute’s background investigation.

PHYSICAL REQUIREMENTS/MENTAL ACTIVITIES/ENVIRONMENTAL CONDITIONS

This position will be constantly keying, seeing, sitting, analyzing, calculating, communicating, reading, reasoning, and writing.

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.