Bioinformatics Analyst II - IGC Core

  • Salk Institute for Biological Studies
  • La Jolla, CA 920371002, USA
  • Apr 07, 2022
Full time Biology/Biotechnology/Life Sciences

Job Description

The Integrative Genomics and Bioinformatics Core provides computational analysis support for genomics projects at the Salk Institute. This includes training in genomics analysis, development of novel algorithms and approaches and active collaboration on research projects with laboratories across the institute.

The Bioinformatics Analyst will work closely with other members of the core and researchers throughout the institute to advance genomics research projects, most notably with next-gen sequencing datasets. The position will leverage a wide range of skills with a focus on contributing to elite scientific research projects. The incumbent will contribute directly to research projects in several laboratories covering a large spectrum of scientific fields (Cancer, Stem Cells, Immunology, etc.) and experimental techniques (RNA-Seq, ChIP-Seq, single cell analysis, machine learning, etc.), with an emphasis on integrating multiple -omics datasets and long-term collaborative projects. The position will also include training in genomics analysis, systems biology, and presentation/publication of scientific work.

This is a great opportunity to work in a flexible academic environment with a small team of Ph.D. bioinformaticians, while developing diverse bioinformatics skills and contributing to cutting edge biology. Website:


Research Design and Presentation (20%)

  • Contribute and assist with project inception, experimental design, analysis, and manuscript presentation.
  • Assist with 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, including experimental design, time, methods, materials, and results.

Bioinformatics Analysis (20%)

  • Assist Institute researchers and contribute to scientific discovery by analyzing genomics/next-gen sequencing data, including, but not limited to: RNA-Seq, ChIP-Seq, GRO-Seq, Hi-C, Bisulfite-Seq, single-cell RNA-Seq and other emerging methods.
  • Work closely with researchers from multiple laboratories and scientific backgrounds simultaneously.
  • Work independently or with limited supervision on informatics research projects under direction from senior core staff or with research collaborators.
  • Use published 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 and genomics fields by reading primary literature and vendor websites and attending scientific talks and conferences.

Advanced Bioinformatics Analysis (30%)

  • Keep abreast of new scientific advances in bioinformatics, genomics, next-generation sequencing, and biological fields related to current projects.
  • Research, implement, and test, and present on new tools and pipelines for high-throughput data analysis.
  • Participate in the 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, scientific conferences, and scientific journals under the supervision of senior core personnel.

ICG Bioinformatics Core Facility Training and Support (15%)

  • Provide assistance and training to researchers on how to analyze and interpret next-gen 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.

ICG Bioinformatics Core Facility Maintenance and Management (5%)

  • Help maintain core scripts, software, website, tools, wiki, and pipelines.
  • Help ensure that core servers and hardware are operating properly and report all possible problems.
  • Help users of core software and servers to troubleshoot potential problems.
  • Liaise with IT department and manufacturers regarding hardware maintenance.
  • Help to ensure the core operates in compliance with all research oversight and institute guidelines.

Help Guide Bioinformatics Projects (10%)

  • Help guide projects of interns and entry-level bioinformatics analysts by making yourself available to them for brainstorming, troubleshooting, and general help with project management.
  • Help IGC interns and entry-level analysts succeed with their projects by providing insights into possible analysis directions, suggesting other tools and pipelines, and providing direct help with projects as needed.
  • Participate in regular internal presentations of complex bioinformatics datasets and projects. Help to ensure the core operates in compliance with all research oversight and institute guidelines


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



  • A minimum of 1 year experience with analysis of large -omics datasets.
  • Programming experience (Python, Java, R, C/C++, Perl, Bash).
  • Strong presentation and communication skills.
  • An ability to work in a high-paced small team environment.


  • Experience working in a Linux operating system in a high-performance computing environment.
  • Experience with machine learning and computational modeling.
  • Firm grasp on statistics/mathematics.
  • Background in biology (aging, cancer, regulation, immunology, neurobiology).
  • Experience working on multi-omics, integrative analyses, or computational modeling.
  • Experience with cloud computing (AWS/GPC) a plus.



  • 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 communication skills (both verbal and written) 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. Skill 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.
  • Experience analyzing genome-wide datasets (specifically from next-gen sequencing experiments).
  • Experience with Standard business office equipment and commonly used software and tools, such as Microsoft Office, electronic mail, and the internet.
  • High proficiency in a scientific programming languages (Perl, Python, C/C++, Java, R or Web applications).


  • Experience applying machine learning approaches for data integration and data mining.
  • Demonstrated knowledge and experience with MAC or Linux/UNIX operating systems.
  • Experience in performing genomics analysis unsupervised and in recommending modifications to algorithms and workflows to meet the needs of research projects.
  • Demonstrated ability to contribute to experimental design and assist with the analysis and interpretation of results.
  • Theoretical and practical knowledge of biological sciences (particularly genetic and molecular biology).


  • Must be willing to work a flexible schedule to support research needs.
  • Successful completion of the Institute's background investigation.
  • Must be willing to sign a confidentiality agreement.


This position will require constant adjusting focus, hearing, keying, lifting 0-20 lbs., seeing, sitting, talking, touching/feeling, analyzing, calculating, communicating, reading, reasoning, writing, and working inside. 

Application Details

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