The Lee Group in the Peptide Biology Laboratory at the Salk Institute focuses on understanding the logic of brain disease using an integrative and whole brain network (e.g., graph theory), multi-scale and multiple-modal approach that include single neurons-barcoding for BRICseq, multiomic sn-RNAseq and sn-ATACseq, spatial transcriptomics and proteinomics, machine learning, circuit mapping, in vivo physiological recording, optogenetics, large-scale unbiased behavioral screen, stem cells and gene-editing in non-rodent species. The Bioinformatics Analyst position will work closely with the PI and other members of the lab to analyze multiomics and multi-modal 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 several collaborators 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.
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 (40%)
- 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.
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 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
- BS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics, or related discipline.
- MS or PhD in any of the above disciplines
- 0-3 years’ 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.
Skills and abilities
- 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).
SPECIAL CONDITIONS OF EMPLOYMENT
- 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.
Salary range for this position is $56,000 to $77,568.
PHYSICAL REQUIREMENTS/MENTAL ACTIVITIES/ENVIRONMENTAL CONDITIONS
The incumbent in this position will be constantly adjusting focus, hearing, keying, lifting up to 20 lbs, reaching, seeing, talking, touching/feeling, analyzing, calculating, communicating, reading, reasoning, writing, and working indoors.