Bioinformatics Analyst I - Integrated Genomics Core
Employment History Include your last ten (10) years of employment history, or length of your employment history if less, including all positions (even those that are not relevant to this position) and periods of unemployment. Incomplete information could disqualify you from further consideration.
The Integrative Genomics and Bioinformatics Core (IGC) provides computational analysis support for omics projects at the Salk Institute. This includes training in genomics analysis, development of novel algorithms and approaches, active collaborative participation in research projects with laboratories across the Institute, maintenance of core resources, and providing training in interpretation and design of high-throughput experiments. The core works closely with the Next Generation Sequencing Core (NGS), Mass spectrometry core (MASS), Information Technology (IT), scientific, administrative, and core leadership to facilitate cutting edge biological research at the Institute.
Under the direction of senior analysts and core director, the Bioinformatics Analyst I 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 leverages Ph.D.-level knowledge in genomics and bioinformatics to design and carry out standard analyses on genomics datasets and present analyses to scientists at the Institute. The Bioinformatics Analyst I will also help maintain core resources (scripts, software, websites, tools), and provide basic training on interpreting data and analyses to Institute scientists. The position may also involve occasional scientific writing, tool development/testing, and presentation of work at scientific conferences.
(25%) Research Design and Presentation
- 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.
(45%) Bioinformatics Analysis
- 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.
(15%) Advanced Bioinformatics Analysis
- 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.
(10%) ICG Bioinformatics Core Facility Training and Support
- 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.
(5%) ICG Bioinformatics Core Facility Maintenance and Management
- 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 with regard to hardware maintenance.
- Ensure core facility is in compliance with EH&S protocols and procedures.
- A minimum of 6 months experience with analysis of large –omics datasets.
- Programming experience (Python, Java, R, C/C++, Perl, Bash).
- 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.
- BS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline, or equivalent.
- MS or PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline.
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.
- Strong presentation and communication skills.
- An ability to work in a high-paced small team environment.
- 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 with Standard business office equipment and commonly used software and tools, such as Microsoft Office, electronic mail, and the internet.
- Experience applying machine learning approaches for data integration and data mining.
- High proficiency in a scientific programming language (Perl, Python, C/C++, Java, R or Web applications).
- 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 clinical 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.
PHYSICAL REQUIREMENTS/MENTAL ACTIVITIES/ENVIRONMENTAL CONDITIONS
This position will be constantly adjusting focus, hearing, keying, lifting 0-20 pounds, seeing, sitting, talking, touching/feeling, analyzing, calculating, communicating, reading, reasoning, writing and working inside.