Bioinformatics Analyst III - Laboratory of Dr. Kuo-Fen Lee

The Lee Group in the Peptide Biology Lab 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. This position will work closely with the PI to analyze multiomics and multi-modal data generated in the lab. BA will be responsible for executing and maintaining current analysis pipelines, building new analysis pipelines, and integrating new genomics tools when appropriate.

Who We Are

The Salk Institute is an internationally renowned research institution that values all members of our scientific community. We seek bold and interactive leaders passionate about exploring new frontiers in science. Our collaborative community embraces perspectives across discipline, professional acumen, 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 has many talented individuals from varied backgrounds, 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

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.

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.

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.

Help Guide Bioinformatics Projects

• 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.
• Performs other related duties as assigned by management.

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 is preferred for this position.
• 6 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.
• Ability to identify, download, install, troubleshoot, and assess new analysis tools.
• Experience analyzing genome-wide datasets (specifically from next-gen sequencing experiments).
• Computer skills required: Microsoft Office, electronic mail, and the internet.

Preferred:

• Master’s degree or PhD preferred.
• 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 in performing genomics analysis unsupervised and in recommending modifications to algorithms and workflows to meet the needs of research
• Experience with cloud computing (AWS/GPC) is a plus.
• 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).

The expected pay range for this position is $100,000 to $131,000 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.

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 (race is inclusive of traits associated with race, including, but not limited to, hair texture and protective hairstyles. Protective hairstyles include, but not limited to, such hairstyles as braids, and twists), 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), reproductive health decision making, 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.

Discrimination is prohibited with any intersectionality of the above-mentioned characteristics, including:

1. Any combination of characteristics.
2. A perception that the person has any of the characteristics or any combination of those characteristics.
3. A perception that the person is associated with a person who has, or is perceived to have, any of those characteristics or any combination of those characteristics.