Stanford University Department of Genetics has an excellent opportunity available for a candidate interested in single-cell genomics and big data management as a part of the Lattice team, coordinating data for the Human Cell Atlas (HCA).
The HCA is a worldwide effort to characterize all human cell types using high-throughput, high-resolution technologies, including single-cell genomics and imaging assays. As the data generated by HCA researchers rapidly increases, computational biologists are beginning to integrate data to form reference maps of the human body, which will make fundamental contributions to our understanding of human biology, disease, and treatments.
One of Lattice’s core responsibilities is to lead the curation of data for CELLxGENE Discover (cellxgene.cziscience.com), a visualization and analysis platform for single-cell data developed by the Chan Zuckerberg Initiative (CZI). The Lattice team, along with computational biologists and software developers at CZI, sets requirements for data hosted at CELLxGENE and collaborates with researchers to populate the CELLxGENE data corpus.
The Associate Biocuration Scientist will join a small team of Ph.D. biologists, computational biologists, and experienced database managers in the Cherry Lab, and will work closely with external researcher and software developer colleagues. In order to ensure CELLxGENE data are formatted in an interoperable manner, the successful candidate will remain current on single-cell bioinformatics tools by interacting with data integrators in the community, attending scientific conferences and workshops, staying current on published research, and through hands-on pipeline execution. They will distill learnings into data resource requirements and features that will improve the usability of data to researchers worldwide.
We look forward to adding a motivated Biocurator to be a valued contributor towards our mission as a part of this ground-breaking project.
Duties include:
- Collect, analyze and interpret information from peer-reviewed scientific journals and/or through direct submissions by applying specific scientific content knowledge. Abstract data into the required format, and verify for accuracy.
- Review complex, scientific submissions to the database for quality and relevancy; abstract information in the required formats. Review, research and resolve quality control reports findings.
- Conduct independent research of scientific literature and other available research to add content to the database and identify upcoming research opportunities.
- Develop documentation regarding effective use of the database for user community, typically professors, students and citizen scientists.
- Research and ensure resolution of user inquiries such as content and web site issues.
- Test new functionality with software to determine issues. Escalate and follow up on identified issues.
- Maintain quality control and integrity of databases and query tools for data mining as part of a collaborative team based on technical content expertise in a scientific field, such as molecular biology or chemistry.
- Contribute to the preparation of reports and publications regarding research progress by researching data/statistics and investigating errors or changes of data are accurate.
- Create and participate in presentations and demonstrations of the database at conferences or other institutions.
* – Other duties may also be assigned
DESIRED QUALIFICATIONS:
- UNIX experience
- Scripting experience
- Strong knowledge of genetics, molecular biology, or bioinformatics
- Strong organizational skills and ability to multitask
Laboratory experience with genomics or imaging techniques - Experience using open data resources
- Experience with modern high-throughput genomics and proteomics experiments
- Experience with python and R
- Experience with data structures, such as pandas
- Experience with both independent and collaborative work environments
EDUCATION & EXPERIENCE (REQUIRED):
Bachelor’s degree in scientific field and one year of related experience, or combination of relevant experience.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
- Solid analytical skills.
- Strong written and oral English communication skills.
- Computer skills, including word processing and spreadsheet applications.
- Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community.
PHYSICAL REQUIREMENTS*:
- Frequently perform desk based computer tasks, seated work and use light/ fine grasping.
- Occasionally stand, walk, and write by hand, lift, carry, push pull objects that weigh up to 10 pounds.
* – Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.
WORKING CONDITIONS:
- May work extended or non-standard hours based on project or business needs. Occasional local travel may be required.
- Some work may be performed in a laboratory setting.
WORK STANDARDS:
- Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
- Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
- Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University’s Administrative Guide, http://adminguide.stanford.edu.
The expected pay range for this position is $67,000 to $98,000 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university 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.
At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website (https://cardinalatwork.stanford.edu/benefits-rewards) provides detailed information on Stanford’s extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process.