The Sonnenburg Lab in the Department of Microbiology and Immunology is seeking a Bioinformatic Scientist with experience in analyzing metagenomic data to join our team. The Bioinformatic Scientist will provide highly specialized technical research and support, expert instruction, and consultation in bioinformatics focused on analyzing metagenomic data from gut bacterial communities; identifying and designing novel pipelines and computational solutions to a wide range of formal and practical problems arising from the management and analysis of associated scientific data. The Bioinformatic Scientist will work in collaboration with senior research staff members, faculty, students, and postdocs. Candidates should be highly organized self-starters, comfortable with autonomy, and embrace opportunities to tackle new problems and challenges as part of a dynamic research group within the University.
Duties include:
- Analyze metagenomic datasets generated from gut microbiome communities. This includes mapping based analysis ofreads to bacterial genome sequences to determine the composition of a sequenced community, and de novo assembly of new microbial genomes from metagenomes.
- Develop new computational pipelines for increasing the accuracy of read mapping and strain identification in microbial communities. Familiarity with Nextflow and/or other cloud-based workflow managers is an essential component of this duty.
- Develop statistically sound approaches to analyzing large sets of metagenomic data (time or perturbation series) to infer strain-strain or strain-perturbation relationships.
- Light system-administration of a Linux lab server, including maintaining backups, on-boarding new users, and helping troubleshoot problems as they arise.
- Participate in collaborations with multiple labs engaged in the initiative; contribute technical expertise, and perform basic bioinformatics research and tool development; act as advisor/consultant in bioinformatics across the initiative.
- Work with users and collaborators to answer questions about the contents of associated databases and computational pipelines/tools; provide assistance with submission of information and analysis.
- Participate in presentations and demonstrations of associated databases and computational tools at conferences or other institutions.
- Create a variety of reports and user demonstrations; collaborate with the users in the discovery of new knowledge; contribute to portions of published articles or presentations; draft and prepare scientific papers.
- Collect and analyze information from peer-reviewed scientific journals and through direct submissions; abstract data into the required format, and verify them for accuracy.
- Supervise and provide technical direction to other research staff, technicians, and/or students, as needed; schedule and assign workload; set appropriate deadlines; review work for quality and timeliness.
– Other duties may also be assigned
DESIRED QUALIFICATIONS:
Bioinformatic Scientist with experience in analyzing metagenomic data. Candidates should be highly organized self-starters, comfortable with autonomy, and embrace opportunities to tackle new problems and challenges as part of a dynamic research group within the University.
EDUCATION & EXPERIENCE (REQUIRED):
Doctor of Medicine, Pharmacy, or Doctor of Philosophy in scientific field and three years of relevant experience, or combination of relevant experience.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
- Strong analytical and computational skills, including experience with Nextflow or other workflow managers, the Linux command line interface, and Python and/or R.
- Demonstrated experience with genomic/metagenomic datasets, relational databases, data integration, and statistics.
- 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 $120,000.00 to $148,000.00 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.