Bioinformatic Scientist

California, United States
31 Jan 2019
End of advertisement period
31 Mar 2019
Contract Type
Full Time

Stanford ChEM-H is a new interdisciplinary institute focused on connecting Chemistry, Engineering, and Medicine for Human Health. The institute is a joint venture of the Schools of Medicine, Engineering, and Humanities and Sciences. The proximity of world-class biologists, chemists, engineers, and clinicians at Stanford presents a unique opportunity to study human biology at a molecular level, to translate this knowledge into groundbreaking products and services that promote human health.

Stanford ChEM-H is developing a new initiative that aims to take advantage of the tremendous promise of the microbiome to treat human disease. We are currently seeking a Bioinformatic Scientist to join our team to support this new multi-investigator initiative. Candidates should be highly organized self-starters, comfortable with autonomy, and embrace opportunities to tackle new problems and challenges as part of a dynamic team in a start-up-like environment within the University.


  • Provide highly specialized technical research and support, expert instruction, and consultation in bioinformatics focused on analyzing metagenomic data from bacterial communities; identify and design novel pipelines and computational solutions to a wide range of formal and practical problems arising from the management and analysis of associated scientific data. Work in collaboration with senior research staff members, faculty, students, and postdocs from engineering, medicine, and other relevant fields engaged in the initiative.


  • Analyze metagenomic datasets generated from natural and synthetic communities.
  • Map reads to bacterial genome sequences to determine the composition of a sequenced community
  • Genome assembly from metagenomes.
  • Develop new computational pipelines for increasing the accuracy of read mapping and strain identification in microbial communities.
  • Develop statistically sound approaches to analyzing large sets of metagenomic data (time or perturbation series) to infer strain-strain or strain-perturbation relationships.
  • 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


Education & Experience:

  • 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:

  • Strong analytical skills.
  • Expertise in programming languages commonly used in Bioinformatics (e.g., Python, R, and C)
  • Fluency with scripting and high performance computing
  • Experience with building and manipulating databases
  • Demonstrated project management experience
  • Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community.
  • A Ph.D. in bioinformatics, computational biology, or a related field.
  • Familiarity with NGS algorithms (e.g., Bowtie, SAMtools).
  • Significant experience in algorithm/pipeline development and pipelines implementation for NGS data analysis.
  • Experience with Amazon-based cloud computing.


  • 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 the job.


  • 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.


  • 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,
  • Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.

Job Family: Information Analytics
Job Series: Scientific Data Curator
Job Code: 4183
Grade: J
Exemption: Exempt