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GENOMICS INSTITUTE: Project Scientist – Genome Assemblies (Open until filled. Apply by 12/2/19)

Recruitment Period

Open date: September 30th, 2019

Last review date: Monday, Dec 2, 2019 at 11:59pm (Pacific Time)
Applications received after this date will be reviewed by the search committee if the position has not yet been filled.

Final date: Tuesday, Jun 30, 2020 at 11:59pm (Pacific Time)
Applications will continue to be accepted until this date, but those received after the review date will only be considered if the position has not yet been filled.


The Genomics Institute at University of California, Santa Cruz (UCSC) invites applications from outstanding scientists for the position of Project Scientist. We seek a self-motivated, creative scientist interested in genomics with a specific focus on phasing and repeat assembly.

Under the direction of Assistant Research Scientist Karen Miga, the incumbent will be expected to contribute and implement the telomere-to-telomere (T2T) assembly pipeline to finish 350 human diploid genomes, which will serve as the pan-human reference genome. In doing so, the Project Scientist will be responsible for the following:

  1. Develop and optimize scalable, cloud-based pipeline to generate complete, telomere-to-telomere assemblies of diploid genomes.
  2. Contribute to the development of tool-kits to evaluate repeat collapse and/or phasing switch error to detect and update errors in assemblies.
  3. Serve as the point of contact between data/analysis and reference evaluation centers: WashU, UW, and Rockefeller to ensure timely production and release of T2T assemblies.
  4. Assist in the management of the high-quality reference genome (HQRG) biorepository and ensure timely public release of assemblies and associated data types.
  5. Work directly with graduate and undergraduate students to harden methods and improve analysis pipelines

In addition to performing research, the incumbent will be expected to write reports summarizing the results of their research that will be used to prepare manuscripts published in scientific journals, presentations for scientific meetings, and grant proposals to further fund the research.

Applicants with expertise in any of the following areas are strongly encouraged to apply: knowledge of genome assembly and analysis methods and/or previous experience with developing cloud-based pipelines.

The successful candidate will have outstanding communication skills and will successfully collaborate with scientists, laboratory scientists, software engineers, and students in developing novel genomics tools, protocols, and resources.

Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC.

Assistant, Associate or Full Project Scientist

Commensurate with qualifications and experience.


  • Ph.D. (or equivalent foreign degree) in bioinformatics, computational biology, genomics, or a related discipline at the time of application.
  • Minimum two-years’ experience in biological data analysis and programming experience to develop computational systems for genomics and precision medicine.

As soon as possible after initial review of the applications.

Initial appointment will be through June 30, 2021, with the possibility of reappointment. Should the hiring unit propose reappointment; a review to assess performance will be conducted. Reappointment is also contingent upon the availability of funding

Applications are accepted via the UCSC Academic Recruit online system. All documents and materials must be submitted as PDFs.

Please refer to Position # JPF00758-20T in all correspondence.

Full consideration will be given to applications completed by December 2, 2019. Applications received after this date will be considered only if the position has not been filled.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. UC Santa Cruz is committed to excellence through diversity and strives to establish a climate that welcomes, celebrates, and promotes respect for the contributions of all students and employees. Inquiries regarding the University’s equal employment opportunity policies may be directed to the Office for Diversity, Equity, and Inclusion at the University of California, Santa Cruz, CA 95064 or by phone at (831) 459-3676.

Under Federal law, the University of California may employ only individuals who are legally able to work in the United States as established by providing documents as specified in the Immigration Reform and Control Act of 1986. Certain UCSC positions funded by federal contracts or sub-contracts require the selected candidate to pass an E-Verify check (see More information is available at the APO website (see or call (831) 459-4300.

UCSC is a smoke & tobacco-free campus

If you need accommodation due to a disability, please contact the Academic Personnel Office at (831) 459-4300.

Visit the Apo Web Site at


Job location

Santa Cruz, California


Document requirements
  • Cover Letter - Letter of application that briefly summarizes your qualifications and interest in the position

  • Curriculum Vitae - Your most recently updated C.V.

  • Copy of peer-reviewed publication which may be co-authored - One of two required publications

  • Copy of peer-reviewed publication which may be co-authored - Two of two required publications