Project Scientist – Genome Assemblies

University of California, Santa Cruz
Santa Cruz, CA, United States
Job Type:
  • Investigator (Academic Title: Assistant, Associate or Full Project Scientist)
Degree Level Required:
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Project Scientist – Genome Assemblies

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. 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.


The Project Scientist will be responsible for the following:

  • Develop and optimize scalable, cloud-based pipeline to generate complete, telomere-to-telomere assemblies of diploid genomes.
  • Contribute to the development of tool-kits to evaluate repeat collapse and/or phasing switch error to detect and update errors in assemblies.
  • 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.
  • Assist in the management of the high-quality reference genome (HQRG) biorepository and ensure timely public release of assemblies and associated data types.
  • 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.


  • 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.

Additional Information

Evaluation of applications will begin on October 30th, and submissions will be accepted until November 30th

POSITION AVAILABLE As soon as possible after initial review of the applications.

DURATION OF POSITION 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

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

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