Assistant Project Scientist

The Department of Computer Science and Engineering at UC San Diego (https://cse.ucsd.edu/) seeks a candidate for the position of Project Scientist (non-tenured Assistant) in the broad area of computational cancer genomics. The project scientist will lead the development of methods for exploring focal amplifications in cancer genomes in the Center for Precision Genomics, and to interface with members of team eDyNAmiC, an interdisciplinary group investigating the

occurrence and properties of extrachromosomal DNA in cancer.

The Center for Precision Genomics laboratory is housed in the Franklin Antonio Hall of the Jacobs School of Engineering, houses 5 principal investigators and 50+ research staff analyzing data from a multitude of advanced genomic technologies. Team eDyNAmiC had identified ecDNA as a dominant mechanism of oncogene amplification in cancer. To aid that effort, the Bafna and Mesirov laboratories are developing technologies for identifying ecDNA from genome sequencing data. Specifically, they have developed the Amplicon Suite pipeline for identifying ecDNA, which has been used to analyze over 30,000 genomes (1.5 Petabyte of data),

across many cancer subtypes. They have also developed the Amplicon Repository, a community editable resource for archiving and retrieving information on ecDNA in cancer cells. The selected candidate will contribute to and support the laboratory's research mission of ecDNA analysis. They will collaborate with scientists in launching large scale computational experiments that utilize AmpliconSuite and Amplicon Repository, will lead a group of software engineers to enable new developments and updates to these software tools. They will guide graduate student researchers in ensuring that prototypes of their algorithms and software are

programmed to best practices, and eventually incorporated into the AmpliconSuite pipelines.

https://jacobsschool.ucsd.edu/news/release/3495?id=3495

Finally, they will assist PIs Bafna and Mesirov in collecting data and in writing future grant applications, and manuscripts.

At UC San Diego, Project scientists are academic researchers who are expected to make significant and creative contributions to a research program. They are not required to carry out independent research or develop an independent research program but are expected to engage in creative research and publication under a faculty member's supervision associated with the Center.

The successful candidate must have the following skills

1. Ph.D. in a relevant field (Computer Science or Bioinformatics) with at least 2 years of postdoctoral experience working in cancer genomics.

• 2-4 letters of reference required

The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, covered veteran status, or other protected categories covered by the UC nondiscrimination policy.

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