Assistant, Associate or Full Project Scientist in MED of Genomic Research
University of California San Diego, School of Medicine
United States


The Department of Medicine ( at University of California San Diego is committed to academic excellence and diversity within the faculty, staff, and student body and is currently recruiting a Project Scientist.

The Department of Medicine is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego and employs 500+ full-time salaried faculty members and 150+ academic appointees. Staff personnel include 800+ staff in 9 bargaining units, students, and volunteers. There are over 250 clinical faculties practicing at multiple sites and hospitals. Professional fee billings for the department exceed $50 million with collections of over $19 million per year. The total annual budget is approximately $170 million, which includes contract and grant revenues, clinical practice and medical center funds, and other state and private endowment funds.

The Mesirov Lab in the UCSD Department of Medicine seeks an exceptional candidate who is passionate about helping genomics investigators accelerate the pace of biomedical research through the use of advanced software tools to analyze their data. The Project Scientist will work with a team developing a number of software tools for biomedical research that have been used by more than 450,000 investigators worldwide. These tools include GenePattern Notebook, an environment that integrates the Jupyter Notebook online system with the user-friendly GenePattern integrative genomics analysis platform.

Under general supervision, the Project Scientist's responsibilities will cover the broadest range of bioinformatics activities including software development; adding complex analysis methods to GenePattern; modifying algorithms for application to particular scientific projects; and collaborating with scientists and computational biologists to implement and integrate new methodologies developed by the lab and with collaborating labs, and engaging the UCSD biomedical research community to maintain awareness of its analytical requirements. Specifically, the Project Scientist will develop and test GenePattern notebooks – complete research narratives containing interactive analytic workflows and associated textual and graphical exposition. Responsibilities will include designing and developing the broad structure of an analysis workflow as well as incorporating the individual analysis and documentation components.

Research responsibilities will include working with scientists from collaborating laboratories, initiating new collaborations, and independently discussing analysis results with other experts. These studies will give rise to GenePattern notebooks, and the Project Scientist will participate in the publication of the methods and results in the appropriate journals.

The Project Scientist's research responsibilities will also include the support of a multidisciplinary tumor board as required to analyze patient RNA-Seq and other genomic data with the goal of suggesting candidate compounds for treatment, to continuously enhance and expand the associated analysis pipelines, to ensure HIPAA compliance, to draft written reports, and to present cases to the board.

The Project Scientist's training responsibilities will include mentoring and onboarding short-term and long-term interns whose levels of experience ranges from high school students to PhD and MD students. As a member of the development team, the incumbent will participate in user support, including answering email help questions, writing documentation and training materials, and presenting at training workshops.

Candidates must have a PhD degree in the life sciences, bioinformatics, or related discipline, or a combination of education and experience. Candidates must be capable of in-depth review and understanding of the biomedical literature. Candidates must have experience with analysis of genomic data, including work with gene expression or other functional data, demonstrable experience with machine learning approaches, and extensive experience with the GenePattern Notebook environment. The candidate must be able to program in a variety of languages (Python, R, Java), demonstrate experience with a complete web development technology stack (JavaScript, Ant, RDBMS systems), and proficiency with statistical methods and biological concepts. Experience with public genomics resources, including experimental data repositories, annotation tools, biological pathway databases, is preferred.

Appointment will be at Assistant, Associate or Full Project Scientist level based on background and years of experience. Salary is commensurate with qualifications and based on University of California pay scales.

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