Critical Assessment of Genome Interpretation (CAGI)
Research Group of Steven Brenner
University of California, Berkeley
Establish the state-of-the-art in genome interpretation
We are seeking a leader for the Critical Assessment of Genome Interpretation (CAGI, /'kā-jē/), a community experiment to evaluate the prediction of phenotypes from genetic variation. CAGI objectively assesses computational methods for predicting the phenotypic impacts of genomic variation. In this experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genotypic data and make predictions of resulting molecular, cellular, or organismal phenotype
These predictions are evaluated against experimental and clinical characterizations, and independent assessors perform the evaluations. Community workshops are held to disseminate results, assess our collective ability to make accurate and meaningful phenotypic predictions, and better understand progress in the field. From this experiment, we identify bottlenecks in genome interpretation, inform critical areas of future research, and connect researchers from diverse disciplines whose expertise is essential to methods for genome interpretation. The CAGI experiments have engaged hundreds of researchers and led to two journal special issues with >60 papers.
The CAGI Lead Scientist will be primarily responsible for operating the CAGI experiment, from developing challenges to managing prediction submissions and assessments to dissemination of results. Each new challenge requires extensive interactions with the data set provider to develop the most informative challenge. Supervision of assessment includes interacting with assessors, developing standard and automated assessment protocols, and ensuring that uniform standards are applied and that proposed assessment methods are appropriate, as well as reviewing assessment results and ensuring that the necessary technical support is provided.
Prediction management includes engaging a broad and diverse community, providing tutorials, editing necessary web resources, distributing challenges, robustly accepting predictions, providing comprehensive access to results and analysis, and ensuring data security. The CAGI Lead Scientist will organize the CAGI conference culminating each experiment, at which results are initially presented and other meetings. They will take a lead role in working with participants to coordinate publications about CAGI experiments and facilitate presentations to ensure broad dissemination.
The CAGI Lead Scientist will write papers describing research findings; create effective figures, slides, and posters; and present research including travel as appropriate. They will draft grant reports and grant applications, as well as apply for fellowships, grants, and engage in other career development activities. They will work collaboratively in the research group and with collaborators and provide mentorship. They will promote diversity in science in the lab and CAGI experiment and through outreach. They will follow all University policies and lab practices such as: following all safety guidelines and ensuring safe conduct of research; maintaining security of data and resources entrusted to us; keeping meticulous detailed records of research in routine laboratory notebook entries and triennial reports; participating in weekly group and subgroup meetings; and performing lab jobs to facilitate lab operations.
Brenner Research Group:
The Brenner Laboratory is an interdisciplinary research group at the University of California, Berkeley, one of the world's premiere research universities. We are associated with the Center for Computational Biology, the Department of Plant and Microbial Biology, the Department of Molecular and Cell Biology, the Department of Bioengineering and the California Institute for Quantitative Biosciences. We are also affiliated with the Chan Zuckerberg Biohub; the Institute for Human Genetics and the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco; and Lawrence Berkeley National Lab.
The University of California, Berkeley ranks first nationally in the number of graduate programs in the top 10 in their fields, according to the most recent National Research Council study. This year Forbes ranked UC Berkeley as the #1 Top College in America, and the Times Higher Ed placed UC Berkeley first among US public universities.
The Brenner Research Group is committed to creating an inclusive community of belonging that enables every member to achieve their potential. We value the diversity of our members' unique backgrounds, experiences, and perspectives; their synergy and complementarity is fundamental to our group's effort to advance our research—which aims to benefit all people.
Basic qualifications (required at time of application)
Doctorate degree or equivalent international degree
• Ph.D., M.D. or equivalent international degree in computational biology, human genetics, or a related discipline.
• Demonstrated ability to work and communicate with an extensive array of collaborators.
• Experience in managing large data sets, developing standard and automated assessment protocols, managing data set QC, performing human genetic data analyses, ethics of human research participants, publishing in high quality journals, event organization.
• Ability to manage multiple and conflicting obligations and deadlines.
• Curriculum Vitae - Your most recently updated C.V.
• Cover Letter
• Statement on Contributions to Advancing Diversity, Equity, and Inclusion - Statement on your contributions to diversity, equity, and inclusion, including information about your understanding of these topics, your record of activities to date, and your specific plans and goals for advancing equity and inclusion if hired at Berkeley. /shortcuts/ofew_contributions_diversity.
• Statement of Research (Optional)
• 3-5 required (contact information only)
Apply link: https://apptrkr.com/4593188
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UC Berkeley is committed to diversity, equity, inclusion, and belonging. The excellence of the institution requires an environment in which the diverse community of faculty, students, and staff are welcome and included. Successful candidates will demonstrate knowledge and skill related to ensuring equity and inclusion in the activities of their academic position (e.g., teaching, research, and service, as applicable).
The University of California, Berkeley 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. For the complete University of California nondiscrimination and affirmative action policy see: http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct
In searches when letters of reference are required all letters will be treated as confidential per University of California policy and California state law. Please refer potential referees, including when letters are provided via a third party (i.e., dossier service or career center), to the http://apo.berkeley.edu/ucb-confidentiality-policy prior to submitting their letter.
As a University employee, you will be required to comply with all applicable University policies and/or collective bargaining agreements, as may be amended from time to time. Federal, state, or local government directives may impose additional requirements.
To apply, visit https://apptrkr.com/4593188
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