Variant Impact Predictor Database (VIPdb)
Steven Brenner, Professor
Plant and Microbial Biology
Closed. This professor is continuing with Fall 2024 apprentices on this project; no new apprentices needed for Spring 2025.
Genome sequencing identifies a vast number of genetic variants. Predicting these variants’ molecular and clinical effects is one of the preeminent challenges in genetics. Accurate prediction of the impact of genetic variants improves our understanding of how genetic information yields molecular and cellular functions and is an essential step toward precision medicine. Over four hundred tools/resources have been developed specifically for this purpose. The Brenner lab has summarized these tools based on their characteristics in the genetic Variant Impact Predictor Database (VIPdb) (Hu et al., 2019; Lin et al., 2024). This database has helped researchers and clinicians explore appropriate tools and inform the development of improved methods.
Role: In this project, the student will enhance VIPdb by (1) adding new ClinGen calibration (Bergquist et al. 2024), (2) incorporating new fields to increase transparency, such as reporting of molecular mechanisms (Karchin et al., 2024), (3) incorporating model information (e.g., training data, date, and methods), (4) adding new or previously overlooked VIPs, (5) building VIP submission and update infrastructure, (6) creating a searchable database, and (7) surveying the community and literature for recommendations on new category fields to add. The student will update the database and website as needed. The student will develop modules to automate the search and categorization of VIPs to support these tasks, and will manually validate the results.
Qualifications: (1) Willing to learn and conduct research in a fast-paced environment.
(2) Knowledge of next-generation sequencing (NGS) data analysis or programming languages (R or Python) is a plus.
(3) Candidates must:
• Attend a 3-hour lab meeting every week.
• Attend a research subgroup meeting every week.
• Adhere to all lab policies (including weekly notebooks to track research and semester reports).
• Must register for credits, regardless of program-specific requirements.
(4) The student is required to continue the project during the Spring 2025 semester and full time in Summer 2025, if the student is invited to do so by the lab.
(5) Applicants with GPA under 3.6 will be considered only in exceptional circumstances.
Day-to-day supervisor for this project: Yu-Jen (Jennifer) Lin, Graduate Student
Hours: 12 or more hours
Related website: http://compbio.berkeley.edu
Related website: http://compbio.berkeley.edu