Head of Computation and Bioinformatics , CRISPR Cures Core

Head of Computation and Bioinformatics (5229C), CRISPR Cures Core - #85890

The Innovative Genomics Institute (IGI) is a non-profit, academic research organization formed through the partnership of UC Berkeley and UC San Francisco, and located on the UC Berkeley campus. A key focus of the IGI is accelerating translation of CRISPR-based approaches to address real-world problems in human health, agriculture, and climate.

The Bioinformatics Programmer develops and utilizes computational tools and systems to analyze and interpret biological and other research data. The incumbent will utilize and develop algorithms, computational techniques, and statistical methodologies. Assists IGI scientists at all levels (PI, postdoc, graduate student, undergraduate student) in the design of new experiments. Implements end‑user needs in database searching and integration. Maintains computational pipelines and tracks the flow of samples and information for large-scale studies.

Provides web‑based bioinformatics and access to public and proprietary databases.

• Develops new algorithms and bioinformatic processing pipelines for the analysis of high throughput sequencing data from genome editing experiments.
• Creates processing pipelines in order to scale to massive dataset sizes.
• Develops bioinformatic methods so they can be broadly applicable to data from different genome editing modalities and sequencing platforms. This includes development tools that process data from base editing, prime editing, and homology-directed repair strategies, and data from both long and short read sequencing platforms.
• Creates open-source bioinformatic software to be deployed across heterogenous computing systems and to be disseminated and supported for use by users not part of the group.
• Guides institute members in selection of appropriate bioinformatic analyses.
• Assists members of the group with analysis methods applying various data types and analyses. Analysis includes selection of pipelines that will effectively take advantage of compute infrastructure while maintaining data and analysis integrity.
• Applies advanced statistical knowledge of the analysis of genome editing experiments that includes the selection of correct wet‑lab and field protocols that will affect downstream bioinformatic method selection and analyses.
• Train staff, graduate students, and postdoctoral researchers in directly performing bioinformatic programming development.
• Utilizes both direct one‑on‑one and group interactions with members of the group with varying degrees of bioinformatic expertise.
• Directly communicates and trains group members that are primarily biologists that have varying degrees of experience in computational systems and bioinformatic understanding.
• Perform independent and group research with the goal of novel biological discoveries.
• Develops methods that incorporate both biological and computational knowledge to facilitate the rapid identification of safe and effective editing strategies for the correction of pathogenic mutations of interest. Central to this is the facilitation of methods for the improvement and optimization of new genome editing tools.
• Focuses on main research goals for the group that include the integration of different types of data from many large scale screening campaigns.
• Utilizes modern data science tools to integrate large sequencing datasets with heterogenous data types.
• Authors manuscripts for publication in research journals; presents oral and poster presentations at research conferences.
• Authors scientific level publications in high-level journals.
• Responsible for quality graphics and figures from complex scientific data.
• As needed, collaborates with other members of the group and non‑group collaborators with publications and presentations.
• Develops a comprehensive strategy for integrating data from a wide range of experimental systems into rules for identifying optimal editing strategies for correction of pathogenic mutations of interest.
• Develops computational approaches for the nomination and evaluation of potential off‑target effects of genome editing strategies.
• Develops and…