Head of Computation and Bioinformatics (5229C), CRISPR Cures Core - #85890 Departmental Overview 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. Position Summary 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. Responsibilities 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 implements strategies with executive personnel for computational biological programs for large research groups, departments, and institutes. This will involve work at the Innovative Genomics Institute, Division Chiefs at at UCSF, UCLA, and Stanford, Program Officers at Advanced Research Projects Agency for Health (ARPA‑H), the Chief Technology Officer at Danaher Corporation - among others - to define strategic goals for computational / bioinformatic pipelines for CRISPR Cures and lead on implementation of these strategies both intramurally and across other centers for CRISPR Cure excellence (UCSF, UCLA, Stanford, Penn). Manages data access and priorities for members of the group and international collaborators. Verifies the quality, standardization, and providence of new data. Monitors large amounts of novel sequencing data that is constantly being generated. The new data entering the lab must be processed in a way that is both standardized and usable by the whole group. Develops practices and methods that ensure that all incoming data to the lab conforms to robust and standardized quality control. Process new data in a way that is translatable to a large multi‑user group with varying degrees of technical training. This can mean ensuring that new data is tagged in a way that is understandable by everyone in the lab to ensuring that data processing pipelines are compatible with existing analysis infrastructure. In collaboration with development partners and IGI leadership, participates in development of proposals and funding requests. This position will identify funding opportunities strategically aligned with IGI priorities, develop a proposal strategy, draft specific sections that require position‑appropriate technical expertise and provide technical input for other sections of the proposal. In other complementary settings this position will be responsible for specific subunits of larger proposals that have to comprise a substantial computational / bioinformatics component. Leads a team of bioinformatics programming professionals. This will involve project leading and direct oversight of lower‑level Bioinformatics Programmers. Responsible for project budgets and financial reporting. This applies to budgets for the following funded CRISPR Cures programs at the IGI: IGI‑Danaher Beacon for CRISPR Cures; CZI‑IGI Center for Pediatric CRISPR Cures; MRC Center for Research Excellence in Therapeutic Genomics; and the newly funded ARPA‑H THRIVE AEGIS effort. The duties will involve managing allocations and monitoring expenditures, with report preparation delegated to designated project managers within those efforts. Required Qualifications Expert knowledge of bioinformatics methods, applications programming, web development and data structures. Expert understanding of relational databases, web interfaces and operating systems. Highly developed project management skills. Expert knowledge of modern biology and applicable field of research. Highly developed interpersonal skills in order to work with both technical and non-technical personnel at all levels internally and externally to the organization, including ability to effectively communicate and interface with campus, departmental, and institute leadership. Advanced familiarity with online bioinformatic databases and systems, such as NCBI and EMBL ENA. Expert knowledge of therapeutically relevant human genome editing technologies, including base editing and prime editing. Data science experience, specifically integrating biological and non-biological data. Understanding of database and search systems, such as SQL, MongoDB, and Elasticsearch. Experience with effectively analyzing large data with modern visualization tools. Experience synthesizing biological and informatic themes. Has demonstrated development of tools for analyzing large scale sequence datasets. Advanced statistical knowledge of analysis of high-throughput screening data. Thorough knowledge of high throughput sequencing technologies, related experimental workflows and protocols, and data processing. Bachelor's degree in related area and / or equivalent experience / training. Communication skills to work with both technical and non‑technical personnel in multiple fields of expertise and at various levels including ability to guide both bioinformatic and non‑bioinformatic researchers; Ability to effectively communicate and interface with campus, departmental, and institute leadership. Preferred Qualifications Advanced knowledge of CRISPR-based functional genomics, including design, execution, and analysis of novel screening protocols and/or ability to learn. High-level understanding of DNA repair mechanisms relevant to genome editing. Ability to develop independent research themes and assist in the acquisition of funding from governmental agencies and private donors. Ability to communicate through research articles and presentations. Demonstrated history publishing in a research journal. Experience presenting orally at scientific conferences. PhD degree in related area and / or equivalent experience / training. Salary & Benefits The budgeted annual salary that the University reasonably expects to pay for this position is $155,900.00 - $310,900.00. This is an exempt, monthly-paid position. Equal Opportunity Employer The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law. #J-18808-Ljbffr