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

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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.

The IGI is committed to hiring and developing staff who want to work in a high-performing culture that supports the outstanding work of our faculty and students. The IGI is interested in candidates who will contribute to our commitment to excellence, diversity, and inclusion in academia. The IGI is also interested in applicants who may have had non-traditional career paths, taken time off for family/personal reasons, or excelled in careers outside academia. Most of our job postings list "required" and "preferred" qualifications. We encourage individuals to apply who do not meet every preferred qualification, but who could grow and thrive in the role.

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.

Application Review Date

The First Review Date for this job is: TBD (Must be 14 days from when the posting goes live, TA will input). For full consideration, please apply on or before the first review date.

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.

• 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 nonbioinformatic researchers; 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.

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

For information on the comprehensive benefits package offered by the University, please visit the University of California's Compensation & Benefits website.

Under California law, the University of California, Berkeley is required to provide a reasonable estimate of the compensation range for this role and should not offer a salary outside of the range posted in this job announcement. This range takes into account the wide range of factors that are considered in making compensation decisions, including but not limited to experience, skills, knowledge, abilities, education, licensure and certifications, analysis of internal equity, and other business and organizational needs. It is not typical for an individual to be offered a salary at or near the top of the range for a position. Salary offers are determined based on final candidate qualifications and experience.

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.

How to Apply

• To apply, please submit your resume and cover letter.

Other Information

• This position is covered by the collective bargaining agreement between UAW, United Auto Workers, and the University of California Regents for RPSP.
• This is not a visa opportunity. This position does not include sponsorship of a new consular H-1B visa petition that would require payment of the $100,000 supplemental fee.
• This position is eligible for up to 25% remote work. Exact arrangements are determined in partnership with your supervisor to meet role responsibilities and department needs and are subject to change.

Misconduct

SB 791 and AB 810 Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts a conditional offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; received notice of any allegations or are currently the subject of any administrative or disciplinary proceedings involving misconduct; have left a position after receiving notice of allegations or while under investigation in an administrative or disciplinary proceeding involving misconduct; or have filed an appeal of a finding of misconduct with a previous employer.

"Misconduct" means any violation of the policies or laws governing conduct at the applicant's previous place of employment, including, but not limited to, violations of policies or laws prohibiting sexual harassment, sexual assault, or other forms of harassment, discrimination, dishonesty, or unethical conduct, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct:

UC Sexual Violence and Sexual Harassment Policy

UC Anti-Discrimination Policy

Abusive Conduct in the Workplace

Equal Employment Opportunity

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.