Annual Report 2022-23

Executive Summary

“This year, our institute co-lead a consortium to create a draft human pangenome – a better, more diverse reference for human genomic research that will reduce reference bias and open up new insights into human variation. It is hard to overstate just how monumental this will be for our field.”

David Haussler

Scientific Director UC Santa Cruz Genomics Institute

Quick Numbers

$28.4M

In federal funding awards

$3.8M

In industry and non-profit funding awards

49.4K

Citations in 2022 and an overall h-index of 298

45

Affiliate faculty

6

Unique mentoring/ training programs to reduce barriers to STEM

1.2K

Animal genomes added to our Browser’s Genark genome system

240

Mammal genomes compared using our Cactus software tool

15M

Pathogen genomes visualized with phylogenetic trees

119 Billion

Bases added to the existing human genome reference through the pangenome

“We are introducing more diversity and equity into the reference by sampling diverse human beings… One genome isn’t enough to represent everybody — the pangenome will ultimately be something that is inclusive and representative.”

– Benedict Paten

Associate Director for Computational Genomics UC Santa Cruz Genomics Institute

Top Headlines

First human pangenome reference better represents human diversity

Zoonomia release offers fresh insights into mammal evolution

Braingeneers develop method to automate brain organoids growth

SSPsyGene sets out to study 250 genes linked to neuropsychiatric conditions

Treenome Browser provides new tool for displaying millions of genome sequences

Beth Shapiro announces plans to de-extinct the dodo bird

Community Outreach

We are committed to educating the next generation of scientists, and making sure that genomic research careers are accessible to everyone. Our training programs and outreach events provide pathways to majors such as bioinformatics and bioengineering, and will develop a more robust pipeline of diverse learners into our undergraduate majors.

Research Mentoring Internship
(Undergraduate)

Bilingual Bioinformatics & Coding Short Course (Community College)

GREAT Summer Research Program (Undergraduate)

Bioinformatics Summer Bridge Program (Undergraduate)

Remote Project-Based Learning With Organoids (High School – Undergraduate)

Treehouse Undergraduate Bioinformatics Immersion
(Undergraduate)

Priorities for 2023/24

1

Understanding mechanisms of disease and developing strategies to improve human health

Use our strengths in data acquisition, data mining, data sharing, and technology development to improve the human reference genome and study neuropsychiatric disorders, cancer, and infectious disease. Continue our work with state and national public health agencies to bring the power of genomics to community and public health. Create a multidisciplinary Research Biosphere where genomic, epigenomic, transcriptomic, and other “omic” data can be combined with phenotype and other health-related data to greatly increase our understanding of biological systems, and empower breakthrough discoveries with critical impact on human health.

Using Conservation Genomics to Protect Our Planet

Ramp up our efforts to understand and reverse species extinction by cataloging genomic diversity, and setting up networks to save it before it disappears. Develop a broad conservation genomics program that capitalizes on UCSC strengths in genomics, marine systems, and ecology and evolution studies to develop and distribute resources towards conservation efforts and facilitate broad community engagement.