Projects
Applications in Review
Single-Cell Resolution of the Epigenomic Basis of Adaptation in the Wild
NIH NIGMS R01 (2026-2031) | $2,187,344 | PI: William Cresko
Using threespine stickleback fish to understand epigenomic mechanisms underlying adaptation in natural populations at single-cell resolution.
Current Research Funding
Male Pregnancy and its Effects on the Brood Pouch Microbiome
NSF (2020-2025) | $1,070,484 | PI: William Cresko
Investigating the unique biology of male pregnancy in syngnathid fishes and how it shapes host-microbiome interactions in the brood pouch.
Recent Major Research Projects
Mathematical Models of Host-Symbiont Ecology and Evolution
Moore Foundation (2022-2025) | $564,000 | PI: William Cresko
Developing mathematical frameworks to understand the evolutionary dynamics of host-microbiome interactions.
NIH P50 Reducing Opioid Addiction in Mothers
NIH P50 (2019-2025) | $11,190,603 | Co-Investigator
Multi-institutional center grant focused on understanding and reducing opioid use disorder in pregnant and parenting mothers.
NIH Center Grant (2012-2018) | $10,298,725 | PI: William Cresko
Established the Microbial Ecology and Theory of Animals Center to study host-microbiome interactions across multiple model systems.
COVID-19 Response Projects
SARS-CoV-2 Testing Infrastructure and Scale-up
Oregon Health Authority (2020-2022) | $4,364,823 | PI: William Cresko
Major equipment purchase and infrastructure development for high-throughput COVID-19 testing at UO and throughout Oregon.
Optimizing SARS-CoV-2 Testing in Latinx Communities
NIH RADx-UP (2021-2023) | $1,832,583 | MPI: William Cresko
Increasing COVID-19 testing access and efficacy in underserved Latinx populations throughout Oregon.
Scaling up SARS-CoV-2 Testing in Latinx Communities
NIH RADx-UP (2020-2022) | $4,166,575 | MPI: William Cresko
Large-scale implementation of culturally appropriate testing strategies for Oregon’s Latinx communities.
Genomics and Transcriptomics Research
Advancing Transcriptomics in Aquatic Models
NIH (2011-2019) | $2,647,451 | PI: William Cresko
Developed novel transcriptomic tools and CRISPR applications for aquatic model organisms. Included major supplement for CRISPR technology development.
The Study of Cancer Development as an Evolutionary Process
W.M. Keck Foundation (2011-2015) | $1,000,000 | PI: William Cresko
Applied evolutionary theory to understand cancer progression and treatment resistance.
Functional and Population Genomics of Small RNA Regulation
NIH (2011-2016) | $1,484,689 | PI: William Cresko
Investigated the role of small RNAs in developmental plasticity and evolutionary adaptation.
Evolution and Development Studies
Evolutionary Genomics of Rapid Adaptation in Stickleback
NSF (2009-2013) | $364,756 | PI: William Cresko
Documented genomic changes underlying rapid evolutionary responses to environmental change.
Evolution of Development of Facial Bone Morphology
NSF (2008-2012) | $555,016 | PI: William Cresko
Uncovered developmental genetic mechanisms controlling craniofacial variation in natural populations.
Microevolution of Craniofacial Development in Stickleback
NIH (2007-2011) | $473,944 | PI: William Cresko
Identified genetic variants affecting skull morphology with implications for understanding human craniofacial disorders.
Infrastructure and Educational Support
Major Renovation of UO Animal Facilities
NIH C06 (2010-2012) | $9,117,040 | PI: William Cresko
Complete modernization of animal research facilities supporting campus-wide biomedical research.
NSF IGERT - Evolution, Development and Genomics
NSF (2005-2010) | $2,399,988 | PI: William Cresko
Established interdisciplinary graduate training program combining evolutionary biology with genomics.
Computational Instrument for Scientific Synthesis
NSF MRI (2009-2011) | $1,971,109 | PI: William Cresko
Acquisition of high-performance computing infrastructure supporting genomics research across campus.
Graduate Internship Program Support
ETIC (2013-2015) | $1,299,109 | PI: William Cresko
Renewable funding establishing industry partnerships for graduate student training.
X-ray Microscope Capabilities
Murdock Charitable Trust (2019-2020) | $500,000 | PI: William Cresko
Advanced imaging infrastructure for biological and materials science research.
Methodological Developments
Years: 2008-present | Impact: 10,000+ users worldwide
Developed Restriction site Associated DNA sequencing for cost-effective genome-wide SNP discovery and genotyping.
Years: 2010-present | Downloads: 50,000+
Created comprehensive software suite for building loci from short-read sequences in organisms without reference genomes.
Years: 2020-present
Pioneered single-cell isoform sequencing methods for understanding cell-type-specific transcript variation.
Fellowship and Student Support
Postdoctoral Fellowship Support
Successfully mentored 8 NIH-funded postdocs including Kirchstein NRSA Fellows
Total postdoctoral fellowship funding secured: >$1,000,000
Graduate Student Support
Secured funding for 5 NSF Doctoral Dissertation Improvement Grants
Mentored NSF Graduate Research Fellowship recipients
NIH F31 Fellowship advisor for multiple students
Collaborative Networks
National & International: Stanford Hopkins Marine Station | Max Planck Institute | Swedish Museum of Natural History | University of Alaska | Lund University | OHSU
Campus Collaborations: Institute of Ecology and Evolution | Knight Campus for Accelerating Scientific Impact | META Center | Genomics and Cell Characterization Core Facility | Prevention Science Institute
Industry Partnerships: Two spin-off companies utilizing next-generation sequencing technologies
Data & Resources
All genomic data publicly available through:
NCBI BioProject | Dryad | GitHub
Software Tools: Stacks | RAD-seq protocols | scISOr-seq pipelines
Total Research Funding
Career Total: >$60 million in federal, foundation, and state funding
Current Active Funding: >$1.6 million
Leadership Roles: PI on >25 major grants | Co-I on >10 collaborative grants
For collaboration inquiries or data access: wcresko@uoregon.edu