Summer Program Past Participants
2024

PI: Stan Fields
project: Mapping substrate specificities of human rhinovirus 3C protease in vitro using RNA-barcoded proteins

PI: Christine Queitsch & Josh Cuperus
project: Mapping the chromatin accessibility of plasmids with varying enhancer arrangement within maize

PI: Leo Pallanck
project: Automating a Climbing Assay to Study Neurodegeneration in Drosophila

PI: Brian Beliveau
project: Machine Learning for Cell Cycle Stage Classification in Mouse Embryo Tissue

PI: David Hawkins
project: CRISPR validation of cis-regulatory element interactions

PI: Lea Starita
project: Expanding variant effect assays to stem cell phenotypes

PI: Devin Schweppe
project: Towards quantitative phosphoproteomics in murine models

PI: Andrew Stergachis
project: Testing Protein Stability of NOTCH2tv in Human Cells

PI: Cole Trapnell
project: Building a Neural Network Capable of Predicting Fluorescent Markers in Gastruloid Images

PI: Maitreya Dunham
project:
2023

PI: Devin Schweppe
project:

PI: Christine Queitsch & Josh Cuperus
project:

PI: David Hawkins
project:

PI: Bill Noble
project:

PI: Lea Starita
project:

PI: Brian Beliveau
project:

PI: Maitreya Dunham
project:

PI: Jay Shendure
project:

PI: Andrew Stergachis
project:

PI: Cole Trapnell
project:

PI: Doug Fowler
project:
2022

PI: Evan Eichler
project: Human Structural Diversity of Complex Inverted Region at 17q21.31

PI: Doug Fowler
project: Deep mutational scanning reveals epistasis in CYP2C19

PI: Lea Starita
project: Conserved intronic region of MYBPC3 functions as a strong enhancer in iPSC cardiomyocyte reporter assay

PI: Christine Queitsch, Josh Cuperus
project:

Fort Lewis College
PI: Judit Villen
project:

PI: Stan Fields
project:

PI: Brian Beliveau
project:

PI: Christine Queitsch, Josh Cuperus
project: Investigating Genetic Insulation Mechanisms in Plants

PI: Devin Schweppe
project:
PI: David Hawkins
project:
2021

PI: Brian Beliveau
project: Visualizing Satellite DNA Repeats with Tigerfish

PI: Doug Fowler
project: Alternating Nuclear Localization Signals to Optimize Bxb1 Recombinase

PI: Mike MacCoss
project: Optimization of limited proteolysis-mass spectrometry on cerebrospinal fluid

PI: Lea Starita
project: Identification of CRISPR prime edited resistance mutations in the EGFR gene

PI: David Hawkins
project: Verifying Enhancers Interactions through Deletion of the Enhancers

PI: Cole Trapnell
project: Building an Atlas of Lung Cell Types in Hereditary Pulmonary Alveolar Proteinosis

PI: Bill Noble
project: Avocado model uses HFFc6 cell type to make predictions for missing assays

PI: Devin Schweppe
project:
PI: Christine Queitsch, Josh Cuperus
project: Identifying photoperiod sensitivity across Camelina sativa accessions

PI: Christine Queitsch, Josh Cuperus
project: Short-day conditions significantly affect growth of Camelina sativa

PI: Maitreya Dunham
project: Haplotype modifies variant function in G6PD
2019
PI: David Hawkins
project: Functional validation of Human T-cells and Macrophage specific Cis-Regulatory Elements
PI: Celeste Berg
project: Investigation of Novel Gene Interaction in D. melanogaster Tube Formation
PI: Stan Fields
project: Identifying Inhibitory Fragments of E. coli Dihydrofolate Reductase with a Sequencing-based Assay
PI: Evan Eichler
project: Characterizing the Gene HNRNPH2 in Neurodevelopmental Disorders
PI: Maitreya Dunham
project: Identification of genes that impact fitness of aneuploid S. cerevisiae strains
PI: Cole Trapnell
project: Single Cell Investigation of npas41 Zebrafish Mutants
PI: Christine Queitsch
project: Developing Methods for Characterizing Plant Enhancers
PI: Jay Shendure
project: Optimizing Conditions for Single Cell Lineage Tracing in a Mammalian Model
PI: Bonny Brewer
project: Does the mcm4 helicase mutation increase genome instability in yeast?

PI: Paul Valdmanis
project:
PI: Christine Queitsch
project: Mapping Cell Lineages with scATAC-seq

PI: Lea Starita
project:
2018

PI: Celeste Berg
project:

PI: Cole Trapnell
project: Dissecting Kinase Networks with Targeted Single-Cell Genomics and Proteomics

PI: Willie Swanson
project: Genetic Variation in Sperm Lysin in Pacific Abalone

PI: David Hawkins
project: Understanding Gene Expression via Enhancers

PI: Stan Fields
project: Mistranslation as a Method to Measure the Impact of Mutations on Protein Interactions

PI: Sam Miller
project:

PI: Doug Fowler
project: Identifying Inhibitor-Specific Resistance Mutations in Src Kinase

PI: Bill Noble
project: Generating Representative Subsets from Single Cell Hi-C Data Using Submodular Optimization

PI: Judit Villen
project: Identifying and Understanding Phosphorylation Patterns on Insulin Receptor Substrate 1 Using Targeted Mass Spectrometry

PI: Bonny Brewer
project: Sequence Specificity of Yeast Origins
2017

PI: Jay Shendure
project:

PI: Evan Eichler
project:

PI: Leo Pallanck
project:

PI: Bob Waterston
project:

PI: Jim Bruce
project:

PI: Celeste Berg
project:

PI: Doug Fowler
project:

PI: Stan Fields
project:

PI: Jim Bruce
project:
PI: Cole Trapnell
project:

PI: David Hawkins
project:
2016

PI: Evan Eichler
project: The evolutionary history and transcript diversity of a Homo sapiens specific segmental duplication
PI: Sam Miller
project: The second messenger cyclic-di-GMP regulates biofilm formation, motility, antibiotic resistance, and outer membrane permeability of multidrug-resistant Acinetobacter baumannii

PI: Bob Waterston
project: Analyzing single cell gene expression in Caenorhabditis elegans

PI: Mike MacCoss
project: Quantifying phosphorylation events in the insulin signaling pathway using MS/MS

PI: Doug Fowler
project: Validating Amyloid-Beta Deep Mutational Scan data using a yeast growth assay
PI: Cole Trapnell
project: Visualization of myoblast fusion to uncover underlying mechanisms
2015

PI: Cole Trapnell
project:

PI: Bob Waterston
project:

PI: Jim Bruce
project:

PI: Jay Shendure
project: Measuring Cellular Growth Response to 6-MP Treatment and Protein Stability in all Possible Nonsynonymous Mutations in TPMT

PI: Sam Miller
project:

PI: Doug Fowler
project:
2014

PI: Bob Waterston
project:

PI: Evan Eichler
project:

PI: Ray Monnat
project:

PI: Jim Bruce
project:

PI: Bonny Brewer
project:

PI: Celeste Berg
project:

PI: Jay Shendure
project: Saturation mutagenesis methods for evaluating the effects of all possible nonsynonymous mutations in TPMT in response to thiopurine drugs

PI: Stan Fields
project: The effect of synonymous codon pair changes on HIS3 expression in yeast
2013

PI: Mary-Claire King
project:

PI: Evan Eichler
project:

PI: Leo Pallanck
project:

PI: Maitreya Dunham
project:

PI: Bonny Brewer
project:

PI: Bill Noble
project:

PI: Doug Fowler
project:
2012

PI: Bonny Brewer
project: Amplification of SUL1 in diploid yeast cells grown in sulfate-limited conditions

PI: Josh Akey
project: Whole Genome Analysis of Siblings by comparing SNPs with Identity by Descent

PI: Evan Eichler
project: Identification of Copy Number Variants Contributing to Neurological Disorders of Human Specific Neuronal SRGAP2

PI: Sam Miller
project: Indentifying phoP mutants involved in regulating Salmonella's outermembrane permeability barrier

PI: Celeste Berg
project: Exploring the role of putative Tramtrack69 targets in Drosophila tube morphogenesis

PI: Stan Fields
project: Isolation and characterization of ethanol-tolerant yeast strains

PI: Bob Waterston
project: Can Partially Redundant Genes Compensate for the Loss of their Partner? Examination of the Roles of the Tbx8 and Tbx9 Genes in Embryonic Nematode Development

PI: Judit Villen
project: Evolutionary Protein Phosphorylation in Yeast Species
2011

PI: Judit Villen
project: Signaling Patterns in the Saccharomyces cerevisiae Proteome under Oxidative Stress

PI: Christine Queitsch
project:

PI: Evan Eichler
project: The Discovery and Validation of Copy Number Variations in Autism

PI: John Stamatoyannopoulos
project:

PI: Josh Akey
project: A High-Resolution Genome Wide Map of Structural Variation in the Modern Domesticated Dog

PI: Celeste Berg
project: On the Shark quest: Role of Shark tyrosine kinase in tube formation

PI: John Stamatoyannopoulos
project: A Novel Method for Detection and Quantification of Genome-Wide Methylation

PI: Willie Swanson
project: Population Sequencing of a Rapidly Evolving Sperm Protein, SP6

PI: Bob Waterston
project: Identification of Regulatory Relationships of hnd-1 in Muscle Differentiation and of elt-1 in Hypodermal Differentiation in the Caenorhabditis elegans Embryo
2010

PI: Elhanan Borenstein
project: "An analysis of the topological properties of the metabolic networks of gut-dwelling microbes"

PI: Mike MacCoss
project:

PI: Evan Eichler
project:

PI: Leo Pallanck
project: "Mitochondrial quality control in dopaminergic neurons"

PI: Jay Shendure
project: "Progress towards massively parallel single cell sequencing of T-cell receptors"

PI: Gail Jarvik
project: "Challenging the Powerful Gene: An Investigation of Muscle Hypertrophy"

PI: Celeste Berg
project: "Probing the Role of Stretch cells during Dorsal Appendage Tube Formation in Drosophila"

PI: Bonny Brewer
project: "Genome Mapping Identifies Genomic Inversion in Kluyveromyces walti"
2009

PI: Bob Waterston
project:

PI: Bill Noble
project:

PI: Evan Eichler
project:

PI: Maitreya Dunham
project:

PI: Debbie Nickerson
project: