Department of Genome Sciences
Foege Building S-250, Box 355065
3720 15th Ave NE, Seattle WA 98195-5065
phone: (206) 221-7377 | fax: (206) 685-7301
non-academic questions:
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How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin
Mike Doud and Juhye Lee are lead authors on paper in Nature Communications.

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome
Giancarlo Bonora is lead author on paper in Nature Communications.

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition
Tim Durham is lead author on paper in Nature Communications.

On the design of CRISPR-based single-cell molecular screens
Andrew Hill and Jose McFaline are lead authors on paper in Nature Methods.

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
This ms documents DNA damage repair deficiencies across 33 cancer types, and links between DDR deficiency, genomic instability and clinical outcomes. Ray Monnat was part of the leadership team of three, and a corresponding author for the team of 38 co-authors with 24 different affiliations.
Cell Reports


Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data
Former grad Vanessa Gray is lead author on paper in Cell Systems.

Hepatic Abundance and Activity of Androgen and Drug Metabolizing Enzyme, UGT2B17, are Associated with Genotype, Age, and Sex
Steven Lee is author on paper in Drug Metabolism and Disposition.

Two Drosophilids exhibit distinct EGF pathway patterns in oogenesis
Kenley O'Hanlon and Rachel Dam are co-first authors on paper in Development, Genes, and Evolution.

The cis-regulatory dynamics of embryonic development at single-cell resolution
Darren Cusanovich is lead author on paper in Nature.
Nature | UW Medicine

Using Genotype Abundance to Improve Phylogenetic Inference
Will DeWitt is lead author on paper in Molecular Biology and Evolution.

BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data
Borenstein Lab members Alex Eng, Colin McNally, and Cecilia Noecker are co-first authors on paper in Frontiers in Microiology.

Taxa-function robustness in microbial communities
Alex Eng is first author on paper in Microbiome.




Complex relationships between chromatin accessibility, sequence divergence, and gene expression in A. thaliana.

Queitsch Lab members Cristina Alexandre, Ken Jean-Baptiste, Mike Dorrity, and Kerry Bubb, along with Fields Lab member Josh Cuperus, are authors on paper in Molecular Biology and Evolution.

Determinants and Regulation of Protein Turnover in Yeast
Miguel Martin-Perez is first author on paper in Cell Systems.

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C
Caiti Smukowski Heil, Josh Burton, and Ivan Liachko are co-first authors on a paper in Yeast.

The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition
Adrian Verster is lead author on paper in Cell Host & Microbe. | UW Medicine Newsroom

Reversed graph embedding resolves complex single-cell trajectories
Xiaojie Qiu is lead author on paper in Nature Methods.

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements
Naresh Doni Jayavelu is co-first/lead author on a paper in Stem Cell Reports.

Comprehensive single-cell transcriptional profiling of a multicellular organism
Junyue Cao and Jonathan Packer are lead authors on paper in Science, along with other members of the Shendure, Trapnell, and Waterston Labs.
Science | NY Times

Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics
Fowler Lab members are authors on paper in Nature Methods.

A statistical framework for analyzing deep mutational scanning data
Hannah Gelman and former grad Alan Rubin are lead authors on paper in Genome Biology

Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions
Vanessa Gray is lead author on paper in Genetics.

Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation
Emma Timmins-Schiffman is lead author on paper in Journal of Proteome Research.

Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases
Cristina Valensisi is lead author on paper in Cell Reports.

phydms: software for phylogenetic analyses informed by deep mutational scanning
Sarah Hilton is first author on a paper in PeerJ describing software for performing phylogenetic analyses informed by deep mutational scanning.

Parallel evolution of influenza across multiple spatiotemporal scales
Katherine Xue is lead author on paper in eLife.
eLife | The Atlantic | Wired

The dynamic three-dimensional organization of the diploid yeast genome
Seungsoo Kim is lead author on paper in eLife.

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast
Former grad Elyse Hope is lead author on paper in Genetics.

Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in Drosophila melanogaster
Sandra Zimmerman is lead author on paper in Genetics.

Mining microbes: Creating genomic tools to fight disease
Borenstein Lab research is featured in Science.

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants
the 2016 paper on rDNA copy number variation in yeast by Liz Kwan (postdoc), Summer Wang and Haley Amemiya (former undergrads) has been featured in a GSA Journals Spotlight booklet.

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
Former grad Ryan Emerson and incoming grad William DeWitt are lead authors on paper in Nature Genetics.

Loss of heterozygosity drives adaptation in hybrid yeast
Caiti Smukowski Heil is lead author on paper in Molecular Biology and Evolution.

The birth of a human-specific neural gene by incomplete duplication and gene fusion
Max Dougherty and Xander Nuttle are lead authors on paper in Genome Biology.

A platform for functional assessment of large variant libraries in mammalian cells
Kenny Matreyek is lead author on paper in Nucleic Acids Research.

Single-cell mRNA quantification and differential analysis with Census
Xiaojie Qiu is lead author on paper in Nature Methods.

Complete mapping of viral escape from neutralizing antibodies
Mike Doud's complete mapping of virus antibody escape is published in PLoS Pathogens.

Seeking to unravel DNA
Tim Durham's research is featured on UW IT website.





Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases
Former Eichler Lab members Holly Stessman and Bo Xiong are lead authors on paper in Nature Genetics.

Differential paralog divergence modulates genome evolution across yeast species
Monica Sanchez is lead author on paper in PLoS Genetics.




Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome

Borenstein Lab paper is in Microbiome.

Thursday, May 24
Heather Machkovech (Ph.D. in Genome Sciences)
"Translation initiation during influenza virus infection and its role in cellular immunity"
2:00, Pelton Auditorium, FHCRC | flier

Friday, May 25
Max Dougherty (Ph.D. in Genome Sciences)
"Transcription of human-specific duplicate genes"
11:00, Foege Auditorium | flier

Wednesday, May 30
Jorgen Nelson
(Ph.D. in Genome Sciences)
"High-throughput protein design and optimization for antimicrobial applications"
9:00, Health Sciences T-733

Human genetics pioneer, Dr. Arno G. Motulsky, 94, remembered

UW Medicine | Division of Medical Genetics | NY Times










GS Distinguished Faculty interview:

Dr. Jesse Bloom has been selected as an HHMI Investigator.

Katherine Xue has received the Crow Early Career Award at the 2018 Population, Evolutionary and Quantitative Genetics Conference.

Juhye Lee has been awarded an F30 from the NIAID to support her thesis project "Comprehensive antigenic mapping of seasonal influenza viruses.

Introducing the Genome Sciences 2018 incoming class:

Elizabeth Aguilar - DePauw University
Ryan Carlson - UW MSTP
Shawn Fayer - Brandeis University
Sayeh Gorjifard - Johns Hopkins University
Allie Greaney  - UW MSTP
Hyeon-Jin Kim - University of Washington
Michelle Noyes - University of Chicago
Phoebe Parrish - Davidson College
Chengxiang Qiu - Peking University
Sam Regalado - UW MSTP
Sam Smukowski - University of Wisconsin

Clara Amorosi has been awarded an Amgen Scholars Alumni Travel award.

Dr. Mary-Claire King has been awarded the Shaw Prize in Life Science and Medicine.

Sarah Hilton has been selected to attend the Heidelberg Laureate Forum.

Dr. Mary-Claire King has been awarded the Dan David Prize.

Molly Gasperini has been named to the Husky 100.

Dr. Cole Trapnell has been awarded the ISCB Overton Prize.

Berg Lab undergraduate researcher Bernice Lin has received the Thomas Sedlock Icon Scholarship.

Katherine Xue has been awarded the Weintraub Graduate Student Award from FHCRC.

Dr. Jay Shendure to lead the Brotman Baty Institute for Precision Medicine.

UW Medicine | Seattle Times

Xiaojie Qiu has been awarded the China Scholarship Council Award.

Dr. Caiti Smukowski Heil has been awarded a DeLill Nasser Award from the Genetics Society of America.

Dr. Kelley Harris has been awarded the Science & SciLifeLab Prize for Young Scientists.

Former UW Genetics Ph.D. student Jeffrey Hall has been awarded the Nobel Prize.

NY Times | UW News

Dr. Marsha Wheeler has been awarded an ASH Abstract Achievement Award by the American Society of Hematology.

Dr. Evan Eichler has been elected to the National Academy of Medicine.

Dr. Douglas Fowler has been selected as a CIFAR Azrieli Global Scholar.

Vijay Ramani has been selected as a Sandler Fellow at UC San Francisco

2017 department retreat | large photo | Ethan Ahler and Tychele Turner have received the Parker Travel Award for best poster at the Genome Sciences department retreat

Emily Killingbeck has been awarded an NRSA fellowship from the NIH.

Genome Sciences Education Outreach has received funding from a Science Education Partnership Award (SEPA) to support our new project Genes, the Environment, and Me: Health and STEM Network (GEMNet). This project will build on our successful GEM program to develop a cross-disciplinary approach for teaching and learning about type 2 diabetes in high school biology, health, and family and consumer sciences classes. GEMNet and GEM have been supported by a Science Education Partnership Award (SEPA) from the National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health.

Recent papers:

Socratic Seminar with Data: A Strategy to Support Student Discourse and Understanding

How Do You Like Your Science, Wet or Dry? How Two Lab Experiences Influence Student Understanding of Science Concepts and Perceptions of Authentic Scientific Practice

The Paul G. Allen Frontiers Group announces center to map cell lineages
$10 million grant will create an Allen Discovery Center at UW Medicine to generate the first global maps of cell lineage in complex organisms
UW Health Sciences | Paul G. Allen Frontiers Group

Eliah Overbey has been awarded an Amazon Catalyst grant to work on direct RNA sequencing using the Oxford Nanopore MinION.

Dr. Kelley Harris has received a Burroughs Wellcome Fund Career Award at the Scientific Interface fellowship.

Liesl Strand, a recent UW undergraduate student doing research in the Berg lab, earned a “Best Poster” prize in the PhD division at the International Society for Developmental Biology in Singapore.

Introducing the Genome Sciences 2017 incoming class:

David Bacsik, UW MSTP
Danielle Boley, University of Notre Dame
Florence Chardon, UC Berkeley
Emma De Neef, University of South Carolina
William DeWitt, University of Vermont
Philip Dishuck, Washington & Lee University
Kate Dusenbury, UW MSTP
Michael Goldberg, Brown University
Jose Pineda, UW MSTP
Deanna Plubell, Walla Walla University
Nick Popp, UW MSTP
David Read, University of Michigan

Former GS grad Keolu Fox named one of 2017 National Geographic Emerging Explorers

UW ranked 5th in the world for genetics by the Center for World University Rankings.

Dr. Damien Wilburn selected as the 2017 Postdoc Mentoring Award Winner

Jolie Carlisle, Martin Mathay, Anna Minkina, Jared Mohr, Bianca Ruiz, and Cindy Yeh have been awarded NSF fellowships. Gesine Cauer, Emma Hoppe, Alberto Rivera, and Ian Smith received honorable mention.

Berg Lab undergraduate researcher Liesl Strand is one of 60 undergraduates nationwide selected to present her research to Congress at a two-day symposium “Posters on the Hill”. Liesl also received a GSA Victoria Finnerty Travel Award to present her work at the National Drosophila Conference in San Diego and will be featured in this year's Husky 100.

Bill Noble has been selected as an International Society for Computational Biology fellow.

Benjamin Brandsen and Greg Findlay have been awarded NRSA fellowships from the NIH.

Max Dougherty, Jason Klein, and Brian Searle have been awarded NRSA fellowships from the NIH.

Ethan Ahler has been awarded an American Association for Cancer Research -June L. Biedler Scholar-in-Training Award.





2016 Highly Cited Researchers list from Thomson Reuters includes Drs. Evan Eichler, William Noble, Jay Shendure, John Stamatoyannopoulos, and Judit Villen | UW Today

2016 summer students McCauley Eddy (MacCoss Lab) and Floriane Ngako-Kameni (Fowler Lab) received awards for their research presentations at the 2016 ABRCMS.

Molly Gasperini has been selected as a 2016 Epstein Trainee Award Recipient by the American Society of Human Genetics.

Former GS grad Sharon Greenblum is featured in the Stanford CEHG blog.

Former GS grad Katrina Claw is featured in UW Health Sciences News Beat.

Music by GS grad Bianca Ruiz is featured on the GSA Genes to Genomes blog.

Lucas Cary (Queitsch Lab), Liesl Strand (Berg Lab), and Cynthis Wong (Malik Lab) have been awarded the Herschel Roman Undergraduate Scholarship. Liesl Strand (pictured) has also been awarded a Levinson Emerging Scholars Award.

Former Berg Lab member and grad student Nate Peters earned the cover on a book titled “Oogenesis” for our chapter “In vitro culturing and live imaging of Drosophila egg chambers: A history and adaptable method”

Drs. Maitreya Dunham and Jesse Bloom have been selected as HHMI Faculty Scholars.

Lindsay Pino has been awarded an NRSA individual fellowship.

Katherine Xue and Adrian Verster have received the Parker Travel Award for best poster at the Genome Sciences department retreat.

2016 department retreat | large photo

Dr. Brian Beliveau

Genome Sciences is pleased to welcome Dr. Brian Beliveau to the department in September 2018 as our newest faculty member. Dr. Beliveau develops and applies super-resolution microscopy methods and programmable molecular technologies to map the 3D organization of the genome in single cells.

Dr. Kelley Harris

Dr. Kelley Harris joined Genome Sciences in 2018. Dr. Harris uses population genetic theory and high-throughput biological sequence analysis to study recent evolutionary history in humans and other species. Please visit her faculty page to learn more about her research.