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:
gsadmin [ a t ]
academic / web: bgiebel [ a t ]

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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.




Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry
Bruce Lab paper is in PNAS.







Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome
Borenstein Lab paper is in featured on the cover of Cell Host & Microbe. | UW Health Sciences NewsBeat

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
Martin Kircher is lead author on paper in Genome Research.




Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns

Emma Timmins-Schiffman and Damon May are lead authors on paper in The ISME Journal.

Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Former grad Rachel Gittelman is lead author on paper in Current Biology.
Daily Mail | USA Today | Gazeta Wyborza

Detecting Sources of Transcriptional Heterogeneity in Large-Scale RNA-Seq Data Sets
Brian Searle is lead author on paper in Genetics.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075
Xia Wu and Juan Chavez are lead authors on paper in Nature Communications, along with members of the Bruce, Manoil, and Singh Labs.

denovo-db: a compendium of human de novo variants
Denovo-db paper has been selected as an NAR Breakthrough Article.
Nucleic Acids Research | denovo-db

Deciphering the Mysterious Microbiome
Borenstein Lab research is featured in IEEE Pulse.

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA
Tychele Turner is lead author on paper selected as a Best of AJHG 2015 and 2016.

Evolution of protein phosphorylation across 18 fungal species
Dr. Ricard Rodriguez-Mias is lead author on paper in Science, along with other Villen and Dunham Lab members.

Population genetics: A map of human wanderlust
Nature | NY Times
Serena Tucci is author on commentary in Nature.

Analysis of exome sequencing data sets reveals structural variation in the coding region of ABO in individuals of African ancestry
Keolu Fox is lead author on paper in Transfusion.

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants
Liz Kwan, Summer Wang, and Haley Amemiya are authors on paper in G3.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility
Xander Nuttle is lead author on paper in Nature.
Nature | UW Health Sciences NewsBeat

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast
Caitlin Gamble is lead author on paper in Cell.





In Vivo Conformational Dynamics of Hsp90 and Its Interactors
Juan Chavez, Devin Schweppe, Jimmy Eng, and Jim Bruce are authors on paper in Cell Chemical Biology. | UW Health Sciences NewsBeat

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin
Mike Doud is first author on a paper in Viruses describing improved deep mutational scanning of influenza hemagglutinin.




Whole organism lineage tracing by combinatorial and cumulative genome editing
Greg Findlay and Aaron McKenna are lead authors on paper in Science.
Science | The Atlantic | BBC

Evolutionary assembly patterns of prokaryotic genomes
Max Press is lead author on paper in Genome Research.

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation
Ivan Liachko is co-first author on paper in G3

Long-read sequence assembly of the gorilla genome
Eichler Lab members are authors on paper in Science.





Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry
Rob Lawrence is lead author on paper in Nature Methods.

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Former grad Benjamin Vernot is lead author on paper in Science.
Science | NY Times

Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture
Katherine Xue is first author on a paper showing that flu viruses can cooperate in eLife.




The mechanistic underpinnings of an ago1-mediated, environmentally-dependent, and stochastic phenotype

Alex Mason is lead author on paper in Plant Physiology.

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis
Ohad Manor is lead author on paper in Nature Scientific Reports.

An algorithm for designing minimal microbial communities with desired metabolic capacities
Alex Eng is lead author on paper in Bioinformatics.




Homing Endonuclease Genes: New Tools for Mosquito Population Engineering and Control

Dynamin-mediated endocytosis is required for tube closure, cell intercalation, and biased apical expansion during epithelial tubulogenesis in the Drosophila ovary
Former grad Nate Peters is lead author on paper in Developmental Biology.

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation
Cecilia Noecker is lead author on paper in mSystems.

Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae
Former grad Anna Sunshine is lead author on paper in Aging Cell.

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin
Matthew Snyder and Martin Kircher are lead authors on paper in Cell.
Cell | NY Times

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification
PLOS Genetics

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Host-Microbe Protein Interactions during Bacterial Infection
Devin Schweppe is lead author on paper in Chemistry & Biology, along with members of the Bruce, Manoil, and Singh Labs. | UW Health Sciences NewsBeat

Making Indigenous Peoples Equal Partners in Gene Research
Research by Keolu Fox and the Nickerson Lab is featured in The Atlantic.

Searching for the Genes That Are Unique to Humans
Research by Max Dougherty and the Eichler Lab is featured in The Atlantic.

Taking the Uncertainty Out of Genetic Screening for Cancer Risk
Dr. Lea Starita's talk at the ASHG conference is profiled in The Atlantic.

Physiological responses of a Southern Ocean diatom to complex future ocean conditions
Emma Timmins-Schiffman and Brook Nunn are authors on paper in Nature Climate Change.

An integrated map of structural variation in 2,504 human genomes
former grad student Peter Sudmant is lead author on paper in Nature, along with other Eichler lab members including programmer John Huddleston who is a shared first author.

Human genomics: The end of the start for population sequencing

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

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

2015 Highly Cited Researchers list from Thomson Reuters includes Drs. David Baker, Evan Eichler, Deborah Nickerson, William Noble, and Judit Villen | UW Today | interviews now available via the UW Medicine website

Aaron Seo has been awarded an NRSA individual fellowship.

Dr. Stanley Gartler has been awarded the 2016 Victor McKusick Leadership Award from the American Society for Human Genetics.

The very model of a classical geneticist:
See Stan Fields' Genes to Genomes post for a slight twist on The Pirates of Penzance, as performed by Vijay Ramani and Ian Blumenthal.

Graduate student Mike Doud has won the award for the best abstract in virology at the Options for the Control of Influenza meeting.

Dr. Michael MacCoss has been awarded the HUPO 2016 Award for Discovery in Proteomic Sciences for fostering the development of Skyline and its resulting impact within the proteomics community.

Vanessa Gray has been awarded a DeLill Nasser Award from the Genetics Society of America.

Ethan Ahler has won best poster at FASEB Cell Signaling in Cancer: From Mechanisms to Therapy.

Dr. Judit Villen has been profiled in Nature Methods.

Steven Lee has been awarded a KSEA-KUSCO Graduate Scholarship.

Brewer-Raghuraman Lab undergrad researcher Haley Amemiya has been featured in the Husky 100.

Introducing the Genome Sciences 2016 incoming class:

Gesine Cauer, Haverford College
Andria Ellis, Boston University
Nick Hasle, UW MSTP
Emma Hoppe, Creighton University
Daniel Lawrence, UW MSTP
Fong Shun Lo, Johns Hopkins University
Martin Mathay, Swarthmore College
Anna Minkina, Carleton College
Jared Mohr, Cornell University
Alberto Rivera, Harvard University
Bianca Ruiz, California State University, Fullerton
Ian Smith, Muhlenberg College
Sanjay Srivatsan, UW MSTP
Anthony Valente, Western Washington University
Mitchell Vollger, Princeton University
Chiann-Ling Yeh, New Mexico State University

Dr. Su-In Lee has been awarded a National Science Foundation Career Award.

GSA supports symposia organized by student and postdoc members

Dr. Elizabeth Kwan and Dr. Elizabeth Morton have been awarded funding by the Genetics Society of America to organize the "New Investigations into Ribosomal DNA" symposium, to be held August 11, 2016 in Foege Auditorium.

Berg Lab members Liesl Strand (People's Choice Award - best poster from all categories, including postdocs, grads, and undergrads) and Bernice Lin (Second Place Undergraduate poster) received awards at the Northwest Developmental Biology meeting.

Keolu Fox has been selected as a 2016 TED Fellow.
BBC | Wired | Forbes

UW ranked #3 in genetics by US News.

Public Lecture Series

7:00 pm | Foege Auditorium | free admission | poster

July 19
Matt Kaeberlein
"A biologist and his dogs: The quest to slow aging in man's best friend"

July 26
Doug Fowler
"New approaches to understanding variation in human genomes"

Dr. Kelley Harris

Genome Sciences is pleased to welcome Dr. Kelley Harris to the department in 2018 as our newest faculty member. 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.





Background research image courtesy of the Berg Lab and Jennie Dorman, Ph.D.