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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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

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana
Former grad student Jennifer Lachowiec is lead author on paper in PLOS Genetics.

Nuclear and organellar genomes of Chrysochromulia algae
Two first-author ms. in PLoS Genetics and BMC Genomics report former GS grad student Blake Hovde's sequencing of the genomes of Chrysochomulina tobin, a newly defined algal species of high evolutionary and biotech interest.

How Wasps Use Viruses to Genetically Engineer Caterpillars
Research by Jim Thomas and Sean Schneider is featured in The Atlantic.

Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages
Heather Machkovech is lead author on paper in Journal of Virology.

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
Sonia Ting and Jarrett Egertson are lead authors on paper in Molecular & Cellular Proteomics.

Using data independent acquisition to model high-responding peptides for targeted proteomics experiments.
Brian Searle and Jarrett Egertson are lead authors on paper in Molecular & Cellular Proteomics.

Global diversity, population stratification, and selection of human copy number variation
Former graduate student Peter Sudmant is lead author on paper in Science.

High-throughput determination of RNA structure by proximity ligation
Vijay Ramani is lead author on paper in Nature Biotechnology.

Quantitative interactome analysis reveals a chemoresistant edgotype
Juan Chavez is lead author on paper in Nature Communications.

Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs
Mike Doud is lead author on paper in Molecular Biology & Evolution.




Proteomics of Colwellia psychrerythraea at subzero temperatures – a life with limited movement, flexible membranes and vital DNA repair

Brook Nunn, Krystal Slattery, and Emma Timmins-Schiffman are authors on paper in Environmental Microbiology.

Comprehensive identification and analysis of human accelerated regulatory DNA
Rachel Gittelman is lead author on paper in Genome Research.

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:

Michelle Berry, Stanford University
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.

Brendan MacLean has been awarded the Gilbert S. Omenn Computational Proteomics Award.

Matthew Snyder has been selected as a recipient of the Harold M. Weintraub Graduate Student Award for outstanding achievement in graduate studies by the Fred Hutchinson Cancer Research Center.

Drs. Kate Cook and Adrian Verster have been awarded NSERC postdoctoral fellowships.

2015 Highly Cited Researchers list from Thomson Reuters includes Drs. David Baker, Evan Eichler, Deborah Nickerson, William Noble, and Judit Villen | UW Today

Dr. Mary-Claire King has been awarded the Szent-Györgyi Prize for Progress in Cancer Research by the National Foundation for Cancer Research.

Dr. Mary-Claire King to receive National Medal of Science
NSF | UW Health Sciences


The UW SACNAS chapter has received the UW School of Medicine 2016 Martin Luther King Community Service Award.

The UW SACNAS chapter has received the Outstanding Chapter of the Year award at the 2015 SACNAS conference.

William Edelman has received the award for best Oral Graduate Presentation in Developmental Biology/Cancer Biology at the 2015 SACNAS conference.




Researchers awarded $12 million to study the human genome in 4-D
HS NewsBeat

Reuters has named the University of Washington the world's most innovative public university.

Dr. Cole Trapnell has received a New Innovator Award from the NIH.

The Big Data for Genomics and Neuroscience Training Grant has been funded by the National Cancer Institute.

Jarrett Egertson and Matthew Snyder have received the Parker Travel Award for best poster at the Genome Sciences department retreat.

Introducing the Genome Sciences incoming class of 2015:

Jolie Carlisle,  UC Berkeley
Khrystyna Dilai, Clarkson University
Sarah Hilton, George Washington University
Ken Jean-Baptiste, Princeton University
Juhye Lee, UW Medical Scientist Training Program / Rice University
Seungbeen Steven Lee, University of Washington
Andy Lin, University of Michigan
Eliah Overbey, UC San Diego
Jonathan Packer, Columbia University



Monica Sanchez has been awarded a Robert D. Watkins Graduate Research Fellowship from the American Society for Microbiology.

Dr. Mary-Claire King has been awarded the Prix Galien 2015 Pro Bono Humanum Award.

Altius Institute for Biomedical Sciences to be led by Dr. John Stamatoyannopoulos

Dr. Jesse Bloom has received a Burroughs Wellcome Young Investigator in the Pathogenesis of Infectious Diseases award.

Dr. Jay Shendure has been selected as a Howard Hughes Medical Institute Investigator.

Dr. Stan Fields has been named to the American Academy of Arts & Sciences.

Dr. Michael MacCoss has been awarded the Biemann Medal by the American Society for Mass Spectrometry.

Dr. Wenqing Fu has been awarded a K99 Career Transition Award from NHGRI.

Katherine Xue has been awarded a Hertz Fellowship.



Friday, June 3, 2016: David Young (Ph.D. in Genome Sciences)
"High throughput determination of sequence-function relationships in protein and RNA"
1:00, Foege Auditorium

Wednesday, June 8, 2016: Jennifer McCreight (Ph.D. in Genome Sciences)
1:30, Foege Auditorium

Friday, June 10, 2016: Michael Duyzend (Ph.D. in Genome Sciences)
3:00, Foege Auditorium





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