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
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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.

Dynamic proteome response of Pseudomonas aeruginosa to tobramycin antibiotic treatment
Xia Wu is lead author on paper in Molecular & Cellular Proteomics along with members of the Bruce, Manoil, and Singh labs.

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas
Emma Timmins-Schiffman and Brook Nunn are authors on paper in BMC Genomics.

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects
Anna Sunshine is lead author on paper in PLOS Biology.

Multiplexed peptide analysis using data-independent acquisition and Skyline
Jarrett Egertson is lead author on paper in Nature Protocols.

Students Present Research at Annual Symposium
Dunham Lab undergrad Erica Alacantara is featured in UW Daily article.

Machine learning applications in genetics and genomics
Max Libbrecht is lead author on paper in Nature Reviews Genetics.

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Darren Cusanovich is lead author in paper in Science.

Where the Wild Ideas Are -- A Chat with James E. Bruce: Biology in 3D

New Genetic Tests for Breast Cancer Hold Promise
NY Times

The Proteomic Landscape of Triple-Negative Breast Cancer
Rob Lawrence is lead author on paper in Cell Reports.

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
Ohad Manor is lead author on paper in Genome Biology.

Copy-Number Variation and False Positive Prenatal Aneuploidy Screening Results
Matthew Snyder is lead author on paper in The New England Journal of Medicine.
NEJM | Seattle Times

Feasibility of protein turnover studies in prototroph S. cerevisiae strains
Miguel Martin-Perez is lead author on paper in Analytical Chemistry.

A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae
Josh Cuperus is lead author on paper in ACS Synthetic Biology.

Escape from X Inactivation Varies in Mouse Tissues
PLOS Genetics

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression
Max Libbrecht is lead author on paper in Genome Research.

Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry
Arti Navare is lead author on paper in Structure, along with members of the Bruce, Manoil, and Singh labs.

UW, Bloodworks Northwest Team Designs NGS-based Blood Typing Panel

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
Current grad Max Press and former grads Keisha Carlson and Peter Sudmant are authors on paper in Genome Research.

Complex History of Admixture between Modern Humans and Neandertals
Benjamin Vernot and Josh Akey are authors on paper in The American Journal of Human Genetics.
AJHG | NY Times | Daily Mail | genomeweb

Project Sheds Light on What Drives Genes
NY Times

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species
Sharon Greenblum, Rogan Carr, and Elhanan Borenstein are authors on paper in Cell.
Cell | UW News | genomeweb

A Never-Ending Genetic Quest
New York Times

The Top 100 Papers
Joe Felsenstein's research is included in Nature's list of the most-cited research of all time.

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.

Introducing the Genome Sciences incoming class of 2015:

Jolie Carlisle,  UC Berkeley
Alexandra Gesine Cauer, Haverford College
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

Matt Rich has been awarded a Japanese Society for the Promotion of Science Fellowship.

Damon May has been awarded a National Defense Science & Engineering Graduate Fellowship.

Ivan Liachko has won the genomics poster award at the Fungal Genetics conference of the Genetics Society of America.

Melissa Chiasson, Claudia Espinoza, Andrew Hill, and Hannah Pliner have been awarded NSF fellowships. Tim Durham, Serena Liu, Damon May, Cecilia Noecker, Vijay Ramani, Amanda Watts, and Aaron Wolf received honorable mention.

Stephanie Battle has been awarded a Ford Foundation fellowship. William Edelman has received honorable mention.

Dr. Sandra Zimmerman has won third place for posters at the Genetics Society of America 56th Annual Drosophila Research Conference.

Dr. Cole Trapnell has been awarded a Sloan Fellowship.

Benjamin Vernot 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.

Dr. Ron Hause has received a Damon Runyon Cancer Research Foundation fellowship.

Dr. Ivan Liachko has received a DeLill Nasser Award from the Genetics Society of America.

Postdoctoral fellow Dr. Matt Maurano has been selected as a winner of the 2014 Charles J. Epstein Trainee Awards for Excellence in Human Genetics Research at the 64th annual meeting of the American Society of Human Genetics.

The UW SACNAS chapter has received the 2014 Graduate Chapter of the Year award.

Noted geneticist once was turned away from U.S. shores
Dr. Arno Motulsky fled Nazi Germany and became a global leader in medical genetics
UW Health Sciences News Beat

Dr. Stan Fields (senior editor) and Dr. Jay Shendure (associate editor) have been appointed to the editorial board of Genetics.

Dr. Stan Fields has been elected Vice President / President Elect of the Genetics Society of America.

Dr. Douglas Fowler has received a 2014 Alzheimer’s Association New Investigator award.

Dr. Mary-Claire King has been awarded the Lasker~Koshland
Special Achievement Award in Medical Science.

NY Times | Forbes | UW Today

The Department of Genome Sciences is excited to welcome Dr. Cole Trapnell as its newest Assistant Professor. Dr. Trapnell studies stem cells and differentiation, primarily using high throughput transcriptome sequencing.  He comes to UW from a postdoc at John Rinn’s lab at Harvard and before that, earning his Ph.D. in Computer Science from the University of Maryland, College Park working with both Steven Salzberg and Lior Pachter.














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