Research

Please visit the faculty section for individual faculty research descriptions.

 

Recent research highlights:

>> 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.

>> 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
CrossTalk

>> 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
genomeweb

>> 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
John Stamatoyannopoulos' research is featured in the 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
Mary-Claire King's research is featured in the 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.

>> Massively parallel single-amino-acid mutagenesis
Former and current Genome Sciences trainees Jacob Kitzman and Lea Starita are authors on paper in Nature Methods.

>> Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
Jeff Vierstra is lead author on paper in Science.

>> Conservation of trans-acting circuitry during mammalian regulatory evolution
Andrew Stergachis and Shane Neph are lead authors on paper in Nature.
Nature | Nature commentary

>> Resolving the complexity of the human genome using single-molecule sequencing
Mark Chaisson is lead author on paper in Nature.
Nature | Business Standard | Nature News

>> The contribution of de novo coding mutations to autism spectrum disorder
Former and current Genome Sciences trainees Brian O'Roak (shared first author), Nik Krumm and Holly Stessman are authors on a paper in Nature.
Nature | Newsweek | NBC News | Time

>> Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability
Megan Dennis is lead author on paper in Nature Genetics.

>> Heritable variation of mRNA decay rates in yeast
Jenny Andrie is lead author on paper in Genome Research.

>> Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations
Wenqing Fu is lead author on paper in the American Journal of Human Genetics.

>> Refining analyses of copy number variation identifies specific genes associated with developmental delay
Brad Coe is lead author on paper in Nature Genetics.

>> Hsp90 promotes kinase evolution
Jennifer Lachowiec and Tzitziki Lemus are lead authors on paper in Molecular Biology and Evolution.

>> Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
Alessandra Sullivan is lead author on paper in Cell Reports.

>> The modENCODE consortium consisting of multiple labs across the globe published 5 papers in Nature this past week accompanied by 15 additional papers in Genome Research, Genome Biology and Proc. Nat. Acad. Sci. USA. These papers present the progress made in defining the functional elements in C. elegans and D. melanogaster over the past 5 years. The three Nature research letters compare the features found in fly and worm with those of human, delineating conserved features of the transcriptome (Gerstein et al.), regulatory factor binding (Boyle et al.) and chromatin (Ho et al.). The two Nature articles describe the Drosophila transcriptome and the C. elegans regulatory landscape.
New York Times | Nature | NHGRI

>> Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae
Elyse Hope is lead author on paper in G3: Genes, Genomes, and Genetics.

>> The Conserved PFT1 Tandem Repeat is Crucial for Proper Flowering in Arabidopsis thaliana
Pauline Rival, Max Press, Jacob Bale, and Tanya Grancharova are authors on paper in Genetics.

>> The overdue promise of short tandem repeat variation for heritability
Max Press and Keisha Carlson are authors on paper in Trends in Genetics.

>> Study of Jewish Women Shows Link to Cancer Without Family History
New York Times

>> Saturation editing of genomic regions by multiplex homology-directed repair
Greg Findlay and Evan Boyle are lead authors on paper in Nature.

>> Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome
Ohad Manor, Roie Levy, and Elhanan Borenstein are authors on paper in Cell Metabolism.

>> Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
Rogan Carr and Elhanan Borenstein are authors on paper in PLOS One.

>> Primate evolution of the recombination regulator PRDM9
Jerrod Schwartz, David J. Roach, Jim Thomas and Jay Shendure are authors on paper in Nature Communications.

>> Emergent Biosynthetic Capacity in Simple Microbial Communities
Hsuan-Chao Chiu, Roie Levy, and Elhanan Borenstein are authors on paper in PLOS Computational Biology.

>> Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton
MacCoss Lab member and GS Research Professor Brook Nunn is author on paper in PNAS.

>> Computing exact p-values for a cross-correlation shotgun proteomics score function
Jeff Howbert and Bill Noble are authors on paper in Molecular & Cellular Proteomics.

>> The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection
Dunham Lab member Celia Payen is lead author on paper in G3: Genes, Genomes, Genetics

>> Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps
Josh Burton, Ivan Liachko, Maitreya Dunham, and Jay Shendure are authors on paper in G3: Genes, Genomes, Genetics

>> Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
Noble Lab member Ferhat Ay is lead author on paper modeling the dynamic genome architecture of a malarial parasite in Genome Research.

>> An autonomously replicating sequence for use in a wide range of budding yeasts
Dunham Lab members Ivan Liachko and Maitreya Dunham are authors on paper in FEMS Yeast Research.

>> GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris
Dunham Lab member Ivan Liachko is lead author on paper in PLOS Genetics, along with GS co-authors Kerry Bubb, Christine Queitsch, Bonny Brewer, M.K. Raghuraman, and Maitreya Dunham.

>> Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex
Brewer-Raghuraman Lab members Gina Alvino, Bonny Brewer, and M.K. Raghuraman are authors on paper in Genes and Development.

>> A Higher Mutational Burden in Females Supports a "Female Protective Model" in Neurodevelopmental Disorders
Eichler Lab members Sebastien Jacquemont (visiting scientist), Brad Coe (postdoc), Nik Krumm and Michael Duyzend (graduate students) are authors on paper in American Journal of Human Genetics
AJHG | The Economist | BBC

>> Fit-Hi-C: Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
Postdoc Ferhat Ay is lead author on paper in Genome Research.

>> A general framework for estimating the relative pathogenicity of human genetic variants
Postdoc Martin Kircher is lead author on paper in Nature Genetics.

>> Resurrecting Surviving Neanderthal Lineages from Modern Human Genomes
Grad Benjamin Vernot is lead author on paper in Science.
Science
| NY Times | National Geographic | The Weather Channel | UW Today

>> Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Andrew Stergachis is lead author on a paper in Science describing the discovery of "duons" -- dual-use codons that simultaneously encode protein sequence and regulatory information.
Science | perspective | US News & World Report | UW Today

>> Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
Grad Jeff Vierstra is lead author on a paper in Nature Methods.

>> Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Grad Josh Burton is lead author. Grad Andrew Adey and former grads Jacob Kitzman and Rupali Patwardhan are co-authors on paper in Nature Biotechnology.

>> Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation
MacCoss Lab member Brook Nunn is lead author on paper in PLOS One.

>> Optimized RNA ISH, RNA FISH and protein-RNA double labeling (IF/FISH) in Drosophila ovaries
Berg Lab members Sandra Zimmerman, Nate Peters, and Ariel Altaras are authors on paper in Nature Protocols.

>> Computer-designed proteins recognize and bind small molecules
GS grad Jorgen Nelson is author on paper in Nature.
Nature | UW Today

>> Developmental fate and cellular maturity encoded in regulatory DNA patterns  
Andrew Stergachis, PhD, is lead author on a paper in Cell reporting that cells 'remember' key developmental decisions and track their progress through normal development.  The paper also provides new insights into how cancer cells differ from normal cells via altered regulatory programs. 
Cell

>> Autism’s Unexpected Link to Cancer Gene
NY Times

>> UW researchers report on genome of aggressive cervical cancer that killed Henrietta Lacks
Grads Andrew Adey, Josh Burton, and Jacob Kitzman are co-first authors on paper in Nature.
Nature | NY Times | NIH | UW Today

>> UW scientists make breakthrough in understanding schizophrenia
Puget Sound Business Journal | NIH

>> Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
MCB grad Roie Levy is lead author on paper in PNAS.
PNAS | UW Today

>> Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90
GS grad Max Press is lead author on paper in PLoS Genetics.

>> Great ape genetic diversity and population history
GS grad Peter Sudmant is lead author on paper in Nature. Nature | UW Today

>> Interaction of exons with promoters and enhancers influences gene splicing patterns.  
Tim Mercer, PhD, a postdoctoral fellow with the Stamatoyannopoulos lab and the Mattick lab at the Garvan Institute in Australia, is lead author on a publication in Nature Genetics demonstrating that the 3-dimensional folding of the human genome impacts gene products by influencing how exons are spliced into mature transcripts. | 6/23/13

>> A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan
Liz Kwan, a former MCB graduate student in Toni Bedalov's lab at FHCRC and now a postdoctoral fellow in the Brewer/Raghuraman lab, is the lead author on a study linking lifespan in yeast with replication of the rDNA locus in PLoS Genet. | 3/7/13

>> The Protein Chaperone HSP90 Can Facilitate the Divergence of Gene Duplicates
Grads Jennifer Lachowiec and Tzitziki Lemus-Vergara are lead authors on paper in Genetics | 2/14/13

>> High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast
Genome Research | 12/11/12

>> Harmful protein-coding mutations in people arose largely in the past 5,000 to 10,000 years
Nature | UW Today | 11/28/12

>> Integrative annotation of chromatin elements from ENCODE data
Nucleic Acids Research | 11/10/12

>> Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3
GS postdoc Soledad Undurraga and GS grad Max Press are lead authors on paper in PNAS.
PNAS | 10/9/12

>> Encyclopedia of DNA elements compiled; UW a key force in Project ENCODE
Nature | NY Times | Washington Post | UW Today | 9/5/12

>> Widespread plasticity in transcription factor occupancy linked to DNA methylation
GS fellows Hao Wang and Hongzhu Qu and grad Matt Maurano are co-first authors on this paper in Genome Research.
Genome Research | 9/5/12

>> Differences in regulatory DNA between people and human populations
GS grad Ben Vernot is first author on this paper in Genome Research.
Genome Research | UW Today | 9/5/12

>> Millions of DNA switches that power human genome's operating system are discovered
GS scientist  Shane Neph and grad Andrew Stergachis  are co-first authors on this paper in Cell.
Cell | Seattle Times | UW Today | 9/5/12

>> Researchers unlock disease information hidden in genome’s control circuitry
GS grad Matt Maurano and scientists Rich Humbert and Eric Rynes are co-first authors on this paper in Science
Science | US News & World Report | UW Today | 9/5/12

>> Researchers construct the first extensive map of protein docking sites on the human genome
GS Grads Jeff Vierstra and Andrew Stergachis, and scientists Shane Neph and Alex Reynolds are co-first authors on this paper in Nature.
Nature | UW Today | 9/5/12

>> The first detailed map of human regulatory DNA exposes the switches that control the cell
GS scientists Bob Thurman, Eric Rynes and Rich Humbert are co-first authors on this paper in Nature.
Nature | Bloomberg News | UW Today | 9/5/12

>> Genetic Mutation May Have Allowed Early Humans to Migrate Throughout Africa
Science Daily

>> Germ Cell Migration Across Sertoli Cell Tight Junctions
Recent GS Grad Ben Smith is first author on paper in Science.
Science

>> Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers
GS grad Benjamin Vernot is second author on paper in Cell
Cell | NY Times | Washington Post | Science

>> Exome sequencing of health condition extremes can reveal susceptibility genes
Nature Genetics | UW Today

>> Prenatal genome deciphered from parents’ lab tests
GS grads Jacob Kitzman and Matthew Snyder are lead authors on paper in Science Translational Medicine
NY Times | MSNBC | Nature | UW Today

>> Slew of rare DNA changes following population explosion holds clues to common diseases
Science | Nature | UW Today

>> Scientists Link Gene Mutation to Autism Risk
NY Times | UW Today

>> Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication
GS senior fellow Dr. Megan Dennis and grad student Xander Nuttle are first authors on paper in Cell
Cell | UW Today

>> Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Nature Methods | Noble Lab Segway page

>> Gorilla genome offers insights into great ape and human evolution
UW Today

>> Massively parallel functional dissection of mammalian enhancers in vivo
GS grads Rupali Patwardhan and Joe Hiatt are first authors on Nature Biotechnology paper
Nature Biotechnology

>> Treatment for TB can be guided by patients’ genetics
UW Today | Cell

>> Gut microbe networks differ from norm in obese people, systems biology approach reveals
GS grad Sharon Greenblum is first author on PNAS paper.   UW Today | PNAS | 1/10/12

>> Modern genetics answers age-old question on Garrod's fourth inborn error of metabolism
UW Today | PNAS | 10/31/11

>> Genome map of advanced, lethal prostate cancers reveals 'hypermutations'
GS grad Akash Kumar is first author on PNAS paper.
UW Today | PNAS | 9/28/11

>> "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project"
Science | 12/22/10

>> Difference in Gene Numbers Responsible for Wide Variations in the Human Genome
GS grads Jacob Kitzman and Peter Sudmant are first authors on paper in Science.
Science | Nature | Reuters | University Week

>> Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome
American Journal of Human Genetics | 7/29/10

>> Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing
Proc Natl Acad Sci USA | 7/13/10

>> Genetic alterations common to Kabuki syndrome discovered through streamlined DNA sequencing
University Week | 8/19/10

>> Tracing Evolution's Recent Fingerprints
Science | 8/13/10

>> Adventures in Very Recent Evolution
New York Times | 7/19/10

>> People with autism have more duplicated and deleted DNA sequences in their genomes than do those without the disorder
University Week | 6/9/10

>> Genome comparison tools found to be susceptible to slip-ups
University Week | 5/27/10

>> Neandertal genome sequencing reveals new clues on human-specific gene changes
University Week | 5/20/10

>> Genetic Heterogeneity in Human Disease
Cell | 4/16/10

>> A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay
Nature Genetics | 2/14/10

>> A three dimensional model of the yeast genome
Nature | 11/17/09

>> New methods identify thousands of new DNA sequences missing from reference map of the human genome
University Week | 4/19/10