Replaying germinal center evolution on a quantified affinity landscape
Will DeWitt is lead author in a paper in Cell.
Research Highlights
Please visit the faculty section for individual faculty research descriptions.
Recent Research Highlights
A global map for introgressed structural variation and selection in humans
PingHsun Hsieh, David Porubsky, and other current and former Eichler Lab members are authors on publication in Science.
Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects
Sriram Pendyala is lead author on a publication in Cell.
Recurrent mutations drive rapid HIV escape from two broadly neutralizing antibodies in vivo
Elena Romero is lead author on a publication in PNAS.
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications
Taylor Real is lead author, along with other Eichler and Stergachis Lab members, on a publication in Cell Genomics.
NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development
Yash Sonthalia is lead author on a publication in Nature Neuroscience.
Context dependency is essential for predicting intrahost evolution
Alison Feder and Will DeWitt are authors on a comment in Nature Ecology & Evolution.
Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA.
Michelle Noyes is lead author, along with other Eichler Lab members, on a paper in Nature Communications.
Using the linear references from the pangenome to discover missing autism variants
Yang Sui is lead author, along with other Eichler Lab members, on a paper in Nature Communications.
Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast
Amanda Ro and Lauren Ackermann are lead authors on a paper in microPublication Biology.
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
Alex Robertson is lead author on a paper in Nature Ecology & Evolution.
Mapping single-cell diploid chromatin fiber architectures using DAF-seq
Elliott Swanson is lead author, along with other Stergachis Lab members, on a paper in Nature Biotechnology.
CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity
Yash Sonthalia is an author on a paper in eLife.
Mechanisms underlying thermally induced growth plasticity in juvenile Pacific halibut
Nunn Lab members are authors on a paper in Journal of Experimental Biology.
Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk
Hunter Colegrove is lead author on a paper in PLOS Computational Biology.
Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP
Nick Popp and Rachel Powell are lead authors on a paper in Nature Structural and Molecular Biology.
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
Connor Kubo, former grad Chris Large, and current and former Waterston Lab members are authors on a paper in Science.
Accelerating Biomolecular Modeling with AtomWorks and RF3
IPD members, including GS grad student Yash Sonthalia, are authors on a paper posted on bioRxiv.
Complex genetic variation in nearly complete human genomes
Former Eichler Lab member Glennis Logsdon is lead author, along with current and former Eichler Lab members David Porubsky, DongAhn Yoo, Katy Munson, Kendra Hoekzema, Arvis Sulovari and William Harvey, on a paper in Nature.
Gene clusters linked to insulin resistance identified in a genome-wide study of the Taiwan Biobank population
Noble Lab member Eugene Lin is lead author on a paper in Nature Communications.
Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome
Miranda Mudge is lead author on a paper in Nature Communications. UW Daily
Population size interacts with reproductive longevity to shape the germline mutation rate
Current and former Harris Lab members Luke Zhu and Annabel Beichman are lead authors on a paper in PNAS.
Protein signatures predict coral resilience and survival to thermal bleaching events
Nunn Lab members are lead authors on a paper in Nature Communications Earth & Environment. UW News
A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data
Justin Sanders and Bo Wen are lead authors, along with other MacCoss and Noble Lab members, on paper to be published in Nature Methods.
Complete sequencing of ape genomes
DongAhn Yoo, a postdoc in the Eichler lab, led an effort of 123 scientists from 64 labs from around the world to completely sequence and annotate 6 non-human ape genomes, on a paper in Nature.
Predicting cell cycle stage from 3D single-cell nuclear-stained images
Gang Li and Eva Nichols are lead authors, along with other Beliveau and Noble Lab members, on a paper in Life Science Alliance.
Proteomic Insights into Psychrophile Growth in Perchlorate-Amended Subzero Conditions: Implications for Martian Life Detection
Anais Gentilhomme is lead author, along with Nunn Lab members, on a paper in Astrobiology.
Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching
Emma Timmins-Schiffman is lead author, along with MacCoss and Nunn Lab members, on a paper in Journal of Proteome Research.
Structural polymorphism and diversity of human segmental duplications
Current and former Eichler Lab members Hyeonsoo Jeong, Philip Dishuck, and DongAhn Yoo are lead authors on a paper in Nature Genetics.
Multiplex generation and single-cell analysis of structural variants in mammalian genomes
Sudarshan Pinglay is lead author on a paper in Science, along with Shendure Lab members.
Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition
Mitchell Vollger is lead author on a paper in Nature Genetics, along with other Stergachis Lab members.
An In-Depth Coho Salmon (Oncorhynchus kisutch) Ovarian Follicle Proteome Reveals Coordinated Changes Across Diverse Cellular Processes during the Transition From Primary to Secondary Growth
Emma Timmins-Schiffman is lead author on a paper in Proteomics.
A maternal germline mutator phenotype in a family affected by heritable colorectal cancer
Candice Young is lead author on a paper in Genetics.
Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER
Sahar Attar is lead author on a paper in Nature Methods.
Reproductive resilience: pathways to gametogenic success in Montipora capitata after bleaching
Emma Timmins-Schiffman is lead author on a paper in Nature Scientific Reports.
Experimental evolution of Saccharomyces cerevisiae for caffeine tolerance alters multidrug resistance and target of rapamycin signaling pathways
Renee Geck is lead author, along with other Dunham Lab members, on a paper in G3.
Chromatin context-dependent regulation and epigenetic manipulation of prime editing
Xiaoyi Li is lead author on paper in bioRxiv.
A single-cell time-lapse of mouse prenatal development from gastrula to birth
Chengxiang Qu is lead author on paper in Nature.
Single-cell, whole-embryo phenotyping of mammalian developmental disorders
Chengxiang Qu and Xingfan Huang are lead authors on paper in Nature.
Best practices for collecting and preserving marine mammal biological samples in the ‘omics era
Emma Timmins-Schiffman is co-author on an article in Marine Mammal Science.
Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod
Emma Timmins-Schiffman is lead author on paper in Journal of Proteome Research.
The variation and evolution of complete human centromeres
Glennis Logsdon and other Eichler Lab members are authors on paper in Nature.
Systematic profiling of ale yeast protein dynamics across fermentation and repitching
Riddhiman Garge, along with current and former Dunham, Harris, and Villen Lab members, are authors on paper in G3.
Structurally divergent and recurrently mutated regions of primate genomes
Current and Former Eichler Lab members Yafei Mao, David Porubsky, William Harvey, Katy Munson, and Kendra Hoekzema are authors on paper in Cell.
Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod
Nunn Lab members are authors on paper in Molecular Ecology.
A unifying model that explains the origins of human inverted copy number variants
Brewer/Raghuraman and Dunham Lab members are authors on paper in PLOS Genetics.
Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA
Rebecca Martin and Claudia Espinoza are lead authors on paper in PLOS Genetics., along with other Brewer/Raghuraman and Dunham Lab members.
Elevated HIV Viral Load is Associated with Higher Recombination Rate In Vivo
Elena Romero is lead author on paper in Molecular Biology and Evolution.
Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection
Jarvik Lab members are authors on paper in Scientific Reports.
An Atlas of Variant Effects to understand the genome at nucleotide resolution
Fowler and Starita Lab members are authors on paper in Genome Biology.
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease
Gennifer Merrihew, Jea Park, Deanna Plubell, and other MacCoss Lab members are authors on paper in Nature Communications.
A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer’s disease
Gennifer Merrihew, Jea Park, Deanna Plubell, and other MacCoss Lab members are authors on paper in Scientific Data.
Increased mutation and gene conversion within human segmental duplications
Mitchell Vollger and Philip Dishuck are lead authors on a paper in Nature along with other Department of Genome Sciences members.
Gaps and complex structurally variant loci in phased genome assemblies
David Porubsky is lead author on a paper in Genome Research along with former (Mitchell Vollger) and current Eichler Lab members (William Harvey and Allison Rozanski)
Inversion polymorphism in a complete human genome assembly
David Porubsky is lead author on a paper in Genome Biology along with Eichler Lab members William Harvey and Allison Rozanski.
Sampling the proteome by emerging single-molecule and mass spectrometry methods
MacCoss Lab members are authors on a paper in Nature Methods.
State-dependent evolutionary models reveal modes of solid tumour growth
Bedford Lab member Maya Lewinsohn is lead author on a paper in Nature Ecology and Evolution, along with other Beford and Feder Lab members.
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
Beliveau Lab and Noble Lab member Robin Aguilar is lead author on a paper in bioRxiv, along with other Beliveau and Noble Lab members.
Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast
Brewer-Raghuraman Lab member Liz Kwan is lead author on a paper in Cell Reports, along with other Brewer-Raghuraman and Queitsch-Cuperus Lab members.
Skeletal muscle mitochondrial interactome remodeling is linked to functional decline in aged female mices
Bruce Lab member Anna Bakhtina is lead author on a paper in Nature Aging.
Association of Genetic Diagnoses of Childhood-Onset Hearing Loss With Cochlear Implant Outcomes
King Lab member Ryan Carlson is lead author on a paper in JAMA Otolaryngology – Head & Neck Surgery.
Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants
Dunham Lab postdoctoral trainee Renee Geck is lead author on a paper in AJHG.
yEvo: Experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in S. cerevisiae
Former Dunham Lab postdoctoral trainee Bryce Taylor is lead author on a paper in G3.
Unique Cell Subpopulations and Disease Progression Markers in Canines with Atopic Dermatitis
Hawkins Lab members are authors on a paper in The Journal of Immunology.
Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart
Research in the Bruce Lab reveals mitochondrial interactome changes in heart failure. Nature Cardiovascular Research
High-throughput approaches to functional characterization of genetic variation in yeast
Cindy Yeh and Pengyao Jiang are lead authors on a paper in Current Opinion in Genetics and Development.
An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging
Beliveau Lab member Lily Deng is lead author on a paper in HardwareX.
A time-resolved, multi-symbol molecular recorder via sequential genome editing
Junhong Choi is lead author on a paper in Nature, along with other Shendure Lab members.
Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges
Brook Nunn and Emma Timmins-Schiffman are authors on a paper in Limnology and Oceanography.
From Canvases to Microscopes: Building Uplifting Community and Research Spaces Within and Beyond Genomics
Robin Aguilar is author and artist on a paper in ACS Chemical Biology .
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders
David Porubsky is lead author on a paper in Cell, along with Benson Hsieh, William Harvey, and other Eichler Lab members.
Segmental duplications and their variation in a complete human genome
Mitchell Vollger, Xavi Guitart, Philip Dishuck, and other Eichler Lab members are lead authors on a paper in Science.
The complete sequence of a human genome
Mitchell Vollger, Glennis Logsdon, and other Eichler lab members are lead authors on a paper in Science.
PacRAT: A program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment
Cindy Yeh and Clara Amorosi are lead authors on a paper in Bioinformatics.
Familial long-read sequencing increases yield of de novo mutations
Michelle Noyes is lead author on a paper in AJHG, along with Eichler Lab members William Harvey, David Porubsky, Katy Munson, Kendra Hoekzema, and Alex Lewis.
Closing the gap: Systematic integration of multiplexed functional data resolves variants of uncertain significance in BRCA1, TP53, and PTEN
Shawn Fayer is lead author on a paper in AJHG.
Precise genomic deletions using paired prime editing
Junhong Choi and Wei Chen, along with other Shendure Lab members, are authors on a paper in Nature Biotechnology.
Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity
Alison Feder and colleagues are authors on a paper in eLife.
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
Pengyao Jiang is lead author on a paper in eLife, along with other Dunham and Harris Lab members.
Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
PingHsun Hsieh is lead author on a paper in Nature Communications, along with other Eichler Lab members Phil Dishuck, Mitchell Vollger, Stella Huang and Yafei Mao.
Massively parallel characterization of CYP2C9 variant enzyme activity and abundance
Clara Amorosi and Melissa Chiasson are lead authors on a paper in AJHG, along with other Dunham and Fowler Lab members.
Recent ultra-rare inherited variants implicate new autism candidate risk genes
Amy Wilfert is lead author on a paper in Nature Genetics, along with other Eichler Lab members.
Embryo-scale, single-cell spatial transcriptomics
Sanjay Srivatsan is lead author on a paper in Science
PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments
Elliot Hershberg and Conor Camplisson are lead authors on a paper in Nature Methods.
Robustness of phylogenetic inference to model misspecification caused by pairwise epistasis
Will DeWitt and Sarah Hilton are authors on a paper in Molecular Biology and Evolution.
Nonparametric coalescent inference of mutation spectrum history and demography
Will DeWitt is lead author on a paper in PNAS.
A high-quality bonobo genome refines the analysis of hominid evolution
Yafei Mao is lead author on a paper in Nature, along with other Eichler Lab members Phil Dishuck, Benson Hsieh and David Porubsky.
Multiplexing Mutation Rate Assessment: Determining Pathogenicity of Msh2 Variants in S. cerevisiae
Anja Ollodart is lead author on a paper in Genetics.
The structure, function and evolution of a complete human chromosome 8
Glennis Logsdon is lead author, along with Mitchell Vollger, Yafei Mao, David Porubsky, PingHsun Hsieh, Phil Dishuck, and other Eichler Lab members, on a paper in Nature.
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Peter Audano is lead author, along with David Porubsky and PingHsun Hsieh on a paper in Science.
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
David Porubsky is lead author, along with Mitchell Vollger, Arvis Sulovari and other Eichler Lab members on a paper in Nature Biotechnology
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility
Mitchell Vollger, Phil Dishuck, David Porubsky, and Yafei Mao are authors on a paper in Science.
A human cell atlas of fetal chromatin accessibility
Silvia Domcke, Riza Daza, Andrew Hill, and Darren Cusanovich are lead authors on a paper in Science.
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
Tianyun Wang is lead author on a paper in Nature Communications, along with Madelyn Gillentine, Arvis Sulovari, Kendra Hoekzema, and Brad Coe.
Detecting New Allies: Modifier Screen Identifies a Genetic Interaction Between Imaginal disc growth factor 3 and combover, a Rho-kinase Substrate, During Dorsal Appendage Tube Formation in Drosophila
Claudia Espinoza is lead author on a paper in G3.
Inferring evolutionary dynamics of mutation rates through the lens of mutation spectrum variation
Jed Carlson and Will DeWitt are authors on a paper in Current Opinion in Genetics & Development.
Long-read human genome sequencing and its applications
Glennis Logsdon is lead author on a review in Nature Reviews Genetics, along with Mitchell Vollger.
Recurrent inversion toggling and great ape genome evolution
David Porubsky is lead author on a paper in Nature Genetics, along with with Benson Hsieh, Arvis Sulovari, David Gordon, and Melanie Sorensen.
Mitochondrial protein interaction landscape of SS-31
Bruce Lab members are authors on a paper in PNAS.
Candidate silencer elements for the human and mouse genomes
Naresh Doni Jayavelu is lead author on a paper in Nature Communications.
Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2
Emma Timmins-Schiffman is lead author on a paper in Ecology and Evolution.
Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi
Nunn Lab members are authors on a paper in Scientific Data.
Human-specific tandem repeat expansion and differential gene expression during primate evolution
Arvis Sulovari is lead author on a paper in PNAS.
The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast
Kelsey Lynch is lead author on a paper in PLOS Genetics.
Temperature preference can bias parental genome retention during hybrid evolution
Dunham Lab members are authors on a paper in PLOS Genetics.
Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
Dunham Lab members are authors on a paper in Genome Research.
Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
Juhye Lee is lead author on a paper in eLife showing how there is extensive person-to-person variation in how human immunity selects mutations in influenza virus.
Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes
PingHsun Hsieh is first author on a paper in Science. Other authors include GS grad Mitchell Vollger, postdoc David Porubsky, and former postdoc Stuart Cantsilieris.
Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae
Joe Sanchez and Bonny Brewer are lead authors on a paper in Genetics.
Human artificial chromosomes that bypass centromeric DNA
Glennis Logsdon is lead author on a paper in Cell.
Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes
Nunn and Noble Lab members are authors on a paper in Nature’s Journal of Microbial Ecology: ISME.
Calling star alleles with Stargazer in 28 pharmacogenes with whole genome sequences
Steven Lee is lead author on a paper in Clinical Pharmacology & Therapeutics.
A combination of transcription factors mediates inducible interchromosomal contacts
Seungsoo Kim is lead author on a paper in eLife.
Superovulation alters global DNA methylation in early mouse embryo development
Thomas Smith is lead author on a paper in Epigenetics.
Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States
Stephanie Battle is lead author on a paper in Stem Cell Reports.
The single-cell transcriptional landscape of mammalian organogenesis
Jun Cao and Malte Spielmann are lead authors on a paper in Nature.
High-throughput identification of dominant negative polypeptides in yeast
Mike Dorrity is lead author on a paper in Nature Methods.
Dynamics of gene expression in single root cells of A. thaliana
Trapnell, Fields, Queitsch, and Cuperus Lab members Ken Jean-Baptiste, Jose McFaline, Cristina Alexandre, Lauren Saunders, Mike Dorrity, and Kerry Bubb are authors on paper in Plant Cell.
Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective
Evvie Vincow is lead author on a paper in Autophagy.
Reconciling disparate estimates of viral genetic diversity during human influenza infections
Katherine Xue is lead author on a letter in Nature Genetics resolving the question of how much viral genetic diversity is present in human influenza infections.
Comprehensive profiling of translation initiation in influenza virus infected cells
Heather Machkovech is lead author on new study in PLoS Pathogens of translation initiation in influenza-infected cells.
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
Molly Gasperini is lead author on paper in Cell.
Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity
Brad Coe and Madeleine Geisheker are authors on paper in Nature Genetics.
Characterizing the Major Structural Variant Alleles of the Human Genome
Peter Audano and Arvis Sulovari are lead authors on paper in Cell.
Long-read sequence and assembly of segmental duplications
Mitchell Vollger is lead author on paper in Nature Methods.
DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium
Cristina Valensisi is co-lead author on paper in Scientific Reports.
Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
Grad student Sarah Hilton is first author on paper in Virus Evolution examining how deep mutational scanning experiments can be used to inform phylogenetic estimates of divergence times
Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles
Ruth Thomas and Evvie Vincow are lead authors on paper in PLOS Genetics.
Lon protease inactivation in Drosophila causes unfolded protein stress and inhibition of mitochondrial translation
Gautam Pareek is lead author on paper in Cell Death Discovery.
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals
Furlong Lab members are authors on paper in Science. New York Times | The Atlantic | National Geographic
A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function
Lea Starita is lead author on paper in AJHG.
Accurate classification of BRCA1 variants with saturation genome editing
Former grad Greg Findlay is lead author on paper in Nature. New York Times | The Atlantic
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity
Will DeWitt is lead author on paper in eLife.
Variations in Copepod Proteome and Respiration Rate in Association with Diel Vertical Migration and Circadian Cycle
Emma Timmins-Schiffman is co-author on paper in The Biological Bulletin.
Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants
Juhye Lee is lead author on paper in PNAS showing how deep mutational scanning can be used to help forecast fates of influenza virus lineages in nature.
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
Hannah Pliner is lead author on paper in Molecular Cell.
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Darren Cusanovich and Andrew Hill are lead authors on paper in Cell.
STK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS-Mutant Lung Adenocarcinoma
Michael Goldberg is lead author on paper in Cancer Discovery.
MS analysis of a dilution series of bacteria: phytoplankton to improve detection of low abundance bacterial peptides
Emma Timmins-Schiffman is lead author on paper in Scientific Reports.
Precision therapeutic targeting of human cancer cell motility
Bruce Lab members are authors on paper in Nature Communications
A Diverse Lipid Antigen–Specific TCR Repertoire Is Clonally Expanded during Active Tuberculosis
Will DeWitt is lead author on paper in The Journal of Immunology.
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
Colin McNally is lead author on paper in BMC Systems Biology.
Stargazer: a software tool for calling star alleles from next-generation sequencing data using CYP2D6 as a model
Steven Lee is lead author on paper in Genetics in Medicine.
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.
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.
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.
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
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
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.
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.
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.
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.
Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification
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. Technology.org | 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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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
Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90
GS grad Max Press is lead author on paper in PLoS Genetics.
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
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
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
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
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Nature Methods | Noble Lab Segway page
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
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
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