Please visit the faculty section for individual faculty research descriptions.
Recent research highlights:
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.
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.
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.
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.
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.
Taxa-function robustness in microbial communities
Alex Eng is first author on paper in Microbiome.
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.
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.
Comprehensive single-cell transcriptional profiling of a multicellular organism
Junyue Cao and Jonathan Packer are lead authors on paper in Science, along with other members of the Shendure, Trapnell, and Waterston Labs.
Science | NY Times
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.
The dynamic three-dimensional organization of the diploid yeast genome
Seungsoo Kim is lead author on paper in eLife.
Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast
Former grad Elyse Hope is lead author on paper in Genetics.
Proteomics Analysis Identifies Orthologs of Human Chitinase-Like Proteins as Inducers of Tube Morphogenesis Defects in Drosophila melanogaster
Sandra Zimmerman is lead author on paper in Genetics.
Mining microbes: Creating genomic tools to fight disease
Borenstein Lab research is featured in Science.
rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants
the 2016 paper on rDNA copy number variation in yeast by Liz Kwan (postdoc), Summer Wang and Haley Amemiya (former undergrads) has been featured in a GSA Journals Spotlight booklet.
Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
Former grad Ryan Emerson and incoming grad William DeWitt are lead authors on paper in Nature Genetics.
Loss of heterozygosity drives adaptation in hybrid yeast
Caiti Smukowski Heil is lead author on paper in Molecular Biology and Evolution.
The birth of a human-specific neural gene by incomplete duplication and gene fusion
Max Dougherty and Xander Nuttle are lead authors on paper in Genome Biology.
A platform for functional assessment of large variant libraries in mammalian cells
Kenny Matreyek is lead author on paper in Nucleic Acids Research.
Single-cell mRNA quantification and differential analysis with Census
Xiaojie Qiu is lead author on paper in Nature Methods.
Complete mapping of viral escape from neutralizing antibodies
Mike Doud's complete mapping of virus antibody escape is published in PLoS Pathogens.
Seeking to unravel DNA
Tim Durham's research is featured on UW IT website.
Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases
Former Eichler Lab members Holly Stessman and Bo Xiong are lead authors on paper in Nature Genetics.
Differential paralog divergence modulates genome evolution across yeast species
Monica Sanchez is lead author on paper in PLoS Genetics.
Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome
Borenstein Lab paper is in Microbiome.
>> Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry
Bruce Lab paper is in PNAS.
>> Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome
Borenstein Lab paper is in featured on the cover of Cell Host & Microbe. | UW Health Sciences NewsBeat
>> A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
Martin Kircher is lead author on paper in Genome Research.
>> Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns
Emma Timmins-Schiffman and Damon May are lead authors on paper in The ISME Journal.
>> 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.
>> Deciphering the Mysterious Microbiome
Borenstein Lab research is featured in IEEE Pulse.
>> Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA
Tychele Turner is lead author on paper selected as a Best of AJHG 2015 and 2016.
>> Evolution of protein phosphorylation across 18 fungal species
Dr. Ricard Rodriguez-Mias is lead author on paper in Science, along with other Villen and Dunham Lab members.
>> 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.
>> Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast
Caitlin Gamble is lead author on paper in Cell.
>> 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.
>> 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
>> 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.
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.
>> Human genomics: The end of the start for population sequencing
>> 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.
>> Where the Wild Ideas Are -- A Chat with James E. Bruce: Biology in 3D
>> New Genetic Tests for Breast Cancer Hold Promise
>> 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.
>> Feasibility of protein turnover studies in prototroph S. cerevisiae strains
Miguel Martin-Perez is lead author on paper in Analytical Chemistry.
>> Escape from X Inactivation Varies in Mouse Tissues
>> 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
John Stamatoyannopoulos' research is featured in the NY Times.
>> 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.
>> 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.
>> 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.
>> Autism’s Unexpected Link to Cancer Gene
>> 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
>> 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
>> 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
>> 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
>> 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
>> Germ Cell Migration Across Sertoli Cell Tight Junctions
Recent GS Grad Ben Smith is first author on paper in 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
>> 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
>> Gorilla genome offers insights into great ape and human evolution
>> Massively parallel functional dissection of mammalian enhancers in vivo
GS grads Rupali Patwardhan and Joe Hiatt are first authors on Nature Biotechnology paper
>> 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
>> 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