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Saturation Genome Editing
Single Cell Genomics
Retired: Pathogen Detection
Publications
Starita Lab
Home
Our Team
Team Shenanigans
Areas of Practice
Saturation Genome Editing
Single Cell Genomics
Retired: Pathogen Detection
Publications
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Our Team
Team Shenanigans
Folder: Research Projects
Back
Areas of Practice
Saturation Genome Editing
Single Cell Genomics
Retired: Pathogen Detection
Publications
    • P646: Integrating functional data in variant classification: Navigating conflict, calibration, and low-penetrance.

      A McEwen et al 2026.

    • P487: MaveMD: A functional data resource for genomic medicine.

      A McEwen et al. 2026.

    • P155: 260,000 variant effect mapping across the MAPK pathway reveals the importance of molecular and cellular context.

      JJ Simon et al. 2026.

    • P506: Patient perspectives on communication and care after genetic variant reclassification.

      MS Park et al. 2026.

    • Massively scaled variant effect mapping across the MAPK pathway reveals the importance of molecular and cellular context.

      JJ Simon et al. 2026.

    • The IGVF catalog – from genetic variation to function.

      D Li et al. 2026.

    • High-throughput mapping of 6,888 RAD51D variants identifies distinct biochemical functions needed for homologous recombination and olaparib response.

      KE Darrah et al. 2026.

    • Multiplexed assays of variant effect for clinical variant interpretation.

      AE McEwen, M Tejura, S Fayer, LM Starita, DM Fowler. 2026.

    • A scalable approach to resolving variants of uncertain significance.

      M Tejura et al. 2026.

    • Influenza household transmission and genomic diversity in the United States: A prospective cohort study, 2022-2024.

      SN Cox et al 2026.

    • The proteomic landscape and temporal dynamics of human and mouse gastruloid development.

      RK Garge et al. 2026.

    • Genome-wide detection and clinical prioritization of tandem repeat outliers using long-read sequencing.

      SB Gibson et al. 2026.

    • Gene-and domain-aware calibration increases the clinical utility of variant effect predictors.

      Y Chen et al. 2026.

    • A multiplex, prime editing framework for identifying drug resistance variants at scale.

      FMC Abadie et al. 2026.

    • Not Forgotten: Patient Experiences with Genetic Variant Reclassifications.

      P Gupta et al. 2026.

    • Phenotype-Specific Recalibration of MAVE Data Enables Repurposing of BAP1 Functional Assays for Küry-Isidor Syndrome.

      P Gupta et al. 2026.

    • A comparative survey of functional evidence use in hearing and vision loss genetics.

      RA Inan et al. 2026.

    • Chromatin architectures underlying plasmid-based assays for regulatory variant effects.

      BJ Mallory et al. 2026.

    • Saturation Genome Editing reveals the functional impact of RAD51D and XRCC2 variants.

      S Casadei et al. 2026.

    • Image-based, pooled phenotyping reveals multidimensional, disease specific variant effects.

      S Pendyala et al. 2026.

    • Household Transmission of Enterovirus D68, Washington and Oregon, United States, 2022-2024.

      P Roychoudhury et al. 2026.

    • An integrated, scaled approach to resolve TSC2 variants of uncertain significance.

      CG Blair et al. 2026.

    • Combining multiplexed functional data to improve variant classification.

      JD Calhoun et al. 2026.

    • ‘Truthsets’ for clinical validation of large-scale functional assays: Practice recommendations from Cancer Variant Interpretation Group UK (CanVIG-UK).

      S Allen et al. 2026.

    • Clinical validation of large-scale functional assays: insights from 2,120 gene-truthset-assay evaluations.

      KL Hoffman et al. 2026.

    • Immune correlates of risk for SARS-CoV-2 infection in children: a prospective, community-based cohort study.

      TM Babu et al. 2026.

    • Household Transmission of Human Metapneumovirus and Human Parainfluenza Viruses 1-4 in the United States, 2022-2024.

      P Roychoudhury et al. 2026.

    • RSV Molecular Epidemiology Pre-and Post-COVID-19 Pandemic Periods in Seattle, Washington, USA.

      P Roychoudhury et al. 2026.

    • Saturation mutagenesis enables RAD51D clinical variant interpretation and identifies distinct biochemical functions.

      KE Darrah et al. 2026.

    • SARS-CoV-2 diversity and transmission on a university campus across two academic years during the pandemic.

      AM Casto et al. 2025.

    • P713: Survey results reveal barriers and solutions to the use of functional data in variant interpretation.

      MS Park et al. 2025.

    • P656: Using functional data for VUS reclassification in cancer predisposition genes.

      P Gupta et al. 2025.

    • P215: Assessment of factors driving disparities in clinical uncertainty for patients seen in adult medical genetics clinics.

      A Folta et al. 2025.

    • MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays.

      AF Rubin et al. 2025.

    • P-731. Viruses Associated with Acute Respiratory Illness in a Community Cohort of Children and Adults, Oregon and Washington, United States, 2022-2023.

      G Abedi et al. 2025.

    • P-1951. Incidence of SARS-CoV-2 Infection among these 6 Months to 49 Years of Age in the Cascadia Prospective Cohort Study, Oregon and Washington, United States, July 1, 2022 – March 31, 2024.

      MA Schmidt et al. 2025.

    • P-1849. Investigating the impact of SARS-CoV-2 on the Immune Response to Other Pathogens Using VirScan Epitope Profiling.

      LM Sircy et al. 2025.

    • 424. SARS-CoV-2 Positivity and Genetic Relationships among Cases within Households in the Cascadia Prospective Cohort Study, July 2022 to May 2023.

      AM Casto et al. 2025.

    • homeRNA self-blood collection enables high-frequency temporal profiling of presymptomatic host immune kinetics to respiratory viral infection: a prospective cohort study.

      FY Lim et al 2025.

    • Combing multiplexed functional data to improve variant classification.

      VE Alliance et al. 2025.

    • Multiplexed serology reveals age-specific immunodynamics of endemic respiratory pathogens in the wake of COVID-19 pandemic.

      SJ Bents et al. 2025.

    • Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences.

      C Tran-Kiem et al. 2025.

    • Guidelines for releasing a variant effect predictor.

      BJ Livesey et al. 2025.

    • Effectiveness of mRNA COVID-19 vaccines and hybrid immunity in preventing SARS-CoV-2 infection and symptomatic COVID-19 among adults in the United States.

      LR Feldstein et al. 2025.

    • Gene-based calibration of high-throughput functional assays for clinical variant classification.

      D Zeiburg et al. 2025.

    • Insights on improving accessibility and usability of functional data to unlock their potential for variant interpretation.

      MS Park et al. 2025.

    • Consultation informs strategies for improving the use of functional evidence in variant classification.

      RM Villani et al. 2025.

    • Scenario projections of respiratory syncytial virus hospitalizations averted due to new immunizations.

      CL Hansen et al. 2025.

    • Epidemiology of human metapneumovirus infection in a community setting, Seattle, Washington, USA.

      A Elias-Warren et al 2025.

    • Imprecision medicine: Systematic gaps in reporting variants of uncertain significance (VUS) and their reclassifications.

      A Folta et al. 2025.

    • Parental intent to vaccinate children with the updated 2023-2024 COVID-19 vaccine.

      HC Groom et al. 2025.

    • Correlates of risk of respiratory syncytial virus disease: a prospective cohort study.

      C Frivoid et al. 2025.

    • Single-cell, multi-region profiling of the macaque brain across the lifespan.

      W Yang et al 2025.

    • Saturation genome editing of BARD1 resolves VUS and provides insight into BRAC1-BARD1 tumor suppression.

      I Woo et al. 2025.

    • Editing stem cell genomes at scale to measure variant effects in. diverse cell and genetic contexts.

      S Fayer et al. 2025.

    • Household Transmission and Genomic Diversity of Respiratory Syncytial Virus in the United States, 2022-2023.

      SN Cox et al. 2025.

    • O01: Using multiplexed functional data to reduce the VUS burden in populations underrepresented in genomic medicine

      M Dawood et al. 2024.

    • P390: Assessing and addressing the burden of VUSs within adult medical genetics practices

      A Stergachis et al. 2024.

    • Tiny swabs: nasal swabs integrated into tube caps facilitate large-scale self-collected SARS-CoV-2 testing

      B Pfau et al. 2024.

    • Risk of subsequent respiratory virus detection after primary virus detection in a community household study – King County, Washington, 2019-2021

      J Heimonen et al. 2024.

    • CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

      Claussnitzer et al. 2024.

    • Utilizing a university testing program to estimate relative effectiveness of monovalent COVID-19 mRNA booster vaccine versus 2-dose primary series against symptomatic SARS-CoV-2 infection

      JC Bennet et al. 2024.

    • Remote surveillance and detection of SARS-CoV-2 transmission among household members in King County, Washington

      A Emanuels et al. 2024.

    • Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county

      MI Paredes et al. 2024.

    • Multiplexed Functional Assessments of MYH7 Variants in Human Cardiomyocytes

      CE Friedman et al. 2024.

    • Workshop report: the clinical application of data from multiplex assays of variant effects (MAVEs), 12 July 2023

      S Allen et al. 2024.

    • Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre-and post-COVID-19 pandemic years

      AC Perofsky et al. 2024.

    • Evaluation of novel university-based testing platform to increase access to SARS-CoV-2 testing during the COVID-19 pandemic in a cohort study

      JC Bennet et al. 2024.

    • Absenteeism and health behavior trends associated with acute respiratory illness before and during the COVID-19 pandemic in a community household cohort, King County, Washington

      E Chung et al. 2024.

    • Comparative diagnostic utility of SARS-CoV-2 rapid antigen and molecular testing in a community setting

      AE Kim et al. 2024.

    • Single-cell analysis of chromatic and expression reveals age-and sex-associated alterations in the human heart

      DF Read et al. 2024.

    • Calibration of variant effect predictors on genome-wide data masks heterogenous performance across genes

      M Tejura et al. 2024.

    • Assigning credit where it is due: an information content score to capture the clinical value of multiplexed assays of variant effect

      JMO Ranola, C Horton, T Pesaran, S Fayer, LM Starita, BH Shirts. 2024.

    • “I probably shouldn’t go in today”: Inequitable access to paid sick leave and its impact on health behaviors during the emergency of COVID-19 in the Seattle area

      CD Iwu et al. 2024.

    • Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements

      FM Chardon et al. 2024.

    • Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

      JX Chong et al. 2024.

    • CFAP47 is implicated in X-linked polycystic kidney disease

      T Mori et al. 2024.

    • Using multiplexed functional data to reduce variant classification inequities in underrepresented populations

      M Dawood et al. 2024.

    • Understanding genetic variants in context

      N Sinnott-Armstrong et al. 2024.

    • Multiplexed assay of variant effect reveals residues of functional importance in the BRAC1 coiled-coil and serine cluster domains

      G Nagy et al. 2023.

    • Single-cell census of human tooth development enables generation of human enamel

      A Alghadeer et al. 2023.

    •  Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in household in Seattle, WA, USA before and during the COVID-19 pandemic

      JC Bennett et al. 2023.

    • An Atlas of Variant Effects to understand the genome at nucleotide resolution

      DM Fowler et al. 2023. 

    • Care-seeking correlate of acute respiratory illness among sheltered adults experiencing homelessness in Seattle, WA, 2019: a community-based cross-sectional study

      JH Rogers et al. 2023. 

    • Respiratory syncytial virus and other respiratory virus infection in residents of homeless shelters – King County, Washington, 2019-2021

      DJ McCulloch et al. 2023.

    • CRaTER enrichment for on-target gene editing enables generation of variant libraries in hiPSCs

      CE Friedman et al. 2023.

    •  DNA repair function scores for 2172 variants in the BRAC1 amino-terminus

      M Diabate et al. 2023.

    • Evaluation of Commercially Available Rapid RT-PCR Assay’s Detection of SARS-CoV-2 Novel Variants

      L Back et al. 2023.

    •  Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021

      HN Oltean et al. 2023.

    • Beyond the exome: What’s next in diagnostic testing for Mendelian conditions

      MH Wojcik et al. 2023.

    • CASCADIA: a prospective community-based study protocol for assessing SARS-CoV-2 vaccine effectiveness in children and adults using a remote nasal swab collection and web-based survey design

      TM Babu et al. 2023.

    •  P460: Gene- and variant- specific calibration of in silico predictive models results in reclassification of 28% of missense VUS from ClinGen VCEPs

      S Fayer, M Tejura, A McEwen, L Starita, D Fowler. 2023.

    • A single-cell multi-omic atlas spanning the adult rhesus macaque brain

      KL Chiou et al. 2023.

    • SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

      S Srivatsan et al. 2022.

    • Mutliregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment

      KL Chiou et al. 2022. 

    • 1456. Environmental and Nasal Pathogen Surveillance in Seattle Area Homeless Shelters

      NM Franko et al. 2022.

    • 1916. Evaluation of nasal swab collection methods on a university campus during the SARS-CoV-2 pandemic

      JA O’Hanlon et al. 2022.

    • Human Parainfluenza Virus in Homeless Shelters before and during the COVID-19 Pandemic, Washington, USA

      EJ Chow et al. 2022.

    • Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022

      C Hansen et al. 2022.

    • 1904. Health Behavioral Trends and Absenteeism Associated with Acute Respiratory Illness Before and During the SARS-CoV-2 Pandemic in a Community Household Cohort, King County, Washington

      E Chung et al. 2022.

    • 2202. Influenza Surveillance of Families in an Observational Household Study 2019-2021

      TM Babu et al. 2022. 

    • SARS-CoV-2 Screening Testing in Schools: A Comparison of School- Vs. Home-Based Collection Methods

      E Chung et al. 2022.

    • The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters—King County, Washington

      EJ Chow et al. 2022.

    • Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

      AA Weil et al. 2022.

    • Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes

      EC Kline et al. 2022. 

    • Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study

      MI Paredes et al. 2022. 

    • Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow

      GK Gulati et al. 2022.

    • Antibacterial potency of type VI amidase effector toxins is dependent on substrate topology and cellular context

      A Radkov et al. 2022.

    • The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays

      AI Adamovic et al. 2022.

    • Highly Sensitive Immunoresistive Sensor for Point-Of-Care Screening for COVID-19

      T Li et al. 2022. 

    • Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

      R Burstein et al. 2022.

    • Diagnostic Accuracy of an At-Home, Rapid Self-test for Influenza: Prospective Comparative Accuracy Study

      RE Geyer et al. 2022.

    • Phylogenomics of Severe Acute Respiratory Syndrome Coronavirus 2 in Emergency Shelters for People Experiencing Homelessness

      AM Casto et al. 2022.

    • 1359. Human Parainfluenza Epidemiology in Homeless Shelters—King County, Washington

      EJ Chow et al. 2022.

    • The Seattle Flu Study: when regulations hinder pandemic surveillance

      M Boeckh et al. 2021 

    • Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection

      N Panpradist et al. 2021.

    • Closing the gap: Systemic integration of multiplexed functional data resolves variants of uncertain significance in BRAC1, TP53, and PTEN

      S Fayer et al. 2021.

    • SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

      AA Weil et al. 2021.

    • Incidence of Medically Attended Acute Respiratory Illnesses Due to Respiratory Viruses Across the Life Course During the 2018/19 Influenza Season

      ML Jackson et al. 2021.

    • School-Based Surveillance of Respiratory Pathogens on “High-Touch” Surfaces

      AF Murray et al. 2021.

    • Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting

      E Chung et al. 2021.

    • Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

      NF Müller et al. 2021.

    • Comparable Specimen Collection from Both Ends of At-Home Midturbinate Swabs

      M Truong et al. 2021.

    • Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

      AE Kim et al. 2021.

    • Corrigendum to ‘Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays’

      N Panpradist et al. 2021.

    • Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

      ML Jackson et al. 2021.

    • Remote Household Observation for Noninfluenza Respiratory Viral Illness

      A Emanuels et al. 2020.

    • Characteristics of COVID-19 in Homeless Shelters: A Community-Based Surveillance Study

      JH Rogers et al. 2020.

    • Multiplexed Functional Assessment of Genetic Variants in CARD11

      I Meitlis et al. 2020.

    • Point-of-care molecular testing and antiviral treatment of influenza in residents of homeless shelters in Seattle, WA: study protocol for a stepped-wedge cluster-randomized controlled trial

      KL Newman et al. 2020.

    • Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

      T Bedford et al. 2020.

    • The Seattle Flu Study: a mutliarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

      HY Chu et al. 2020.

    • Cryptic transmission of SARS-CoV-2 in Washington state

      T Bedford et al. 2020.

    • Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle

      AA Weil et al. 2020.

    • Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform

      HY Chu et al. 2020.

    • Multimodal single-cell analysis reveals radioresistant stem-like and progenitor cell populations in murine glioma

      J Alexander et al. 2020.

    • Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

      X Deng et al. 2020.

    • Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020

      MJ Jorden et al. 2020.

    • Preliminary support for a “dry swab, extraction free” protocol for SARS-CoV-2 testing via RT-qPCR

      S Srivatsan et al. 2020.

    • COVID-19 SCAN molecular workflow

      Starita. 2020.

    • Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

      SE Brnich et al. 2019. 

    • Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

      H Gelman et al. 2019.

    • MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

      D Esposito et al. 2019.

    • 1775. A Community-wide Study to Evaluate the Accuracy of Self-testing for Influenza: Works in Progress

      M Thompson et al. 2019.

    • LB21. The Seattle Flu Study: A Community-Based Study of Influenza

      HY Chu et al. 2019.

    • Massively parallel single-amino-acid mutagenesis

      JO Kitzman, LM Starita, RS Lo, S Fields, J Shendure. 2015.

    • Deep Mutational Scanning: A Highly Parallel Method to Measure the Effects of Mutation on Protein Function

      LM Starita, S Fields. 2015.

    • Deep Mutational Scanning: Library Construction, Functional Selection, and High-Throughput Sequencing

      LM Starita, S Fields. 2015.

    • Deep Mutational Scanning: Calculating Enrichment Scores for Protein Variants from DNA Sequencing Output Files.

      LM Starita, S Fields. 2015.

    • Functional Analysis of BARD1 Missense Variants in Homology-Directed Repair of DNA Double Strand Breaks

      C Lee et al. 2015.

    • Highly multiplex single amino acid mutagenesis for massively parallel functional analysis

      J Shendure, S Fields, J Kitzman, LM Starita. 2015.

    • S1-PP1: Massively Parallel Experimental Analysis of Missense Mutations in BRAC1 for Interpreting Variants of Uncertain Significance

      LM Starita, M Islam, S Fields, JD Parvin, J Shendure. 2016.

    • The power of multiplexed functional analysis of genetic variants

      M Gasperini, LM Starita, J Shendure. 2016.

    • Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

      TA Manolio et al. 2017.

    • Variant Interpretation: Functional Assays to the Rescue

      LM Starita et al. 2017.

    • Using Multiplexed Genome Editing to Distinguish between Loss- and Gain-of-Function Variants in CARD11

      R James et al. 2017.

    • Accurate classification of BRAC1 variants with saturation genome editing

      GM Findlay et al. 2018.

    • On the design of CRISPR-based single-cell molecular screens

      AJ Hill et al. 2018.

    • A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRAC1 Missense Substitution Variants on Protein Function

      LM Starita et al. 2018. 

    • Multiplex assessment of protein variant abundance by massively parallel sequencing

      KA Matreyek et al. 2018.

Starita Lab

University of Washington
Genome Sciences

lstarita@uw.edu