Pavitra Roychoudhury

Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa

Also affiliated with University of Washington, Fred Hutch Cancer Center

Medicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 64 papers. Top paper: “Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California”.

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

Science(2020)10.1126/science.abb9263

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13.4DataRank · unranked

308 citations

Wei Gu, Scot Federman, Louis du Plessis, Oliver Pybus, Nuno R. Faria +45 more

Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial

The Lancet Infectious Diseases(2022)10.1016/s1473-3099(22)00506-0

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2.0DataRank · unranked

89 citations

An Vandebosch, Jerald Sadoff, Mathieu Le Gars, Carla Truyers, D. Lowson +95 more

Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1)

The Journal of Infectious Diseases(2023)10.1093/infdis/jiad270

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0.990DataRank · unranked

34 citations

Lauren Rodriguez, Pavitra Roychoudhury, Meei‐Li Huang, Keith R. Jerome, Linhui Hao +9 more

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

The Journal of Infectious Diseases(2022)10.1093/infdis/jiac239

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0.603DataRank · unranked

14 citations

Amanda M. Casto, Pavitra Roychoudhury, Peter D. Han, Hong Xie, Brian Pfau +17 more

Viral gene drive spread during herpes simplex virus 1 infection in mice

Nature Communications(2024)10.1038/s41467-024-52395-2

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0.531DataRank · unranked

12 citations

Anoria K. Haick, Rebeccah Riley, Paola A Massa, Daniel E. Strongin, Lindsay M. Klouser +9 more

HIV-SEQ Reveals Global Host Gene Expression Differences Between HIV-Transcribing Cells from Viremic and Suppressed People with HIV

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.17.629023

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0.299DataRank · unranked

5 citations

Sushama Telwatte, Xiaoyu Luo, Natalie Elphick, Reuben Thomas, Douglas V. Arneson +9 more

Cryptic transmission of SARS-CoV-2 in Washington State

medRxiv(2020)10.1101/2020.04.02.20051417

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0DataRank · unranked

86 citations

Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Meei‐Li Huang +52 more

In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.22.165225

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0DataRank · unranked

48 citations

Vikas Peddu, Hong Xie, Lasata Shrestha, Meei‐Li Huang, Megan C. Mears +10 more

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

medRxiv(2020)10.1101/2020.03.27.20044925

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0DataRank · unranked

36 citations

Wei Gu, Scot Federman, Louis du Plessis, Oliver Pybus, Nuno R. Faria +43 more

SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98

mBio(2021)10.1128/mbio.00065-21

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0DataRank · unranked

152 citations

Nicole A. P. Lieberman, Quynh Phung, Tien-Ying Hsiang, Hong Xie, Pavitra Roychoudhury +7 more

A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir

Cell Reports Medicine(2021)10.1016/j.xcrm.2021.100243

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0DataRank · unranked

107 citations

Sean M. Hughes, Pavitra Roychoudhury, Daniel B. Reeves, Chelsea Amstuz, Haiying Zhu +17 more

Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar

PLoS neglected tropical diseases(2021)10.1371/journal.pntd.0010063

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0DataRank · unranked

89 citations

Michelle J. Lin, Hong Xie, Lasata Shrestha, Tien V. Nguyen, Meei‐Li Huang +28 more

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

Science Translational Medicine(2021)10.1126/scitranslmed.abf0202

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0DataRank · unranked

80 citations

Cassia Wagner, Chris Frazar, Pavitra Roychoudhury, Jover Lee, Louise H. Moncla +38 more

Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19

Scientific Reports(2021)10.1038/s41598-021-82850-9

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0DataRank · unranked

70 citations

Jolie Shen, Cecilia S. Lee, Aaron Lee, Emma A. Roberts, Paul D. Simonson +8 more

HIV reservoir quantification using cross-subtype multiplex ddPCR

iScience(2021)10.1016/j.isci.2021.103615

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0DataRank · unranked

47 citations

Carolyn S. Fish, Claire Levy, Pavitra Roychoudhury, Daniel B. Reeves, Sean M. Hughes +9 more

Variants of Concern Are Overrepresented Among Postvaccination Breakthrough Infections of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Washington State

Clinical Infectious Diseases(2021)10.1093/cid/ciab581

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0DataRank · unranked

46 citations

Seth A. Cohen, Chloe Bryson‐Cahn, Catherine Liu, Steven A. Pergam, John B. Lynch +16 more

HIV reservoir quantification by five-target multiplex droplet digital PCR

STAR Protocols(2021)10.1016/j.xpro.2021.100885

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0DataRank · unranked

14 citations

Sean M. Hughes, Pavitra Roychoudhury, Chelsea Amstuz, Haiying Zhu, Meei‐Li Huang +4 more

Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State

medRxiv(2021)10.1101/2021.05.23.21257679

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0DataRank · unranked

31 citations

Seth A. Cohen, Chloe Bryson‐Cahn, Catherine Liu, Steven A. Pergam, John B. Lynch +16 more

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

medRxiv(2021)10.1101/2021.04.05.21254924

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0DataRank · unranked

9 citations

Alexander L. Greninger, Pavitra Roychoudhury, Lasata Shrestha, Hong Xie, Keith R. Jerome +5 more

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report

medRxiv(2021)10.1101/2021.11.08.21266069

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0DataRank · unranked

9 citations

Jon Klein, Alexander J. Robertson, Mario A. Peña-Hernández, Michelle J. Lin, Pavitra Roychoudhury +18 more

Host variation in type I interferon signaling genes ( MX1 ), CCR5 Δ 32 , and MHC class I alleles in treated HIV+ non-controllers predict viral reservoir size

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.31.466670

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0DataRank · unranked

2 citations

Cassandra Thanh, Eunice Wan, Rebecca Hoh, Kristen S. Hobbs, Tony Pan +22 more

Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes

medRxiv(2021)10.1101/2021.10.22.21265255

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0DataRank · unranked

1 citations

Michelle J. Lin, Hong Xie, Margaret G. Mills, Shah A. Mohamed Bakhash, Vinod P. Gaur +9 more

Variants in nucleocapsid protein and endoRNase are found to associate with severe COVID-19 in a case-control study in Washington State, USA

Research Square(2021)10.21203/rs.3.rs-888049/v1

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0DataRank · unranked

0 citations

Pavitra Roychoudhury, Keith R. Jerome, Peter B. Gilbert, Joshua T. Schiffer, Terry P. Lybrand +13 more

Variants in nucleocapsid protein and endoRNase are found to associate with severe COVID-19 in a case-control study in Washington State, USA

Research Square(2021)10.21203/rs.3.rs-888049/v2

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0DataRank · unranked

0 citations

Pavitra Roychoudhury, Keith R. Jerome, Peter B. Gilbert, Joshua T. Schiffer, Terry P. Lybrand +13 more

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

Nature Communications(2022)10.1038/s41467-022-29104-y

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0DataRank · unranked

312 citations

Jon Klein, Alexander J. Robertson, Mario A. Peña-Hernández, Michelle J. Lin, Pavitra Roychoudhury +18 more

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Med(2022)10.1016/j.medj.2022.10.002

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0DataRank · unranked

85 citations

Tracy Basler, Simon White, Andrew Dei Rossi, Dana Wyman, Hang Dai +25 more

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

Clinical Infectious Diseases(2022)10.1093/cid/ciac279

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0DataRank · unranked

80 citations

Stephanie M. Lunn, Michael Famulare, Lauren Frisbie, Ian Painter, Roy Burstein +40 more

Successful Treatment of Prolonged, Severe Coronavirus Disease 2019 Lower Respiratory Tract Disease in a B cell Acute Lymphoblastic Leukemia Patient With an Extended Course of Remdesivir and Nirmatrelvir/Ritonavir

Clinical Infectious Diseases(2022)10.1093/cid/ciac868

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0DataRank · unranked

72 citations

William Simmons, Ellora Karmarkar, Leah H Yoke, Ayodale B Braimah, Johnnie J. Orozco +15 more

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

Virus Evolution(2022)10.1093/ve/veac052

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0DataRank · unranked

21 citations

Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Amin Addetia, Keith R. Jerome +3 more

Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk

Scientific Reports(2022)10.1038/s41598-021-04376-4

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0DataRank · unranked

19 citations

Pavitra Roychoudhury, Peter B. Gilbert, Joshua T. Schiffer, Terry P. Lybrand, Thomas H. Payne +13 more

Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes

Journal of Molecular Diagnostics(2022)10.1016/j.jmoldx.2022.05.007

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0DataRank · unranked

18 citations

Michelle J. Lin, Hong Xie, Margaret G. Mills, Shah A. Mohamed Bakhash, Vinod P. Gaur +9 more

Host variation in type I interferon signaling genes (MX1), C–C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size

AIDS(2022)10.1097/qad.0000000000003428

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0DataRank · unranked

13 citations

Cassandra Thanh, Eunice Wan, Rebecca Hoh, Kristen S. Hobbs, Tony Pan +20 more

Host–pathogen dynamics in longitudinal clinical specimens from patients with COVID-19

Scientific Reports(2022)10.1038/s41598-022-09752-2

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0DataRank · unranked

6 citations

Victoria M. Rachleff, Hong Xie, Lasata Shrestha, Nicole A. P. Lieberman, Vikas Peddu +9 more

Herpes simplex virus lymphadenitis is associated with tumor reduction in a patient with chronic lymphocytic leukemia

Journal of Clinical Investigation(2022)10.1172/jci161109

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0DataRank · unranked

6 citations

Anton M. Sholukh, Andreas Wieland, David L. Jaye, Mary Carrington, Meei‐Li Huang +11 more

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

medRxiv(2022)10.1101/2022.03.09.22272113

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0DataRank · unranked

30 citations

Tracy Basler, Simon White, Andrew Dei Rossi, Dana Wyman, Pavitra Roychoudhury +24 more

A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron

medRxiv(2022)10.1101/2022.01.08.22268865

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0DataRank · unranked

5 citations

David G. Becker, Pius Brzoska, Tyler Cassens, Jeremy Davis‐Turak, Evan Diamond +29 more

Paxlovid-like nirmatrelvir/ritonavir fails to block SARS-CoV-2 transmission in ferrets

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.20.517271

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0DataRank · unranked

5 citations

Carolin M. Lieber, Josef D. Wolf, Amir-Hossein Karimi, Nicole A. P. Lieberman, Zachary M. Sticher +9 more

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.09.479546

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0DataRank · unranked

4 citations

Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Amin Addetia, Keith R. Jerome +3 more

Comparing molnupiravir and nirmatrelvir/ritonavir efficacy and the effects on SARS-CoV-2 transmission in animal models

Nature Communications(2023)10.1038/s41467-023-40556-8

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0DataRank · unranked

35 citations

Carolin M. Lieber, Josef D. Wolf, Amir-Hossein Karimi, Nicole A. P. Lieberman, Zachary M. Sticher +9 more

Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants

Journal of Clinical Microbiology(2023)10.1128/jcm.00138-23

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0DataRank · unranked

18 citations

Adrianna Westbrook, Leda Bassit, Richard Parsons, Eric C. Fitts, Morgan Greenleaf +18 more

Successful Treatment of Persistent Symptomatic Coronavirus Disease 19 Infection With Extended-Duration Nirmatrelvir-Ritonavir Among Outpatients With Hematologic Cancer

Open Forum Infectious Diseases(2023)10.1093/ofid/ofad306

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0DataRank · unranked

13 citations

Leah H Yoke, Pooja Bhattacharyya, Ryan D. Cassaday, Guang‐Shing Cheng, Zahra Kassamali Escobar +8 more

A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size

PLoS Pathogens(2023)10.1371/journal.ppat.1011114

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0DataRank · unranked

8 citations

Germán G. Gornalusse, David Siegel, Alton Barbehenn, Cassandra Thanh, Rebecca Hoh +20 more

Liver-Humanized NSG-PiZ Mice Support the Study of Chronic Hepatitis B Virus Infection and Antiviral Therapies

Microbiology Spectrum(2023)10.1128/spectrum.05176-22

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0DataRank · unranked

7 citations

Daniel Stone, Michelle A. Loprieno, Lindsay M. Klouser, Pavitra Roychoudhury, Tracy K. Santo +8 more

A multiplexed barcode approach to simultaneously evaluate gene delivery by adeno-associated virus capsid variants in nonhuman primates

Hepatology Communications(2023)10.1097/hc9.0000000000000009

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0DataRank · unranked

2 citations

Nadja Meumann, Anne-Sophie Kuhlmann, Christopher W. Peterson, Hong Xie, Pavitra Roychoudhury +16 more

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

medRxiv(2023)10.1101/2023.09.21.23295927

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0DataRank · unranked

3 citations

Kathryn E. Kistler, Garrett A. Perchetti, Noah Baker, Lauren Frisbie, Laura Marcela Torres +9 more

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.10.523535

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0DataRank · unranked

2 citations

David Siegel, Cassandra Thanh, Rebecca Hoh, Kristen S. Hobbs, Tony Pan +16 more

Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.17.549345

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0DataRank · unranked

2 citations

Pavitra Roychoudhury, Anthony L. Cunningham, Keith R. Jerome, David M. Koelle, Paul R. Kinchington +5 more

Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

Research Square(2023)10.21203/rs.3.rs-2743022/v1

N/A

0DataRank · unranked

0 citations

Li Li, Allan C. deCamp, Morgane Rolland, Michal Juraska, Brian D. Williamson +38 more

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution

Nature Communications(2024)10.1038/s41467-024-47599-5

N/A

0DataRank · unranked

27 citations

Kathryn E. Kistler, Garrett A. Perchetti, Noah Baker, Lauren Frisbie, Laura Marcela Torres +9 more

Outcomes in Hematopoietic Cell Transplant and Chimeric Antigen Receptor T-Cell Therapy Recipients With Pre–Cellular Therapy SARS-CoV-2 Infection

Clinical Infectious Diseases(2024)10.1093/cid/ciae116

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13 citations

Leah H Yoke, Pavitra Roychoudhury, Patrick W Flaherty, Masumi Ueda Oshima, Amelia Weixler +7 more

Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features

Nature Communications(2024)10.1038/s41467-024-46536-w

N/A

0DataRank · unranked

12 citations

Li Li, Allan C. deCamp, Morgane Rolland, Michal Juraska, Brian D. Williamson +45 more

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

PLoS Pathogens(2024)10.1371/journal.ppat.1012117

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0DataRank · unranked

10 citations

Amanda C. Perofsky, Lauren Frisbie, Louise H. Moncla, Pavitra Roychoudhury, Hong Xie +26 more

Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice

Journal of Virology(2024)10.1128/jvi.01858-23

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0DataRank · unranked

7 citations

Pavitra Roychoudhury, Anthony L. Cunningham, Keith R. Jerome, David M. Koelle, Paul R. Kinchington +5 more

Clinical outcomes and frequency of persistent infection among immunosuppressed patients treated with bebtelovimab for COVID‐19 infection at an ambulatory cancer center

Transplant Infectious Disease(2024)10.1111/tid.14223

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0DataRank · unranked

6 citations

Elizabeth M. Krantz, Leah M. Yoke, Molly Gallaher, Pooja Bhattacharyya, L L So +14 more

Clinical and Genomic Epidemiology of Coxsackievirus A21 and Enterovirus D68 in Homeless Shelters, King County, Washington, USA, 2019–2021

Emerging infectious diseases(2024)10.3201/eid3011.240687

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0DataRank · unranked

1 citations

Amanda M. Casto, Nicholas Franko, Eric J. Chow, Peter D. Han, Luis Fernando Gamboa +18 more

Reply to Wang et al., “Ample evidence for the presence of HSV-1 LAT in non-neuronal ganglionic cells of mice and humans”

Journal of Virology(2024)10.1128/jvi.00520-24

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0DataRank · unranked

0 citations

Pavitra Roychoudhury, Anthony L. Cunningham, Keith R. Jerome, David M. Koelle, Paul R. Kinchington +5 more

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

Nature(2025)10.1038/s41586-025-08637-4

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0DataRank · unranked

12 citations

Miguel I. Paredes, Amanda C. Perofsky, Lauren Frisbie, Hong Xie, Kevin Kong +21 more

PP4.14 – 00024 HIV RNA+ cells from ART-suppressed PWH exhibit transcriptional profiles distinct from those during active viremia

Journal of Virus Eradication(2024)10.1016/j.jve.2024.100501

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0DataRank · unranked

0 citations

S. Lee, Julie Frouard, Sushama Telwatte, Xiaoyu Luo, Natalie Elphick +9 more

Immune correlates analysis of antibody responses against SARS-CoV-2 variants in the ENSEMBLE vaccine efficacy trial

iScience(2025)10.1016/j.isci.2025.113660

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0DataRank · unranked

1 citations

Youyi Fong, Lars van der Laan, Fei Heng, Ying Huang, Yiwen Lu +61 more

Cryptic transmission of SARS-CoV-2 in Washington state

Science(2020)10.1126/science.abc0523

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0DataRank · unranked

329 citations

Alexander L. Greninger, Pavitra Roychoudhury, Lea M. Starita, Michael Famulare, Meei‐Li Huang +62 more

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

PLoS Biology(2020)10.1371/journal.pbio.3000849

N/A

0DataRank · unranked

303 citations

Vikas Peddu, Hong Xie, Lasata Shrestha, Meei‐Li Huang, Megan C. Mears +10 more

Gene editing and elimination of latent herpes simplex virus in vivo

Nature Communications(2020)10.1038/s41467-020-17936-5

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0DataRank · unranked

77 citations

Daniel E. Strongin, Pavitra Roychoudhury, Michelle A. Loprieno, Anoria K. Haick, Lindsay M. Klouser +11 more

Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection

PLoS Pathogens(2020)10.1371/journal.ppat.1008450

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0DataRank · unranked

48 citations

Julie Frouard, Andrea Gramatica, Guorui Xie, Sushama Telwatte, Guinevere Q. Lee +12 more

Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate

medRxiv(2020)10.1101/2020.08.13.20173161

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0DataRank · unranked

117 citations

Katharine H. D. Crawford, Adam S. Dingens, Haiying Zhu, Pavitra Roychoudhury, Meei‐Li Huang +4 more