Publications by authors named "Ahmed A Quadeer"

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HLA-B*15:01-positive severe COVID-19 patients lack CD8 T cell pools with highly expanded public clonotypes.
Louise C Rowntree, Lilith F Allen, Ruth R Hagen, Hayley A McQuilten, Ahmed A Quadeer

Proc Natl Acad Sci U S A· September 2025

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Back-projection improves inference from sparsely sampled genomic surveillance data.
Elizabeth E Finney, Brian Lee, Syed Faraz Ahmed, Muhammad Saqib Sohail, Ahmed Abdul Quadeer

bioRxiv· July 2025

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Anti-HCV antibodies: A battle for breadth and potency.
Elham Jamali, Ahmed Abdul Quadeer, Nicodemus Tedla, Matthew R McKay, Andrew Lloyd

Antiviral Res· June 2025

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Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.
Brian Lee, Ahmed Abdul Quadeer, Muhammad Saqib Sohail, Elizabeth Finney, Syed Faraz Ahmed

Nat Commun· January 2025

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Seasonal antigenic prediction of influenza A H3N2 using machine learning.
Syed Awais W Shah, Daniel P Palomar, Ian Barr, Leo L M Poon, Ahmed Abdul Quadeer

Nat Commun· May 2024

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Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1.
Muhammad Saqib Sohail, Syed Faraz Ahmed, Ahmed Abdul Quadeer, Matthew R McKay

Viruses· March 2024

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Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis.
Hang Zhang, Ahmed Abdul Quadeer, Matthew R McKay

Nat Commun· November 2023

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HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies.
Hang Zhang, Rowena A Bull, Ahmed Abdul Quadeer, Matthew R McKay

Virus Evol· November 2023

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Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.
Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Daisy Y M Ng, Lydia D J Chang

Nat Commun· March 2023

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Vaccinia-Virus-Based Vaccines Are Expected to Elicit Highly Cross-Reactive Immunity to the 2022 Monkeypox Virus.
Syed Faraz Ahmed, Muhammad Saqib Sohail, Ahmed Abdul Quadeer, Matthew R McKay

Viruses· September 2022

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Within-host diversity of SARS-CoV-2 lineages and effect of vaccination.
Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Daisy Y M Ng, Lydia D J Chang

Res Sq· August 2022

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Identification of Potential SARS-CoV-2 CD8 T Cell Escape Mutants.
Syed Faraz Ahmed, Muhammad Saqib Sohail, Ahmed Abdul Quadeer, Matthew R McKay

Vaccines (Basel)· March 2022

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Evolutionary modeling reveals enhanced mutational flexibility of HCV subtype 1b compared with 1a.
Hang Zhang, Ahmed A Quadeer, Matthew R McKay

iScience· January 2022

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SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron.
Syed Faraz Ahmed, Ahmed Abdul Quadeer, Matthew R McKay

Viruses· January 2022

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Detection of Diabetic Retinopathy from Ultra-Widefield Scanning Laser Ophthalmoscope Images: A Multicenter Deep Learning Analysis.
Fangyao Tang, Phoomraphee Luenam, An Ran Ran, Ahmed Abdul Quadeer, Rajiv Raman

Ophthalmol Retina· November 2021

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Activating Killer-Cell Immunoglobulin-Like Receptors Are Associated With the Severity of Coronavirus Disease 2019.
Enrique Bernal, Lourdes Gimeno, María J Alcaraz, Ahmed A Quadeer, Marta Moreno

J Infect Dis· July 2021

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Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform.
Ahmed Abdul Quadeer, Syed Faraz Ahmed, Matthew R McKay

Cell Rep Med· June 2021

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In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives.
Muhammad Saqib Sohail, Syed Faraz Ahmed, Ahmed Abdul Quadeer, Matthew R McKay

Adv Drug Deliv Rev· April 2021

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Immunodominant epitopes based serological assay for detecting SARS-CoV-2 exposure: Promises and challenges.
Ahmed Abdul Quadeer

EBioMedicine· September 2020

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Cross-serotypically conserved epitope recommendations for a universal T cell-based dengue vaccine.
Syed Faraz Ahmed, Ahmed A Quadeer, John P Barton, Matthew R McKay

PLoS Negl Trop Dis· September 2020

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COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2.
Syed Faraz Ahmed, Ahmed A Quadeer, Matthew R McKay

Nat Protoc· July 2020

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RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins.
Ahmed A Quadeer, David Morales-Jimenez, Matthew R McKay

Bioinformatics· April 2020

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MPF-BML: a standalone GUI-based package for maximum entropy model inference.
Ahmed A Quadeer, Matthew R McKay, John P Barton, Raymond H Y Louie

Bioinformatics· April 2020

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Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies.
Syed Faraz Ahmed, Ahmed A Quadeer, Matthew R McKay

Viruses· February 2020

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Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape.
Ahmed A Quadeer, John P Barton, Arup K Chakraborty, Matthew R McKay

Nat Commun· January 2020

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