Ahmed Abdul Quadeer

Research Assistant Professor
Department of Electronic and Computer Engineering
The Hong Kong University of Science and Technology
Clear Water Bay, Kowloon, Hong Kong
Email: eeaaquadeer (at) ust (dot) hk

Education

  • 2016: PhD in Electronic and Computer Engineering
    The Hong Kong University of Science & Technology, Hong Kong
    Application of statistics and statistical signal processing in virology and immunology
  • 2008: MS in Electrical Engineering
    King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia
    Application of statistical signal processing techniques in communication systems
  • 2006: BE in Electronic Engineering 
    NED University of Engineering & Technology, Karachi, Pakistan

Research and Teaching Experience

  • Sep. 2020 – Present: Research Assistant Professor
    Department of Electronic and Computer Engineering
    The Hong Kong University of Science and Technology, Hong Kong
  • Sep. 2016 – Sep. 2020: Research Associate
    Department of Electronic and Computer Engineering
    The Hong Kong University of Science and Technology, Hong Kong
  • Dec. 2014 – Feb. 2015: Visiting Student
    Arup. K. Chakraborty Lab., Institute for Medical Engineering and Science
    Massachusetts Institute of Technology, USA
  • Sep. 2008 – Aug. 2012: Lecturer
    Electrical Engineering Department
    King Fahd University of Petroleum & Minerals, Dhahran, Saudi Arabia

Publications

Summary

  • 24 Journal papers
  • 16 Conference papers
  • 3 Patents
  • 1 Book chapter
  • H-index: 15
    [Google Scholar]

Selected publications

Altmetric (preprint)

Altmetric (paper)

Dimensions

B. Lee, M. S. Sohail, E. Finney, S. F. Ahmed, A. A. Quadeer, M. R. McKay, and J. P. Barton, “Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data,” medRxiv, 2022.

S. F. Ahmed, A. A. Quadeer, and M. R. McKay, “SARS-CoV-2 T cell responses elicited by COVID-19 vaccines or Infection are expected to remain robust against Omicron,” Viruses, 2022.

H. Zhang, A. A. Quadeer, and M. R. McKay, “Evolutionary modeling reveals enhanced mutational flexibility of HCV subtype 1b compared to 1a,” iScience, 2021.

A. A. Quadeer, S. F. Ahmed, and M. R. McKay, “Landscape of epitopes targeted by T cells in 852 convalescent COVID-19 patients: Meta-analysis, immunoprevalence and web platform,” Cell Reports Medicine, 2021.

E. Bernal, L. Gimeno, M. J. Alcaraz, A. A. Quadeer, …, A. Minguela, on behalf of Murcian COVID19 Study group, “Activating killer-cell immunoglobulin-like receptors are associated with the severity of COVID-19,” The Journal of Infectious Diseases, 2021.

F. Tang, P. Luenam, A. Ran, A. A. Quadeer, S. Sivaprasad, P. Sen, R. Raman, G. Anantharaman, M. Gopalakrishnan, S. Haridas; M. R. McKay, C. Y. Cheung, “Detection of diabetic retinopathy from ultrawide field scanning laser ophthalmoscope images: A multi-center deep learning analysis,” Ophthalmology Retina, 2021.

M.S. Sohail, S. F. Ahmed, A. A. Quadeer, and M. R. McKay, “In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives,” Advanced Drug Delivery Reviews, 2021.

S. F. Ahmed, A. A. Quadeer, and M. R. McKay, “COVIDep: A web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2“, Nature Protocols, 2020.

S. F. Ahmed, A. A. Quadeer, and M. R. McKay, “Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies“, Viruses, 2020.

A. A. Quadeer, J. P. Barton, A. K. Chakraborty, and M. R. McKay, “Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape“, Nature Communications, 2020.

A. A. Quadeer, M. R. McKay, J. P. Barton, and Raymond H. Y. Louie, “MPF-BML: A standalone GUI-based package for maximum entropy model inference,” Bioinformatics, 2019.

A. A. Quadeer, R. H. Y. Louie, and M. R. McKay, “Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them,” Nature Communications, 2019.

A. A. Quadeer, D. Morales-Jimenez, and M. R. McKay, “Co-evolution networks of HIV/HCV are modular with direct association to structure and function“, PLoS Computational Biology, 2018. 

Honours and Awards

  • Sep. 2012 – Aug. 2016: Hong Kong PhD Fellowship Scheme (HKPFS), Hong Kong
  • Jan. 2003 – Dec. 2004: Scholarship from NED University of Engineering & Technology, Karachi, Pakistan
  • Jan. 2002 – Dec. 2005: Scholarship from Federal Board of Intermediate and Secondary Education, Islamabad, Pakistan.

Software

  1. Orthogonal-Clustering [Github link]
    A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery
  2. RoCA [Github link]
    Software for identifying co-evolutionary sectors in proteins using Robust Co-evolutionary Analysis (RoCA)
  3. Maximum-entropy-based simulator of hepatitis C virus E2 evolution [Github link]
    In silico identification of immunologically-vulnerable regions in E2 and broadly neutralizing antibodies that target them
  4. RocaSec [Github link]
    A standalone GUI-based package for robust co-evolutionary analysis of proteins
  5. MPF-BML-GUI [Github link]
    A standalone GUI-based package for maximum entropy model inference
  6. Making-elegant-Matlab-figures [Github link]
    A repository comprising multiple scripts for making elegant publication-quality figures in MATLAB quickly and efficiently