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: 27 Journal papers; 16 Conference papers; 3 Patents; 1 Book chapter; H-index: 17; i10-index: 23 [Google Scholar]
Recent publications
Altmetric (preprint)
Altmetric (paper)
Dimensions
S. A. W. Shah, D. P. Palomar, I. Bar, L. L. M. Poon, A. A. Quadeer, and M. R. McKay, “Seasonal antigenic prediction of influenza A H3N2 using machine learning,” Research Square, 2023.
H. Gu, A. A. Quadeer, …, M. R. McKay, and L. L. M. Poon, “Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals,” Nature Communications, 2023.
H. Zhang, R. A. Bull, A. A. Quadeer, and M. R. McKay, “HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies,” BioRxiv, 2023.
S. F. Ahmed, M. S. Sohail, A. A. Quadeer, and M. R. McKay, “Vaccinia-virus-based vaccines are expected to elicit highly cross-reactive immunity to the 2022 monkeypox virus,” Viruses, 2022.
S. F. Ahmed, M. S. Sohail, A. A. Quadeer, and M. R. McKay, “Identification of potential SARS-CoV-2 CD8+ T cell escape mutants,” Vaccines, 2022.
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
Research awards
- 2022: Paper on SARS-CoV-2 Omicron variant featured as cover article of Viruses Jan. issue
- 2020: Developed SARS-CoV-2 dashboard highlighted on cover of Nature Protocols Jul. issue
- 2020: Paper on SARS-CoV-2 vaccine design featured as cover article of Viruses Mar. issue
- 2020 : Paper on SARS-CoV-2 vaccine design is the most-downloaded (>55,000 times) and the most-cited (>1,200 times) research article of Viruses
- 2020: SARS-CoV-2 research influenced the design of multiple COVID-19 peptide-based vaccines including Vaxxinity, CoVepiT, PolyPEPI-SCoV-2
- 2019: Best poster award in the 24th International Bioinformatics Workshop on VEME
- 2009 – 2012: Recipient of 3 distinguished innovation awards at King Fahd University of Petroleum & Minerals (KFUPM), Saudi Arabia
- Two Highly Cited Papers (ISI Web of Knowledge)
- Research cited in 48 patents as state-of-the-art
- Research mentioned in 2 public policy documents (1 by the WHO)
- Research promoted on international forums (World Economic Forum, World Laureates Forum)
- Research highlighted in scientific magazines (New Scientist, ASEE-PRISM)
- Research featured in >270 news outlets locally (SCMP, China Daily, Xinhua) and internationally (Reuters, The Guardian, The Sun, The Independent)
Education awards
- 2012: Hong Kong PhD Fellowship Scheme (HKPFS), Hong Kong
- 2003, 2004: Scholarship from NED University of Engineering & Technology, Karachi, Pakistan
- 2002-2005: Scholarship from Federal Board of Intermediate and Secondary Education, Islamabad, Pakistan.
Software
- Orthogonal-Clustering [Github link]
A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery - RoCA [Github link]
Software for identifying co-evolutionary sectors in proteins using Robust Co-evolutionary Analysis (RoCA) - 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 - RocaSec [Github link]
A standalone GUI-based package for robust co-evolutionary analysis of proteins - MPF-BML-GUI [Github link]
A standalone GUI-based package for maximum entropy model inference - Making-elegant-Matlab-figures [Github link]
A repository comprising multiple scripts for making elegant publication-quality figures in MATLAB quickly and efficiently