Ahmed Abdul Quadeer
Research Associate
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
Github CV Google Scholar Orcid Research Gate
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. 2016 – Present: 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
- 16 Journal papers
- 16 Conference papers
- 3 Patents
- 1 Book chapter
- H-index: 11
[Google Scholar]
Selected Recent Publications (for a comprehensive list, check detailed CV)
- 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, vol. 12, no. 3, pp. 254, 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, vol. 11, no. 1, pp. 377, 2020.
- A. A. Quadeer, D. Morales-Jimenez, and M. R. McKay, “RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins,” Bioinformatics, 2019.
- 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, vol. 10, no. 1, pp. 2073, 2019.
- S. F. Ahmed, A. A. Quadeer, D. Morales-Jimenez, and M. R. McKay, “Sub-dominant principal components inform new vaccine targets for HIV Gag,” Bioinformatics, vol. 35, no. 20, pp. 3884-3889, Oct. 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, vol. 14, no. 9, pp. e1006409, 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
- 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