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Syed Faraz Ahmed
My current research interests involve developing innovative ways to inform design of next generation vaccines and antivirals drugs against different infectious diseases. My research work adopts a data science perspective and seeks to identify precise targets for next-generation vaccines and drugs for triggering protective immune responses and trapping the pathogen where it hurts. This question is one of the most fundamental questions in vaccine and antiviral development, and one that is broadly applicable to any pathogen.
Project Grants
Chief Investigator - Ideas Grant
Total funding: AUD 1,143,599 from National Health and Medical Research Council (NHMRC)
Australia
2026 - 2023
- Project title: “Using Big Data to Engineer Highly Immunogenic Hepatitis C Virus Envelopes for the Induction of Broad Neutralising Antibodies”
- Chief Investigators: Matthew McKay, Syed Faraz Ahmed - University of Melbourne, Melanie Walker - University of New South Wales, Ahmed Abdul Quadeer - HKUST
- Associate Investigators: Rowena Bull - University of New South Wales, Deborah Burnett - The Garvan Institute of Medical Research
Chief Investigator - Discovery Project
Total funding: AUD 425,000 from Australian Research Council (ARC)
Australia
2025 - 2023
- Project title: “Engineering Methods for Resolving Complex Mutational Networks in Proteins”
- Chief Investigators: Matthew McKay, Syed Faraz Ahmed - University of Melbourne
- Partner Investigators: Ahmed Abdul Quadeer, Daniel Palomar - HKUST
Education
Ph.D., Electronic and Computer Engineering (Research area: Computational Immunology and Bioinformatics)
Hong Kong University of Science and Technology
(HKUST) QS World University Ranking 2025: 47
Hong Kong
Jul-21 - 2016
- Thesis: “Genetic Sequence Analysis to Inform Design of Universal Vaccines against Infectious Diseases”
- Advisor: Prof. Matthew R.McKay
- Medium of instruction: English language
M.S., Electrical Engineering (major Signal Processing)
King Fahd University of Petroleum & Minerals
(KFUPM) QS World University Ranking 2025: 101
Saudi Arabia
2011 - 2008
- Thesis: “A Compressed Sensing Based Channel Estimation of Impulse-Radio UWB Communication System”
- Advisor: Prof. Tareq Y.Al-Naffouri
- Medium of instruction: English language
B.E., Electronic Engineering
NED University of Engineering & Technology
Pakistan
2007 - 2003
- Final Year Project: “QuadHD CMOS Sensor Based Imaging System Design”
Awards and Honors
McKenzie Postdoctoral Fellowship
University of Melbourne
N/A
2025
- Highly competitive three year flagship postdoctoral fellowship at the University of Melbourne for early career stage researchers.
Young Scientist of the Hong Kong Laureates Forum
N/A
2023
- Among the 200 young scientists selected from around the world to participate in the inaugral forum.
PhD Research Excellence Award (Finalist)
School of Engineering, HKUST
QS World University Ranking (Engineering & Technology): 20
N/A
2021
- Awarded as one of the top 4 finalists among 1,100 PhD students across all seven departments within the School of Engineering
Hong Kong PhD Fellowship
Research Grants Council of Hong Kong
N/A
2020 - 2016
- Competitive and highly selective fellowship open to applicants from around the world
Outstanding Performance Award (Staff)
Research Institute, KFUPM
N/A
2015
- Best performance award for staff
Graduate Studies Scholarship
KFUPM
N/A
2011 - 2008
- Fully-funded scholarship to support MS studies
Gold Medal
Govt. Delhi College
N/A
2003
- Top scorer in standardized high school examinations
Research Experience
My research contributed in addressing the fundamental question of vaccine design for three devastating human viruses: HIV, dengue-virus, and SARS-CoV-2 (the causative agent of COVID-19).
McKenzie Fellow
Electrical and Electronic Engineering, University of Melbourne
Australia
Current - 2025
Honorary (Fellow)
Microbiology and Immunology, University of Melbourne
Australia
Current - 2023
Research Fellow
Electrical and Electronic Engineering, University of Melbourne
Australia
2025 - 2022
Post-doctoral Fellow
Electronic and Computer Engineering, HKUST
Hong Kong
2022 - 2021
Graduate Research Assistant
Signal Processing and Computational Biology Lab., HKUST
Hong Kong
2021 - 2016
- Worked on collaborative research projects, analyzed large genetic data sets and developed multiple web platforms.
Visiting Research Student
Barton Lab., University of California, Riverside
USA
2019
- Worked on a research project related to identification of cross-serotypically robust T cell epitopes of Dengue virus.
Research Assistant
Compressive Sensing Lab., KFUPM
Saudi Arabia
2011 - 2009
- Developed a method to estimate UWB wireless channel by exploiting the cluster-sparse structure of the channel model.
Industry Experience
I have contributed in both managing and engineering roles for multiple industry-driven projects.
Engineer-II (Analyst)
Center for Communications & IT, Research Institute, KFUPM
Saudi Arabia
2016 - 2011
- Participated in industry funded projects worth SAR 9.8 million (USD 2.6 million).
- Group leader for RF Radiation Measurements project team. Conducted compliance tests at more than 300 telecom BTS sites in different regions of KSA.
- Team lead of Data Analysis team for KSA National ICT Surveys for 2014 and 2015.
Assistant Manager (Research)
Imaging Payload Systems Lab., SUPARCO
Pakistan
2008
- Developed QuadHD CMOS Sensor based Imaging System with its test-bed on FPGA platform.
IC Design Intern
Digitek Engineering
Pakistan
2007
- Worked on Verilog HDL implementation of Reed-Solomon Codec.
Summer Intern
Pakistan International Airlines
Pakistan
2006
- Worked in Engineering Overhaul Workshop.
Teaching Experience
I co-developed a new Master’s level subject. I served as Tutor and Demonstrator for the subject which received End of Subject Survey scores in top 20% across the School of Electrical, Mechanical, and Infrastructure Engineering.
Demonstrator & Tutor
University of Melbourne
Australia
Current - 2022
- For the EEE course, “Large Data Methods and Applications”
Graduate Teaching Assistant
HKUST
Hong Kong
2019 - 2017
- Assisted in the graduate level course, “Random Matrix Theory and Applications”
- Assisted in two undergraduate level courses.
Teaching Assistant
KFUPM
Saudi Arabia
2011 - 2009
- Conducted laboratory sessions for three undergraduate level courses.
Research Impact
My research work has directly influenced design of peptide pools to assess T cell responses against COVID-19. It has guided multiple vaccine design efforts against COVID-19 and influenced design of a novel HIV vaccine.
COVID-19 vaccine candidate
OSE Immunotherapeutics’s vaccine: CoVepiT
N/A
2024 - 2020
- The design of peptide based T cell vaccine PolyPEPI-SCoV-2 incorporated the research results published in Viruses journal in 2020.
- The design of immunogen in CoVepiT vaccine was influenced by the research results published in Viruses journal in 2020.
Highly cited papers
2 publications among the top 1% articles in the field of Microbiology, Web of Science
N/A
2022
Featured in WHO epidemiological update
WHO epidemiological update on emergence of the Omicron variant
N/A
2022
Featured at World Laureates Forum
Research findings were presented at the session titled, “Learn from the Pandemic: Public Health and Economy”
N/A
2022
Highlighted in Ireland Public Health Policy
Rolling summary of Omicron evidence, epidemiology and guidance
N/A
2022
Highlighted in Asia-Pacific Economic Cooperation Policy document
N/A
2022
Referenced in Mpox Immunisation Guidelines for Ireland
Royal College of Physicians of Ireland
N/A
2022
Most cited research article
Among all articles published in Viruses journal
N/A
2021
- Cited more than 1,480 times (Google scholar)
- Viewed more than 112,500 times (MDPI Viruses)
Referenced in Govt. of Spain Public Health document
Estrategias En La Prevencion Y El Control De La Pandemia De La Covid-19 Causada Por El Sars-cov-2
N/A
2021
Referenced in Switzerland Public Health Review
COVID-19 vaccines and post-vaccination data: Literature update
N/A
2021
Web-based platforms for guiding COVID-19 vaccine research
COVIDep
Dashboard for SARS-CoV-2 T cell epitopes
N/A
2021 - 2020
- COVIDep provides updated vaccine target recommendations.
- Dashobard provides up-to-date landscape of the SARS-CoV-2 T cell epitopes targeted by the immune systems of recovered COVID-19 individuals.
- These web-based platforms are used by researchers from around the world.
Featured in a Public Policy Document on COVID-19
N/A
2020
- Influenced the COVID-19 policy of the African Union, which is a continental body comprised on 55 member states that make up the countries of Africa.
Pre-clinical trial of an HIV vaccine
Adenovirus-vectored vaccine against HIV
N/A
2020
- Pre-clinical trial of an adenovirus-vectored vaccine against HIV has shown to elicit strong T cell response in monkeys; the vaccine immunogen-design aligned with research results published in Bioinformatics journal in 2019.
Commercial Impact
My research had directly guided design of multiple vaccines against COVID-19 as well as design of multiple commercial products for assessing immune responses.
85 patents citing my research have been filed in 26 patent offices, including World Intellectual Property Organization (WIPO), United States (US), and European Patent Office (EP) (Elsevier SciVal).
Product to assess immune responses against COVID
Miltenyi Biotec’s SARS-CoV-2 peptide pools
N/A
2025 - 2020
- Commercially available multiple PepTivator Peptide Pools designed based on research results published in Viruses journal.
- Miltenyi Biotec is a global biotechnology company operating in 28 countries.
Product to assess immune responses against COVID
Mabtech’s SARS-CoV-2 S2 N defined peptide pool
N/A
2025 - 2020
- Commercially available peptide pool for quantification of the number of cytokine secreting cells specific for SARS-CoV-2 S2 and N proteins was based on research results published in Viruses journal in 2020.
- Mabtech is a big biotech company with a focus on developing products for the measurement of immune responses.
Product to assess immune responses against COVID
Anaspec’s SARS-CoV-2 T-cell Peptide Antigens Set
N/A
2025 - 2020
- Commercially available kit contains peptides that are unique T-cell epitopes from the SARS-CoV-2 spike protein and identified from the results published in Viruses journal in 2020.
- AnaSpec is a globally recognized biotechnology company that manufactures and sells proteomic related products.
COVID-19 vaccine design
Treos Bio’s PepTC vaccine: PolyPEPI-SCoV-2
N/A
2024 - 2020
- US patent (US10973909B1) was issued to PepTC Vaccines Ltd (Treos Bio) that refers to the recommended vaccine targets as the state of the art and uses these to benchmark.
Patents citing research work [selected from 85 patents - Elsevier SciVal]
“Peptide vaccines (Treos Bio Ltd.)”
“T cell epitopes and related compositions useful in the prevention, diagnosis, and treatment of beta-coronaviruses (Epivax, Inc.)”
“Coronavirus serology assay (Pfizer Inc.)”
“Pan-coronavirus peptide vaccine (Ose Immunotherapeutics)”
“Diagnosis, prevention and treatment of coronavirus infection (Emergex Vaccines Holding Limited)”
“Coronavirus vaccine (Peptc Vaccines Limited)”
“Virus-like particles for preventing the spreading and lowering the infection rate of viruses (Finncure Oy)”
“Nucleic acids encoding a polypeptide comprising a modified fc region of a human igg1 and at least one heterologous antigen (Scancell Limited)”
“Anti-sars-cov-2 antibodies and uses thereof (Tsb Therapeutics Beijing Co Ltd)”
“CpG-adjuvanted SARS-CoV-2 virus vaccine (Dynavax Tech. Co.;Valneva Austria Gmbh)”
“Recombinant polypeptides containing at least one immunogenic fragment and antibody fc region and uses thereof (Boost Biopharma Inc.)”
“Compositions and methods for improving the immune response to sars-cov2 (Glaxosmithkline Biologicals Sa)”
“Yeast lysate covid-19 vaccine (Immunitybio, Inc.)”
“Amphiphilic polynucleotides (Duke University)”
“SARS-CoV-2 subunit vaccine and microneedle array delivery system (University Of Pittsburgh)”
“Epitopes of sars-cov-2 (Agency For Science, Technology And Research)”
“Developing lateral flow immunochromatography (lfia) peptide-based test strips for rapid detection of antigens and antibodies against specific antigens (KAUST)”
“Polypeptide panels and uses thereof (Oxford University Innovation Limited)”
“Inhaled interferons for viral respiratory infections (New York University)”
“Method of performing structure-based bayesian sparse signal reconstruction (KFUPM)”
“Method and apparatus for enhanced channel estimation using matching pursuit and adaptive cluster tracking (Qualcomm Inc.)”
N/A
2024 - 2015
COVID-19 vaccine design
N/A
2023 - 2020
- The components of the UB-612 vaccine design that were formulated to elicit T cell responses were selected based on recommendations in the paper published in Viruses journal in 2020.
- A commercial first-of-its-kind multiple peptide-based vaccine that is undergoing advanced clinical trials and has reported USD 2.8 billon in advance purchases.
Selected Press
My research work on COVID-19 has received significant media attention, both locally and internationally.
Special Exhibition at Hong Kong Science Museum
“Fighting Viruses” Innovations to Safeguard our Health
N/A
N/A
Cover article of New Scientist magazine
“How soon will we have a coronavirus vaccine? The race against covid-19”
N/A
N/A
HKUST President Prof. Wei Shyy’s article for the World Economic Forum
N/A
N/A
Study International (Interviewed)
N/A
N/A
Medscape
“Important Epitopes Targeted by T Cells in Convalescent COVID-19 Patients Identified”
N/A
N/A
The Medical News
“Will emerging SARS-CoV-2 variants affect T cell immunity? A meta-analysis”
“T cell epitopes from recovered COVID-19 patients identified for vaccine”
“New web-based platform established for reporting vaccine target recommendations for COVID-19”
“HKUST scientists provide leads for guiding research towards COVID-19 vaccine development”
N/A
N/A
MedicalXpress
“Meta-analysis shows SARS-CoV-2 variants unlikely to affect T cell responses”
“A platform of vaccine target recommendations for COVID-19”
“Scientists shed light on COVID-19 vaccine development”
N/A
N/A
ScienMag
“HKUST’s meta-analysis shows SARS-CoV-2 variants unlikely to affect T cell responses”
“HKUST sets up a platform of vaccine target recommendations for COVID-19”
N/A
N/A
Publications
- 4.73 Field-weighted citation impact (FWCI)
- 16 Journal publications
- 4 Conference papers/posters
“Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data”
Nature Communications (IF: 14.7)
N/A
2025
- B. Lee, … S. F. Ahmed et al.
“Single-base tiled screen unveils design principles of PspCas13b for potent and off-target-free RNA silencing”
Nature Structural & Molecular Biology (IF: 12.5)
N/A
2024
- W. Hu, A. Kumar, S. F. Ahmed et al.
“Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1”
N/A
2024
- M.S. Sohail, S. F. Ahmed, A. A. Quadeer, and M. R. McKay
“Computational frameworks guide identification of T cell epitopes: COVID-19 and beyond”
Poster at 2023 Melbourne Emerging Leaders Symposium: Advancing Discovery
N/A
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”
N/A
2022
- S. F. Ahmed, M. S. Sohail, A. A. Quadeer, and M. R. McKay
- Altmetric score: 306; FWCI score: 6.89
“Identification of Potential SARS-CoV-2 CD8+ T Cell Escape Mutants”
N/A
2022
- S. F. Ahmed, M. S. Sohail, 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”
N/A
2022
- S. F. Ahmed, A. A. Quadeer, and M. R. McKay
- Cover article of January 2022 issue.
- Altmetric score: 1,326 ; FWCI score: 10.55
“Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform”
Cell Reports Medicine (IF: 11.7)
N/A
2021
- A. A. Quadeer, S. F. Ahmed, and M. R. McKay
- Altmetric score: 260</a; FWCI score: 2.24
“In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives”
Advanced Drug Delivery Reviews (IF: 15.2)
N/A
2021
- M.S. Sohail, S. F. Ahmed, A. A. Quadeer, and M. R. McKay
- Invited paper for a Special Issue of the journal.
“Cross-serotypically conserved epitope targets for a universal T cell based Dengue vaccine”
PLOS Neglected Tropical Diseases (IF: 3.4)
N/A
2020
- S. F. Ahmed, A. A. Quadeer, J. P. Barton and M. R. McKay
“COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2”
N/A
2020
- S. F. Ahmed, A. A. Quadeer and M. R. McKay
- Highlighted on the cover page of July 2020 issue.
- Altmetric score: 53
“Experimental study on broadband radiofrequency electromagnetic radiations near cellular base stations: a novel perspective of public health”
Journal of Thermal Analysis and Calorimetry (IF: 3.0)
N/A
2020
- S.M. Sait, S. F. Ahmed and M. R. Rafiq
“Sub-dominant principal components inform new vaccine targets for HIV Gag”
N/A
2019
- S. F. Ahmed, A. A. Quadeer, D. Morales-Jimenez and M. R. McKay
“Low-Complexity Bayesian Estimation of Cluster-Sparse Channels”
IEEE Transactions on Communications (IF: 7.2)
N/A
2015
- T. Ballal, T. Y. Al-Naffouri and S. F. Ahmed
“A genetically modified fuzzy linear discriminant analysis for face recognition”
Journal of the Franklin Institute (IF: 3.7)
N/A
2011
- A. Khoukhi and S. F. Ahmed
“Low-Complexity MAP Based Channel Support Estimation for Impulse Radio Ultra-Wide band (IR-UWB) Communications”
2011 IEEE International Conference on Ultra-Wideband
N/A
2011
- S. F. Ahmed, T. Y. Al-Naffouri and A. H. Muqaibel
“Structure Based Bayesian Sparse Reconstruction Using Non-Gaussian Prior”
Forty-Ninth Annual Allerton Conference on Communication, Control, and Computing
N/A
2011
- A. A. Quadeer, S. F. Ahmed and T. Y. Al-Naffouri
- US patent (US-20150139367-A1) was granted to Qualcomm Inc. that refers to this publication.
“Fuzzy LDA for face recognition with GA based optimization”
Annual Meeting of the North American Fuzzy Information Processing Society
N/A
2010
- A. Khoukhi, S. F. Ahmed
“Digital Attendance Recording System”
International Conference on Information and Emerging Technologies
N/A
2007
- A. A. Khan, S. F. Ahmed, et al.
Patents
2 US patents issued
2 US preliminary patents
1 PCT application submitted
“Identification and uses of peptide sequences of sars-cov-2 T cell and B cell epitopes”
PCT Patent Application WO2022148455
N/A
2022
- M. R. McKay, A. A. Quadeer, M. S. Sohail, and S. F. Ahmed
“Identification and uses of peptide sequences of SARS-CoV-2 epitopes derived from SARS-CoV epitopes”
U.S. Provisional Utility Patent Application No. 63/136,175
N/A
2021
- M. R. McKay, A. A. Quadeer and S. F. Ahmed
“Optimized Peptide Pools for Assessing Region-Specific SARS-CoV-2 CD8+ T Cell Responses and Uses Thereof”
U.S. Provisional Utility Patent Application No. 63/229,063
N/A
2021
- M. R. McKay, A. A. Quadeer, M. S. Sohail, and S. F. Ahmed
“Low-Complexity Method for Estimating Impulse-Radio UWB Wireless Channels”
N/A
2015
- S. F. Ahmed and T. Y. Al-Naffouri
“Method of performing facial recognition using genetically modified fuzzy linear discriminant analysis”
N/A
2012
- A. Khoukhi, and S. F. Ahmed
Professional Engagement
International Society for Computational Biology and Bioinformatics (ISCB)
N/A
N/A
Current - 2019
Australia and New Zealand Society for Immunology (ASI)
Presented at the 50th Annual Scientific Meeting of ASI.
N/A
Current - 2022
Australiasian Virology Society (AVS)
Presented at the 12th AVS Meeting.
N/A
Current - 2024
Victorian Infection and Immunity Network (VIIN)
Served as a judge at the VIIN Young Investigator Symposium.
N/A
Current - 2023
Australian Bioinformatics and Computational Biology Society (ABACBS)
Mentoring PhD students through the COMBINE bioinformatics mentoring program.
N/A
Current - 2023
Institute of Electrical and Electronics Engineers (IEEE)
N/A
N/A
Current - 2012
Pakistan Engineering Council
N/A
N/A
Current - 2008
Guest Editor for Vaccines (IF: 5.2)
Special Issue: Diagnostics and Vaccine Development for Emerging Infectious Diseases
N/A
2023 - 2022
Certification
Melbourne Academy
N/A
2022
Standardized Tests
TOEFL-iBT
Score: 112/120
N/A
2015
- Reading: 30/30 Listening: 30/30
- Speaking: 27/30 Writing: 25/30
GRE
Score: 318/340
N/A
2014
- Quantitative: 163/170
- Verbal: 155/170
- Analytical Writing: 4.0/6.0