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Last updated on March 03, 2024.

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Syed Faraz Ahmed

My current research interests involve developing innovative ways to inform design of next generation vaccines against different infectious diseases. My research work adopts a data science perspective and seeks to identify precise fragments of viral proteins that could best trigger a protective immune response. This question is one of the most fundamental questions in vaccine development, and one that is broadly applicable to any virus.

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 2023: 40

Hong Kong

Jul-21 - 2016

M.S., Electrical Engineering (major Signal Processing)

King Fahd University of Petroleum & Minerals
(KFUPM) QS World University Ranking 2023: 160

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

Young Scientist of the Hong Kong Laureates Forum

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

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

During my PhD research, I 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).

Research Fellow

Electrical and Electronic Engineering, University of Melbourne

Australia

Current - 2022

Honorary (Fellow)

Microbiology and Immunology, University of Melbourne

Australia

Current - 2023

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

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.

Research citations: 1,841

Google scholar

N/A

2024

  • H-index: 10

Most cited research article

Among all articles published in Viruses journal

N/A

2021

  • Cited more than 1,430 times (Google scholar)
  • Viewed more than 112,500 times (MDPI Viruses)

COVID-19 vaccine candidate

OSE Immunotherapeutics’s vaccine: CoVepiT

N/A

2021 - 2020

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.

Pre-clinical trial of an HIV vaccine

Adenovirus-vectored vaccine against HIV

N/A

2020

  • Proceedings of the National Academy of Sciences of the United States of America
  • 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.

COVID-19 vaccine design

Vaxxinity’s vaccine: UB-612

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.

Product to assess immune responses against COVID

Miltenyi Biotec’s SARS-CoV-2 peptide pools

N/A

2023 - 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

2023 - 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

2023 - 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

2021 - 2020

  • The design of peptide based T cell vaccine PolyPEPI-SCoV-2 incorporated the research results published in Viruses journal in 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.

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

“From virus-slaying air purifiers to delivery robots, how university inventions are fighting COVID-19”

N/A

N/A

Reuters Health article on research findings related to immune response in COVID patients

“Important Epitopes Targeted by T Cells in Convalescent COVID-19 Patients Identified”

N/A

N/A

Cover article of ASEE-PRISM magazine

“Intensive Care”

N/A

N/A

ScienceDaily

“COVID-19 vaccine development”

N/A

N/A

Publications

  • 13 journal publications
  • 4 conference papers/posters

Field-Weighted Citation Impact (FWCI) score of 7.97.

“Single-base tiled screen reveals new design principles of PspCas13b for potent and off-target-free RNA silencing”

Nature Structural & Molecular Biology (IF: 16.8)
(Accepted)

N/A

2024

  • Wenxin Hu, Amit Kumar, S. F. Ahmed, et al.

“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”

Viruses (IF: 4.7)

N/A

2022

“Identification of Potential SARS-CoV-2 CD8+ T Cell Escape Mutants”

Vaccines (IF: 7.8)

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”

Viruses (IF: 4.7)

N/A

2022

“Landscape of epitopes targeted by T cells in 852 individuals recovered from COVID-19: Meta-analysis, immunoprevalence, and web platform”

Cell Reports Medicine (IF: 14.3)

N/A

2021

“In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives”

Advanced Drug Delivery Reviews (IF: 16.1)

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: 3.8)

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”

Nature Protocols (IF: 14.8)

N/A

2020

“Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies”

Viruses (IF: 4.7)

N/A

2020

  • S. F. Ahmed, A. A. Quadeer and M. R. McKay
  • Cover article of March 2020 issue.
  • Coverage in the cover story (on COVID-19 vaccines) of New Scientist magazine (18 March 2020).
  • Altmetric score: 204; FWCI score: 47.04

“Experimental study on broadband radiofrequency electromagnetic radiations near cellular base stations: a novel perspective of public health”

Journal of Thermal Analysis and Calorimetry (IF: 4.4)

N/A

2020

  • S.M. Sait, S. F. Ahmed and M. R. Rafiq

“Sub-dominant principal components inform new vaccine targets for HIV Gag”

Bioinformatics (IF: 5.8)

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: 8.3)

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: 4.1)

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”

Patent Number US 0280942

N/A

2015

  • S. F. Ahmed and T. Y. Al-Naffouri

“Method of performing facial recognition using genetically modified fuzzy linear discriminant analysis”

Patent Number US 8478005

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, 2022.

N/A

Current - 2022

Victorian Infection and Immunity Network (VIIN)

Served as a judege at the VIIN Young Investigator Symposium 2023

N/A

Current - 2023

Australian Bioinformatics and Computational Biology Society (ABACBS)

N/A

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: 7.8)

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