Signal Processing & Computational Biology

Research Focus

The Signal Processing and Computational Biology Group is an interdisciplinary research group in the Department of Electronic and Computer Engineering at The Hong Kong University of Science and Technology (HKUST). We focus on developing high dimensional statistical and machine learning methods, and applying them to problems in signal processing and computational biology. Our group also works on the theory and applications of random matrices

News

August 2020

Saqib’s paper “Fitness inference from complex evolutionary histories with genetic linkage” has been accepted for publication in Nature Biotechnology. This is a joint work with Raymond Louie (University of New South Wales) and John Barton (University of California-Riverside).

Matthew has been selected to contribute to the 2020 world laureates forum as a young scientist.

Preprint of our recent COVID-19 related work “Epitopes targeted by T cells in convalescent COVID-19 patients” has been posted on bioRxiv. As a part of this work, we have developed a web-dashboard that provides an up-to-date information of the emerging data of SARS-CoV-2 T cell epitopes targeted in convalescent patients.

June 2020

We have developed a web-based platform, “COVIDep“, for real-time reporting of vaccine target recommendations for the COVID-19 coronavirus (SARS-CoV-2). 

Main features:
  • Identification of SARS-derived B-cell and T-cell epitopes that provide vaccine target recommendations for SARS-CoV-2;
  • For T cell epitopes, it reports estimated population coverage using HLA/MHC statistical information;
  • Intuitive graphical interface with flexible parameter setting;
  • Up-to-date reporting based on latest sequence data available (from GISAID).

An article related to the platform “COVIDep: a web-based platform for real-time reporting of vaccine target recommendations for SARS-CoV-2” has been published in Nature Protocols. 

Highlighted on the cover page of Nature Protocols (July issue).

Related bioRxiv preprint: “COVIDep platform for real-time reporting of vaccine target recommendations for SARS-CoV-2: Description and connections with COVID-19 immune responses and preclinical vaccine trials“.

May 2020

Saqib and Ahmed’s paper, “How genetic sequence data can guide vaccine design“, has been published in IEEE Potentials Magazine.

Neil, Faraz, and Awais shared their experience as international PhD students at HKUST in a Study International article.

February – March  2020

​”Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies” has been published in Viruses on 25th Feb. 2020.

Cover article of Viruses (March issue).

Coverage in World Economic Forum article (by Prof. Wei Shyy, President of HKUST).

Coverage in the cover story (on COVID-19 vaccines) of New Scientist.

Selected press coverage (more on News page): The StandardStudy InternationalScience DailyPharmaceutical TechnologiesUST release.

Congratulations to Muhammad Saqib Sohail for successfully defending his Ph.D.!  Saqib’s thesis was entitled “A Stochastic Framework for Inference of Population Genetics Parameters from Time-series Genomic Data”. Saqib is going to continue his research as a post-doctoral fellow in our group.

December 2019
Matthew delivered an invited talk at the Random Matrices and Complex Data Analysis Workshop, held at the Shanghai University of Finance and Economics (SUFE).
November 2019
Ahmed’s paper “Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape” has been accepted to Nature Communications. This is joint work with Arup Chakraborty (MIT) and John Barton (University of California-Riverside).
 
Ahmed’s following 2 papers have been accepted to Bioinformatics:
  • “RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins”.  Joint with David Morales-Jimenez (Queens University, Belfast).
  • “MPF-BML: A standalone GUI-based package for maximum entropy model inference”. Joint with Ray Louie (Kirby Institute, UNSW) and John Barton (University of California-Riverside).
October 2019
We welcome back Faraz and Umer after both spent 3 months visiting John Barton at the University of California (Riverside).
September 2019
Matthew contributed an invited talk at the Physical Concepts and Computational Models in Immunology workshop at MIT and the Ragon Institute of MGH, MIT, and Harvard.
 
Congratulations to Liusha Yang (our group alumni, now at the Shenzhen Big Data Research Institute) for being selected to represent HKUST as a “Rising Star” at the Asia Dean’s Forum Rising Stars Workshop to be held in Seoul, Korea. 
 
Laureano’s paper entitled “Extreme eigenvalue distributions of Jacobi ensembles: New exact representations, asymptotics and finite size corrections” has been accepted to Nuclear Physics B. This is joint work with David Morales (Queens University Belfast).
August 2019
Congratulations to Nicolas Auguin for successfully defending his Ph.D.!  Nicolas’ thesis was entitled Random Matrix Analysis of Gram Matrices and Large Robust Covariance Estimators with Applications.  We wish Nicolas all the best as he takes up his new position in the finance world, joining Qube Research and Technologies in HK.
 
Congrats to Ahmed for receiving the Best Poster Prize for his work on HCV data analysis at the 24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) held at Hong Kong U. 
July 2019
A pre-print of Saqib’s work entitled “Resolving genetic linkage reveals patterns of selection in HIV-1 evolution” has been posted on bioRxiv. This is joint work with Ray Louie (UNSW) and John Barton (University of California, Riverside). 
 
Faraz and Ahmed’s paper “Sub-dominant principal components inform new vaccine targets for HIV Gag” has been accepted for publication in Bioinformatics.  This was joint work with David Morales (Queens University Belfast).
June 2019
Our paper “Asymptotics of eigenstructure of sample correlation matrices for high-dimensional spiked models” has been accepted for publication in Statistica Sinica.  This is joint work with David Morales (Queens University Belfast), Iain Johnstone and Jeha Yang (Stanford).
May 2019
Ahmed’s paper “Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them” has appeared in Nature Communications.  This is joint work with Ray Louie (UNSW).
 
Congrats to our group’s Final Year Project student, Phoomraphee Leunam, whose project was selected as the Best Final Year Project in the ECE Department. He also received the Silver Award for the industry demo competition.  Phoom’s work developed deep learning solutions to detect eye diseases from images extracted from diabetic patients in Hong Kong.  It was a collaboration with the HK Eye Hospital.
January – March 2019
November 2018 
An article related to our group’s research, titled “Fighting disease with data and hope”, is published in The Standard ​newspaper.
September 2018
Matthew was invited to present an “IdeasLab” talk on the use of Big Data Methods to Guide Rational Vaccine Design at the World Economic Forum.  Here is the YouTube link.
 
Matthew was also selected as a Young Scientist of the World Economic Forum.
 
Welcome to Hang Zhang (from Shanghai Jiaotong), Awais Wahab Shah (from KFUPM), and Neel Kanth (from IIT-Delhi) to our group as new Ph.D. students.  Congrats also to Awais and Neel for being selected as recipients of the prestigious Hong Kong Ph.D. Fellowship.
August 2018
Liusha Yang successfully defended her Ph.D. thesis entitled Random-Matrix-Based High-Dimensional Covariance Estimation and Signal Processing Applications. Congratulations to Dr. Yang!  We wish her all the best as she starts her new job at the Shenzhen Big Data Research Institute.
June 2018
We bid farewell to Raymond Louie who had been with our group for five years. He was a core  member of our group’s work related to computational biology. We wish Raymond the best of luck as he moves to the medical school at UNSW, Australia.

Talk at 2018 Artificial Intelligence (AI) in Healthcare Summit, The Ritz Carlton, International Commerce Center, Hong Kong
Title: Inferring the fitness landscape of HIV by unsupervised learning
Speaker: Raymond Louie

May 2018
Talk at 2018 Hospital Authority Convention, Hong Kong Convention and Exhibition Center, Hong Kong
Title: Using data science to find weak spots of Hepatitis C virus: Implications for rational vaccine design
Speaker: Matthew R. McKay
McKay_HAC2
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February 2018
Our work, published in PNAS, has received media attention.  Here are some examples (more complete list on News page):
January 2018
Matthew is now Area Editor (Feature Articles) of the IEEE Signal Processing Magazine.  

Useful Links

— Banner photo taken by HKUST alumnus Terence Pang