Researcher

Dr Raymond Hall Yip Louie

My Expertise

Expertise:  I am a computational biologist and bioinformatician specializing in developing computational tools and analyzing genomics, transcriptomics and proteomics data. I work primarily with immunological and virological data to understand fundamental immunological mechanisms and discover biomarkers for therapeutics and diagnostics. My work involves collaboration with academic, health and industry across NSW, Australia and internationally.

Approaches: I develop computational tools to analyze biological data using my multi-disciplinary background in engineering and statistical machine learning. I also have extensive experience in analyzing single-cell multi-omic datasets.

Impact: My analysis of single-cell data has led to numerous insights into understanding the evolution of immune cells in the context of CAR T immunotherapy and cealiac disease.

Keywords

Fields of Research (FoR)

Immunology, Autoimmunity, Cancer therapy (excl. chemotherapy and radiation therapy), Infectious Diseases, Biological Mathematics, Bioinformatics

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Biography

I am a computational biologist and bioinformatician, with a current focus on applying computational tools to analyze immune cells in patients with HCV, cealiac disease or treated with CAR T therapy.

I received a PhD in Electrical Engineering at the University of Sydney, after which I was an ARC Postdoctoral Fellow focusing on wireless communications. I then moved to the Hong Kong University of Science and Technology, where I focused on...view more

I am a computational biologist and bioinformatician, with a current focus on applying computational tools to analyze immune cells in patients with HCV, cealiac disease or treated with CAR T therapy.

I received a PhD in Electrical Engineering at the University of Sydney, after which I was an ARC Postdoctoral Fellow focusing on wireless communications. I then moved to the Hong Kong University of Science and Technology, where I focused on applying statistical and machine learning tools to viral sequence data, to aid in the design of effective vaccines. My background allows for a unique multi-disciplinary approach to solving biological problems.


My Grants

  • Hong Kong Research Grants Council General Research Fund, Chief  (Primary) Investigator (2017-2019)

    • “Statistical inference of the fitness parameters driving viral evolution using time series data”, HKD 482,605 (AUD 77,168.32)

  • Hong Kong Research Grants Council General Research Fund, Chief (Primary) Investigator (2016-2018),

    • A novel statistical inference framework for big data applications: Identifying hidden multi-variate non-linear associations”, HKD 696,029 (AUD 111,294.72)

  • Australian Research Council Discovery Project grant, Chief (and sole) Investigator (2011-2013). 

    • Design of future cognitive radio relay networks”. AUD 255,000 


My Qualifications

  • PhD. in Electrical Engineering, University of Sydney, Australia

  • B.E/B. Sc. in Electrical Engineering/Computer Science (1st Class Honours), University of New South Wales, Australia


My Research Activities

Journal Papers (Computational biology)

 

  1. Kenneth P Micklethwaite, Kavitha Gowrishankar, Brian S Gloss, Ziduo Li, Janine A Street, Leili Moezzi, Melanie A Mach, Gaurav Sutrave, Leighton E Clancy, David C Bishop, R. H. Y. Louie*, Curtis Cai, Jonathan Foox, Matthew MacKay, Fritz J Sedlazeck, Piers Blombery, Christopher E Mason, Fabio Luciani, David J Gottlieb, Emily Blyth. “Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells”, Blood, 2021
  2. R. H. Y. Louie* and F. Luciani, “Recent advances in single‐cell multimodal analysis to study immune cells”, Immunology and Cell Biology, 2021.
  3. S. Sohail*, R. H. Y. Louie*, J. P. Barton, and M. R. McKay, “MPL resolves genetic linkage in fitness inference from complex evolutionary histories”, Nature Biotechnology, November 2020. *Equal contribution
  4. A. A. Quadeer, M. R. McKay, J.P. Barton, R.H.Y. Louie, “MPF-BML: a standalone GUI-based package for maximum entropy model inference”, Bioinformatics, 36 (7), pp 2278-2279, April, 2020
  5. 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, 10 (1), pp. 1-11, 2019
  6. R. H. Y. Louie, K. J. Kaczorowski, J. P. Barton, A. K. Chakraborty, and M. R. McKay, “The fitness landscape of the human immunodeficiency virus envelope proteins that are the targets of humoral immune responses”, Proceedings of the National Academy of Sciences of the USA (PNAS), 115:E564-E573, Jan 2018.
  7. A. A. Quadeer, R.H.Y. Louie, K. Shekhar, A. K. Chakraborty, I. Hsing, and M. R. McKay, “Statistical linkage of mutations in the non-structural proteins of Hepatitis C virus exposes targets for immunogen design,” Journal of Virology, vol. 88, no. 13, pp. 7628-7644, July 2014

 

 

Journal Papers (Application of signal processing, information theory, game theory, optimization, probability and statistical tools to wireless communication systems)

 

  1. Y. Wu, R. H. Y. Louie, M. R. McKay, “Asymptotic outage probability of MIMO-MRC systems in double-correlated Rician environments”, IEEE Transactions on Wireless Communications, vol. 15, no. 1, pp. 367-376, Jan. 2016

  2. D. M. Jimenez, R.H.Y. Louie, M. R. McKay, and Y. Chen, “Analysis and design of multiple-antenna cognitive radios with multiple primary user signals”, IEEE Transactions on Signal Processing, vol. 63, no. 18, pp. 492954939, September 2015

  3. R.H.Y. Louie, W. Hardjawana, Y. Li and B. Vucetic, “Distributed multiple-access for smart grid home area networks: Compressed sensing with multiple antennas”, IEEE Transactions on Smart Grid, vol. 5, no. 6, pp. 2938-2946, November 2014

  4. S. Bayat, R.H.Y. Louie, Z. Han, B. Vucetic and Y. Li, "Distributed user association and femtocell allocation in heterogeneous wireless networks,” IEEE Transactions on Communications¸ vol. 62, no. 8, pp. 3027-3043, August 2014.

  5. H. Chen, Y. Li, R.H.Y. Louie and B. Vucetic, "Autonomous demand side management with instantaneous load billing: an aggregative game approach,” IEEE Transactions on Smart Grid, vol. 7, no. 4, pp. 1744-1754, April 2014

  6. S. Bayat, R.H.Y. Louie, Z. Han, B. Vucetic and Y. Li, "Physical layer security in distributed wireless networks using matching theory,” IEEE Transactions on Information Forensics and Security¸ vol. 8, no. 5, pp. 717-732, May 2013.

  7. S. Bayat, R. H. Y. Louie, B. Vucetic, Y.  Li, “Dynamic decentralised algorithms for cognitive radio relay networks with multiple primary and secondary users utilising matching theory”, Trans. Emerging Telecommunications Technologies vol. 24, no. 5, pp. 486-502,  2013

  8. Y. Wu, R.H.Y. Louie and M. R. McKay, “Analysis and design of wireless ad hoc networks with channel estimation errors”, IEEE Transactions on Signal Processing¸ vol. 61, no. 6, pp. 1447-1459, March 2013.

  9. Y. Wu, R.H.Y. Louie, M. R. McKay and I. B. Collings, “Generalized framework for the analysis of linear MIMO transmission schemes in decentralized wireless ad hoc networks”, IEEE Transactions on Wireless Communications¸ vol. 11, no. 8, pp. 2815-27, August 2012.

  10. R. Manna, R.H.Y. Louie, Y. Li and B. Vucetic, “Cooperative spectrum sharing in cognitive radio networks with multiple antennas”, IEEE Transactions on Signal Processing¸ vol. 59, no. 11, pp. 5509-22, November 2011.

  11. R.H.Y. Louie, M.R. McKay, and I.B. Collings, “Open-loop diversity and multiplexing communications in ad hoc networks”, IEEE Transactions on Information Theory, vol. 57, no. 1, pp. 317-344, January 2011.

  12. Y. Li , R.H.Y. Louie and B. Vucetic, “Relay selection with network coding in two-way relay channels”, IEEE Transactions on Vehicular Technology, vol. 59, no. 9, pp. 4489-99, November 2010

  13. M. Elkhashlan, P.L. Yeoh, R.H.Y. Louie and I.B. Collings, “On the exact and asymptotic SER of receive diversity with multiple amplify-and-forward relays” IEEE Transactions on Vehicular Technology, vol. 59, no. 9, pp. 4602-08, November 2010

  14. R.H.Y. Louie, Y. Li and B. Vucetic, “Practical physical layer network coding for two way relay channels: performance analysis and comparison”, IEEE Transactions on Wireless Communications¸ vol. 9, no. 1, pp. 764–77, February 2010.

  15. R.H.Y. Louie, Y. Li and B. Vucetic, “Zero forcing in general two-hop relay networks”, IEEE Transactions on Vehicular Technology, vol. 59, no. 1, pp. 191–202, January 2010.

  16. R.H.Y. Louie, M.R. McKay, and I.B. Collings, “Maximum sum-rate of MIMO multiuser scheduling with linear receivers”, IEEE Transactions on Communications, vol. 57, no. 11, pp. 3500–10, November 2009.

  17. R.H.Y. Louie, M.R. McKay, and I.B. Collings, “New performance results for multiuser optimum combining in the presence of Rician fading”, IEEE Transactions on Communications, vol. 57, no. 8, pp. 2348–58, 2009.

  18. R.H.Y. Louie, Y. Li, H. Suraweera and B. Vucetic, “Performance analysis of beamforming in two hop amplify and forward relay networks with antenna correlation”, IEEE Transactions on Wireless Communications, vol. 8, no. 6, pp. 3132–41, 2009.

  19. H. Suraweera , R.H.Y. Louie, Y. Li, George K. Karagiannidis, and B. Vucetic, “Two hop amplify-and-forward transmission in mixed Rayleigh and Rician channels”, IEEE Communications Letters, vol. 13, no. 4, pp. 227–29, 2009.

  20. R.H.Y. Louie, M.R. McKay, and I.B. Collings, “Impact of correlation on the capacity of multiple access and broadcast channels with MIMO-MRC”, IEEE Transactions on Wireless Communications, vol. 7, no. 6, pp. 2397–2407, 2008.

 

Media Coverage

Media coverage includes (see http://www.mckayspcb.com/news/ for a complete list of >20 media articles)

  • SCMP - Breakthrough HKUST-led research on mapping of HIV weak spots paves way for vaccine
    • http://www.scmp.com/news/hong-kong/health-environment/article/2132436/breakthrough-hkust-led-research-mapping-hiv-weak
  • RTHK - Hong Kong Today (Big data analysis helping in development of HIV vaccine)
    • http://news.rthk.hk/rthk/en/news-programmes/this-episode.htm?cmsid=77&episode_id=485231&livetime=20180208063000
  • Eurekalert – Big data methods learn the fitness landscape of the HIV envelope protein
    • https://eurekalert.org/pub_releases/2018-02/hkuo-bdm020618.php

My Teaching

  • ELEC2100H Honors – Signals and Systems (HKUST)
    • Fall 2015, 2016, 2017 (full course)
  • ELEC5450 – Random Matrix Theory and Applications (HKUST)
    • 8/3/2017, 15/3/2017, 16/3/2018 (guest lecturer)
  • BIEN5040 – Introduction to Bioengineering Research (HKUST)
    • 23/9/2015, 30/9/2015, 7/10/2016 (guest lecturer)
  • ELEC2600 - Probability and Random Processes in Engineering (HKUST)
    • Fall 2014 (full course)
    • 8/11/2013 (guest lecturer)
  • ELEC5507 – Error Control Coding (University of Sydney)
    • 2010-2012 (full course)
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