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Academic Staff

Professor HO, Joshua Wing Kei 何永基

Professor HO, Joshua Wing Kei 何永基

  • BSc (Hon), PhD (Sydney)
  • Associate Professor
L4-44, Laboratory Block, 21 Sassoon Road, Hong Kong
+852 3917 9512
+852 2855 9730
  • Bioinformatics
  • Single cell analytics
  • Gut microbiome metagenomics
  • Artificial intelligence and IoT in medicine
  • Digital health

Professor Ho is an Associate Professor in the School of Biomedical Sciences at the University of Hong Kong (HKU). He completed his BSc (Hon 1, Medal) and PhD in Bioinformatics from the University of Sydney, and undertook postdoctoral training in at Harvard Medical School. He is an expert in developing scalable computational methods to analyse single cell omic data, metagenomic data, and digital health data. Professor Ho has over 139 publications, including first or senior papers in leading journals such as Nature, Nature Communications, Genome Biology, Nucleic Acids Research and Cell Systems. Professor Ho is also currently the Programme Co-Director of BSc (Bioinformatics), Deputy Director of EdTech (AI), Academic Lead of the Bioinformatics Core of the Centre for PanorOmic Sciences (CPOS) at HKU, and Lead Scientist of Laboratory Data Discovery for Health. He is an Executive Editor of the journal Biophysical Reviews. He co-founded a digital health company Vitome Limited.

The Ho Laboratory focuses on the use of bioinformatics and systems biology approaches to tackle longstanding problems in basic and translational medicine. A range of specific research projects can be developed within the broad theme of scalable big data analytics for healthcare translation. Here are some major research themes. Multiple projects are available under each theme:

  • Scalable single cell data analytics. Single-cell RNA sequencing (scRNA-Seq) enables researchers to study heterogeneity among tens of thousands of individual cells and define cell types from a transcriptomic perspective. However, fast and reliable analysis of these large and noisy data requires new statistical and computational considerations. In this project we will develop scalable bioinformatics methods to analyze a range of scRNA-seq data to answer important biological questions.
  • Microbiome functional systems biology through metagenomic and multi-omic data analysis. Our laboratory is developing computational and statistical tools that can efficient process large metagenomic data, and integrate them with other omics or deep phenotyping data. Our goal is to understand how the microbiome found in specific location of the body, e.g., the gut, can affect a person's health.
  • Medical artificial intelligence, mobile health and wearable devices. Being able to track the changes of a person's physiological parameters in real time is now increasingly feasible due to the wide availability of consumer-grade smartphones and wearable devices (e.g., fitbit, AppleWatch, etc). Our group is developing new big data machine-learning algorithms extract, de-noise, analyze and correlate physical activity data and heart rate dynamics. Our long-term goal is to establish new non-invasive screening tools to monitor a person's health status.
  1. Wai AKC^, Yip TF^, Wong YH, Chu CK, Lee TTL, Yu KHO, So KWL, Wong JYH, Wong CKH, Ho JWK^, Rainer TH^ (2024) The Effect of COVID-19 Pandemic on Non-COVID-19 Death in Hong Kong: A Population-Wide Retrospective Cohort Study. JMIR Public Health and Surveillance, accepted 
  2. Chen J, Yin D, Wong HYH, Duan X, Yu KHO^, Ho JWK^ (2024) Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data. GigaScience, 13, giad117 
  3. Zheng W, Fong JHC, Wan YK, Chu AHY, Huang Y, Wong ASL, Ho JWK (2023) Discovery of regulatory motifs in 5′ untranslated regions using interpretable multi-task learning models. Cell Systems, 14(12), P1103-1112.E6 
  4. Lin X, Chau C, Ma K, Huang Y^, Ho JWK^ (2023) DCATS: differential composition analysis for flexible single-cell experimental designs. Genome Biology, 24, 151
  5. Wang L, Yao H, Morgan DC, Lau KS, Leung SY, Ho JWK, Leung WK (2023) Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori. Nature Communications, 14, 2196
  6. Virwani PD*, Qian G*, Hsu MSS, Pijarnvanit TKKTS, Cheung CNM , Chow YH, Tang LK, Tse YH, Xian JW, Lam SSW, Lee CPI, Lo CCW, Liu RKC, Ho TL, Chow BY, Leung KS, Tsang HW, Lo EKK, Tung KTS, Chung SK, Yuen MF, Leung SY, Ip P, Hung IFN, Louie JCY, El-Nezami H, Ho JWK^, Lau KK^ (2023) Sex Differences in Association Between Gut Microbiome and Essential Hypertension Based on Ambulatory Blood Pressure Monitoring. Hypertension, 80, 1331–1342
  7. Kwok AWC, Qiao C, Huang R, Sham MH, Ho JWK^, Huang ^ (2022) MQuad enables clonal substrcuture discovery using single cell mitochondrial variants. Nature Communications, 13, 1205
  8. Zhou L*, Yu KHO*, Wong TL*, Zhang Z, Chan CH, Loon JHC, Che N, Yu HJ, Tan KV, Tong M, Ngan ES, Ho JWK^, Ma SKY^ (2022) Lineage tracing and single-cell analysis reveal proliferative Prom1+ tumour-propagating cells and their dynamic cellular transition during liver cancer progression. Gut, 71, 1656-1668 
  9. Wong JYH, Luk LYF, Yip TF, Lee TTL, Wai AKC^, Ho JWK^ (2022) Incidence of Emergency Department Visits for Sexual Abuse Among Youth in Hong Kong Before and During the COVID-19 Pandemic. JAMA Network Open, 5(10), e2236278
  10. Stassen SV, Yip GGK, Wong KKY, Ho JWK, Tsia KK (2021) Generalized and scalable trajectory inference in single-cell omics data with VIA. Nature Communications, 12, 5538

As PI:

  • GRF 2023-2026
  • Guangdong Natural Science Fund General Programme 2023-2025
  • Shenzhen-HK-Macau Science and Technology Programme (Type C) 2022-2024
  • Australia NHMRC Career Development Fellowship 2016-2018
  • Australia National Heart Foundation Future Leader Fellowship 2016-2018
  • Ramaciotti Establishment Grant 2015

As Co-PI:

  • AIR@InnoHK (Laboratory of Data Discovery for Health) 2020-2025
  • CRF 2019-2022
  • Human Frontier Science Program (HFSP) Young Investigator Grant 2014-2017
  • Illumina Early Career Researcher Award, Australian Epigenetics Alliance (2015)
  • NSW Ministerial Award for Rising Stars in Cardiovascular Research (2015)
  • Young Tall Poppy Science Award, Australian Institute of Policy and Science (2016)
  • Research Output Prize, Li Ka Shing Faculty of Medicine, The University of Hong Kong (2022)
  • Faculty Teaching Medal, Li Ka Shing Faculty of Medicine, The University of Hong Kong (2023)

Last updated: 2024-02-09