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PhD Student / PostDoc Recruitment (*self-financing MPhil/PhD is particularly welcomed and prioritized) for
Data Science and Bioinformatics

@ City University of Hong Kong (We are recruiting NOW !!!)
(PhD admission deadline: December every year) Please put down "Ka-Chun Wong" as your potential supervisor in your applications; otherwise, your applications may not reach us. More than 2000 USD can be provided to each fully funded PhD student in Hong Kong every month. Very Top PhD or even PostDoc applicants are encouraged to apply for the Hong Kong PhD Fellowship Scheme which will give at least 3000 USD per month for at least 3 years.


Ka-Chun was born and raised in Hong Kong where he was lucky enough to be immersed in a multi-cultural environment. He received his B.Eng. in Computer Engineering from United College, The Chinese University of Hong Kong in 2008. He has also obtained his M.Phil. degree in the Department of Computer Science and Engineering at the same university in 2010. From 2011 to 2014, he has spent 3.5 years to finish his PhD degree in the Department of Computer Science at the University of Toronto. With exposures to different aspects (academic, industrial, spiritual ,and social), he hopes to strike a balance and contribute to the society.

News: Right after his PhD study, Ka-Chun has started his research lab (web page) in the Department of Computer Science, City University of Hong Kong (4th in QS World University Ranking aged under 50 and 5th in Times University Ranking aged under 50) in 2019/2020. Interested applicants can contact him via email. Especially, PhD applicants are highly encouraged to apply for the Hong Kong PhD Fellowship Scheme (USD$ 3200 per month (tax free)). The scheme is real merit-based and does not have any preference toward nationality, which reflects the open humanity and freedom of Hong Kong. Here are some facts about Hong Kong:

Research Interests

  • Bioinformatics
  • Data Science
  • Artificial Intelligence
  • Natural Computing
  • Computational Science
  • High-Impact Interdisciplinary Research

Publication Highlights since 2020

(More than 100 IEEE Transaction / ACM Transaction / Computing-specific Papers may NOT be listed and can be found in DBLP or Google Scholar

(*(co-)corresponding authorship, #co-first authorship)

Zetian Zheng, Junyi Chen, Xingjian Chen, Lei Huang, Weidun Xie, Qiuzhen Lin, Xiangtao Li*, Ka-Chun Wong* Enabling Single-cell Drug Response Annotations from Bulk RNA-seq using SCAD. Advanced Science (IF=17.5) 2023
Zhuohan Yu, Yanchi Su, Yifu Lu, Yuning Yang, Fuzhou Wang, Shixiong Zhang, Yi Chang, Ka-Chun Wong*, Xiangtao Li* Topological Identification and Interpretation for High-throughput Single-cell Gene Regulation Elucidation across Multiple Platforms using scMGCA. Nature Communications (IF=17.7) 2023
Xingjian Chen, Zifan Zhu, Weitong Zhang, Yuchen Wang, Fuzhou Wang, Jianyi Yang, Ka-Chun Wong*. "Human disease prediction from microbiome data by multiple feature fusion and deep learning." iScience (Cell Press) 25, no. 4 (2022): 104081.
Rahaman, Saifur, Xiangtao Li, Jun Yu, Ka-Chun Wong*. "CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA." Bioinformatics 37, no. 19 (2021): 3319-3327.
Junyi Chen, Ka-Chun Wong* RNCE: Network Integration with Reciprocal Neighbors Contextual Encoding for Multimodal Drug Community Study on Cancer Targets Briefings in Bioinformatics [IF=11.6] 2021
Jiecong Lin, Zhaolei Zhang, Shixiong Zhang, Junyi Chen, Ka-Chun Wong* CRISPR‐Net: A Recurrent Convolutional Network Quantifies CRISPR Off‐Target Activities with Mismatches and Indels Advanced Science [IF=17.5] 2020
Shixiong Zhang, Xiangtao Li, Qiuzhen Lin, Jiecong Lin, Ka-Chun Wong* Uncovering the Key Dimensions of High-Throughput Biomolecular Data using Deep Learning Nucleic Acids Research [IF=17.0] 2020
Shixiong Zhang, Xiangtao Li, Qiuzhen Lin, Ka-Chun Wong* Nature-Inspired Compressed Sensing for Transcriptomic Profiling from Random Composite Measurements IEEE Transactions on Cybernetics [IF=11.4] 2020

Edited Books

[Book 4] Ka-Chun, Wong. Epistasis: Methods and Protocols. [Content: 23 Peer-Reviewed Book Chapters with 46 authors from Australia, Brazil, Canada, China, Denmark, Germany, Hong Kong SAR, India, Netherlands, Singapore, Spain, USA] Methods in Molecular Biology series (Springer, New York). 2020
[Book 3] Xiangtao Li, Ka-Chun Wong: Natural Computing for Unsupervised Learning., Book Series under Unsupervised and Semi-Supervised Learning, Springer (New York) 2019
[Book 2] Ka-Chun Wong: Big Data Analytics in Genomics. Springer (New York) 2017 (Content: 13 Peer-Reviewed Book Chapters with 46 Authors from Argentina, Brazil, China, France, Germany, Hong Kong, India, Japan, Spain, USA)
[Book 1] Ka-Chun Wong: Computational Biology and Bioinformatics: Gene Regulation. CRC Press (Taylor & Francis Group) 2016 (Content: 17 Peer-Reviewed Book Chapters with 52 Authors from Australia, Belgium, Brazil, Egypt, Germany, Hong Kong, India, Japan, USA)

Teaching Course Leaderships

In Hong Kong,
CS8695 : Research in Computer Science (Seasonal)
CS4465 : Computational Biology and Bioinformatics (Spring 2015-now)
CS4480 : Data-Intensive Computing (Fall 2018-now)
CS5488 : Big Data Algorithms and Techniques (Fall 2018-now)
GE1319 : Interdisciplinary Research for Smart Professionals (Seasonal)
GE2324 : The Art and Science of Data (Fall 2015-2017)

Teaching Assistantships

In Toronto,
CSC108 : Introduction to Computer Programming (Fall 2011)
CSC209 : Software Tools and Systems Programming (Summer 2013)
CSC263 : Data Structures and Analysis (Spring 2012)
CSC309 : Programming on the Web (Spring 2014, Summer 2014)
CSC343 : Introduction to Databases (Fall 2012, Spring 2013, Fall 2013)
CSC401/2511 : Natural Language Computing (Spring 2013)
In Hong Kong,
CSC3420 : Computer System Architectures (Spring 2009, Spring 2010)

Awards / Achievements

2023 Elected Governor (APNNS)
2022 Stanford's top 2% most highly cited scientists 2022 Nov
2021 CMES Reviewer Award 2020 (2 Awards in 2020)
2020 Health and Medical Research Fund, Hong Kong (First CS Faculty Ever in History to be Awarded)
2019 Outstanding Supervisor Award, City University of Hong Kong (24 awards in 2019)
2019 ACM Distinguished Speaker Program (2019-2022)
2018 General Research Fund, Research Grant Council (Hong Kong, 57 out of 175 CS professors)
2017 General Research Fund, Research Grant Council (Hong Kong, 56 out of 188 CS professors)
2016 Early Career Scheme, Research Grant Council (Hong Kong, largest ECS grant in CS area)
2015 Assistant Professorship without any Posdoc Placement, City University of Hong Kong
2013 Acres - Joseph Yonan Memorial Fellowship, Computer Science, University of Toronto
2012 Kwok Sau Po Scholarship, School of Graduate Studies, University of Toronto
2012 Acres - Joseph Yonan Memorial Fellowship, Computer Science, University of Toronto
2011-2014 International Research and Teaching Assistantship, University of Toronto
2010 Provost Award. Office of the Provost, KAUST
2007 Dean List, Engineeirng, The Chinese University of Hong Kong
2007 Chiu Fuk San Prize, United College, The Chinese University of Hong Kong
2005 Multiple Scholarships for HK A-level, Concordia Lutheran School
2004 Championship, Computer Game Concept Competition, Sha Tin IVE
2003 Multiple Scholarships for HKCEE, Concordia Lutheran School

Recent Open Software Contributions

MotifHyades FullSignalRanker SignalSpider SNPdryad kmerHMM LatticeModel

Journal Associate Editorship (Sorted by Date)

Computational and Structural Biotechnology Journal (2023-now)
Heliyon [Cell Press] (2023-now)
Frontiers in Genetics (2021-now)
Computer Modeling in Engineering and Sciences (2019-now)
BioData Mining (2016-now)

Journal Editorial Board Memberships (Sorted by Date)

International Journal of Data Science and Analytics (2021-now)
Journal of Biomedical Informatics (2021-now)
PeerJ Computer Science (2020-now)
Applied Soft Computing (2016-now)

Conference Chairships (Sorted by Date)

DSIT 2022 (Publication Co-Chair)
ISCMI 2022 (Publicity Co-Chair)
ISMSI 2022 (Organizing Co-Chair)
ICONIP 2021 (Session Chair)
WSPML 2021 (Conference Co-Chair)
IEEE ICCCS 2021 (Session Chair)
DSIT 2021 (Publication Co-Chair)
ISMSI 2021 (Organizing Co-Chair)
ISCMI 2021 (Publicity Co-Chair)
ICCR 2020 (Session Chair)
DSIT 2020 (Publication Co-Chair)
ICONIP 2020 (Publicity Co-Chair)
ICONIP 2020 (Session Chair)
ISCMI 2020 (Program Co-Chair)
ISMSI 2020 (Program Co-Chair)
DSIT 2019 (Publication Co-Chair)
ISCMI 2019 (Program Co-Chair)
ISMSI 2019 (Publicity Co-Chair)
ISNN 2019 (Registration Co-Chair)
DSIT 2018 (Publication Co-Chair)
ICIST 2018 (Registration Co-Chair)
ICONIP 2018 (Registration Co-Chair)
ISCBI 2018 (Program Co-Chair)
ISCMI 2018 (Publication Co-Chair)
ISMSI 2018 (Program Co-Chair)
ISNN 2018 (Registration Co-Chair)
ICIST 2017 (Registration Co-Chair)
ISCBI 2017 (Program Co-Chair)
ISCMI 2017 (Program Co-Chair)
ISMSI 2017 (Organizing Chair)
ISNN 2017 (Registration Co-Chair)
ICICIP 2016 (Regisration Co-Chair)
ISCBI 2016 (Publication Co-Chair)
ISCMI 2016 (Program Co-Chair)
ISCBI 2015 (Publication Co-Chair)
IEEE SMC 2015 (Session Chair)

Conference Invited Talks (Sorted by Date)

DSIT 2023 (Keynote Speech)
ISMSI 2023 (Keynote Speech)
ICBRA 2022 (Invited Speech)
HKU 2022 (Invited Seminar)
APSCIT 2021 (Keynote Speech)
Lingnan University 2021 (Invited Seminar)
APNNS/IEEE-CIS Education Forum Series: DLAI5 Summer School 2021 (Invited Speech)
ICBBB 2021 (Invited Speech)
IEEE BigData 2020 (Tutorial 1)
HSE Summer School on Machine Learning in Bioinformatics 2020 (Invited Lecture)
BDE 2020 (Invited Speech)

DSIT 2019 (Plenary Speech)
IC-LYCS 2019 (Keynote Speech)
ISACIT 2018 (Keynote Speech)
IWSG 2018 (Invited Speech)
HKU & ND Workshop 2018 (Invited Speech)
ICBCB 2017 (Plenary Speech)
HKU NGS Workshop 2016 (Invited Speech)

Review Service (Sorted by Alphabet)

ACS Nano
Advanced Science
Algorithms for Molecular Biology
Analytical Chemistry
Annals of Translational Medicine
Applied Artificial Intelligence
Applied Soft Computing
Artificial Intelligence Review
Artificial Intelligence in Medicine
Bioinformatics and Biology Insights
Biomedical Engineering and Computational Biology
Biomedical Informatics Insights
Biomedical Signal Processing and Control
Biotechnology and Bioengineering
BMC Bioinformatics
BMC Biology
BMC Genomics
BMC Medical Informatics and Decision Making
Briefing in Bioinformatics
British Journal of Cancer
Cancer Informatics
Cell Regeneration
Cell Reports Methods
Complex & Intelligent Systems
Computational and Structural Biotechnology Journal
Computational Biology and Chemistry
Computer Modeling in Engineering & Sciences
Computer Systems Science and Engineering
Connection Science
Cybernetics and Systems
Engineering Applications of Artificial Intelligence
Engineering Computations
Evolutionary Bioinformatics
Evolutionary Computation
Expert Systems With Applications
Gene Expression to Genetical Genomics
Genome Medicine
Genomics, Proteomics & Bioinformatics
Genomics Insights
IEEE Access
IEEE Journal of Biomedical and Health Informatics
IEEE Transactions on Big Data
IEEE Transactions on Computational Social Systems
IEEE Transactions on Cybernetics
IEEE Transactions on Emerging Topics in Computing
IEEE Transactions on Evolutionary Computation
IEEE Transactions on Fuzzy Systems
IEEE Transactions on Industrial Informatics
IEEE Transactions on Knowledge and Data Engineering
IEEE Transactions on NanoBioScience
IEEE Transactions on Neural Networks and Learning Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics
International Journal of Data Science and Analytics
International Journal of Geographical Information Science
International Journal of Machine Learning and Cybernetics
International Journal of Molecular Sciences
Journal of Bioinformatics and Computational Biology
Journal of Biomedical Informatics
Journal of Computers in Education
Journal of Genomes and Exomes
Journal of Personalized Medicine
Knowledge and Information Systems
Mathematical Biosciences and Engineering
NAR Cancer
NAR Genomics and Bioinformatics
Natural Computing
Nature Communications
Nature Computational Science
Nature Methods
Neural Computing and Applications
Neural Processing Letters
Nucleic Acids Research
Physical Communications
PLoS Computational Biology
PLoS Genetics
Science Bulletin
Scientific Reports
Statistical Analysis and Data Mining
The Computer Journal
Technology in Cancer Research & Treatment
Trends in Genetics

Funding Proposal Review Service (Sorted by Alphabet)

Canada (Natural Sciences and Engineering Research Council, NSERC)
Germany (Deutsche Forschungsgemeinschaft, DFG)
Hong Kong SAR (Universities and Government)
India (The Wellcome Trust/DBT India Alliance)
Israel (U.S.-Israel Binational Science Foundation)
Mainland China (National Natural Science Foundation of China, NSFC)
Poland (Narodowe Centrum Nauki, NCN)
Qatar (Qatar National Research Fund, QNRF)
UK (Biotechnology and Biological Sciences Research Council, BBSRC)
USA (U.S.-Israel Binational Science Foundation)

External Examiner Service (Sorted by Alphabet)

Australia (UNSW)
Canada (UWaterloo)
Hong Kong SAR (CUHK, HKU)
Mainland China (CUHK(SZ))