MPhil / PhD Student / PostDoc Recruitment (*self-financing MPhil/PhD is particularly welcomed and prioritized) forData 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.Biography
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:
- Average IQ: 108, according to Richard Lynn and Tatu Vanhanen .
- Human Deveopment Index (HDI) is 0.933 according to the United Nations in 2017.
- Students are consistently ranked among the top 3 with Finland and Shanghai according to the Programme for International Student Assessment (PISA) in 2012.
- The official language of teaching in universities is English, while Cantonese and British English are commonly used outside schools. It is pretty sure that students will find their studies challenging and enjoyable there.
- Drone Video About Hong Kong:
Research Interests
- Computational Biology & Bioinformatics
- Data Mining & Machine Learning
- Natural Computing
- Computational Science
- Quantitative & Interdisciplinary Research
Selected Publications
(More than 70 IEEE Transaction / ACM Transaction / Computing-specific Papers may NOT be listed and can be found in DBLP)
(*corresponding authorship, #co-first authorship)
[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)
[J32] 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=16.8] 2020
[J31] 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] 2020
[J30] 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
[J29] 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
[J28] Shankai Yan, Ka-Chun Wong* Context awareness and embedding for biomedical event extraction Bioinformatics 2020
[J27] Ka-Chun Wong*, Junyi Chen, Jiao Zhang, Jiecong Lin, Shankai Yan, Shxiong Zhang, Xiangtao Li et al. Early Cancer Detection from Multianalyte Blood Test Results. iScience 15 (2019): 332-341
[J26] Ka-Chun Wong*, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam Kwong, Cheng Liang DNA Sequencing Technologies: Sequencing Data Protocols and Bioinformatics Tools ACM Computing Surveys (CSUR) 2019
[J25] Ka-Chun Wong*, Jiecong Lin, Xiangtao Li, Qiuzhen Lin, Cheng Liang, YQ Song Heterodimeric DNA Motif Synthesis and Validations Nucleic Acids Research 2019
[J24] Xiangtao Li, Shixiong Zhang, Ka-Chun Wong* Single-cell RNA-seq Interpretations using Evolutionary Multiobjective Ensemble Pruning
Bioinformatics 2019
[J23] Shixiong Zhang, Xiangtao Li, Qiuzhen Lin, Ka-Chun Wong* Synergizing CRISPR/Cas9 Off-Target Predictions for Ensemble Insights and Practical Applications Bioinformatics 2019
[J22] Ka-Chun Wong* DNA Motif Recognition Modeling from Protein Sequences iScience 2018
[J21] Jiecong Lin, Ka-Chun Wong* Off-target predictions in CRISPR-Cas9 gene editing using deep learning (ECCB 2018) Bioinformatics 2018
[J20] Xiangtao Li, Ka-Chun Wong* Evolutionary Multiobjective Clustering and Its Applications to Patient Stratification IEEE Transactions on Cybernetics 2018
[J19] Ka-Chun Wong* MotifHyades: Expectation Maximization for de novo DNA Motif Pair Discovery on Paired Sequences Bioinformatics 2017
[J18] Jiao Zhang, Sam Kwong, Yuheng Jia, Ka-Chun Wong*: NSSRF: global network similarity search with subgraph signatures and its applications. Bioinformatics 2017
[J17] Ka-Chun Wong*, Yue Li, Chengbin Peng: Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. Bioinformatics 2016, 32(3): 321-324
[J16] Ka-Chun Wong*, Yue Li, Chengbin Peng, Alan M Moses, Zhaolei Zhang*: Computational Learning on Specificity-Determining Residue-Nucleotide Interactions. Nucleic Acids Research 2015, 43 (21): 10180-10189
[J15]
Ka-Chun
Wong,
Yue
Li,
Chengbin
Peng,
Zhaolei
Zhang*:
SignalSpider:
Probabilistic
Pattern
Discovery
on
Multiple
Normalized
ChIP-Seq
Signal
Profiles.
Bioinformatics
2015,
31
(1):
17-24
Supplementary
Data
Website
Link
[J14]
Graham
Cromar,
Ka-Chun
Wong,
Noeleen
Loughran,
Tuan
On,
Hongyan
Song,
Xuejian
Xiong,
Zhaolei
Zhang,
John
Parkinson.
New
tricks
for
olddomains:
How
novel
architectures
and
promiscuous
hubs
contributed
to
the
organization
and
evolution
of
the
ECM.
Genome
Biology
and
Evolution
2014,
Vol.
6
2897-2917
[J13]
Yue
Li#*,
Liang
Cheng#,
Ka-Chun
Wong,
Jiawei
Luo,
Zhaolei
Zhang*:
Mirsynergy:
detecting
synergistic
miRNA
regulatory
modules
by
overlapping
neighbourhood
expansion.
Bioinformatics
2014,
30
(18):
2627-2635
[J12]
Ka-Chun
Wong*,
Chengbin
Peng,
Yue
Li,
Tak-Ming
Chan:
Herd
Clustering:
A
synergistic
data
clustering
approach
using
collective
intelligence.
[J11]
Yue
Li,
Liang
Cheng,
Ka-Chun
Wong,
Ke
Jin,
Zhaolei
Zhang*:
Inferring
probabilistic
miRNA-mRNA
interaction
signatures
in
cancers:
a
role-switch
approach.
[J10]
Ka-Chun
Wong,
Zhaolei
Zhang*:
SNPdryad:
Predicting
Deleterious
Non-synonymous
human
SNPs
Using
Only
Orthologous
Protein
Sequences.
[J9]
Yue
Li*,
Anna
Goldenberg,
Ka-Chun
Wong,
Zhaolei
Zhang*:
A
probabilistic
approach
to
explore
human
miRNA
targetome
by
integrating
miRNA-overexpression
data
and
sequence
information.
[J8]
Ka-Chun
Wong,
Tak-Ming
Chan,
Chengbin
Peng,
Yue
Li,
Zhaolei
Zhang*:
DNA
Motif
Elucidation
using
Belief
Propagation.
[J7]
Ming
Fan,
Ka-Chun
Wong,
Taewoo
Ryu,
Timothy
Ravasi,
Xin
Gao*:
SECOM:
A
Novel
Hash
Seed
and
Community
Detection
Based-Approach
for
Genome-Scale
Protein
Domain
Identification.
[J6]
Chengbin
Peng,
Xiaogang
Jin,
Ka-Chun
Wong,
Meixia
Shi,
Pietro
Lio*:
Collective
Human
Mobility
Pattern
from
Taxi
Trips
in
Urban
Area.
[J5]
Ka-Chun
Wong*,
Chun-Ho
Wu,
Ricky
K.P.
Mok,
Chengbin
Peng,
Zhaolei
Zhang:
Evolutionary
multimodal
optimization
using
the
principle
of
locality.
[J4]
Y.Leung*,
M.H.Wong,
K.C.Wong,
W.Zhang,
K.S.Leung:
A
Novel
Web-based
System
for
Tropical
Cyclone
Analysis
and
Prediction.
[J3]
Tak-Ming
Chan*,
Ka-Chun
Wong,
Kin-Hong
Lee,
Man-Hon
Wong,
Chi-Kong
Lau,
Stephen
K.
W.
Tsui,
Kwong-Sak
Leung:
Discovering
approximate-associated
sequence
patterns
for
protein-DNA
interactions.
[J2]
Ka-Chun
Wong*,
Chengbin
Peng,
Man-Hon
Wong,
Kwong-Sak
Leung:
Generalizing
and
learning
protein-DNA
binding
sequence
representations
by
an
evolutionary
algorithm.
[J1]
Kwong-Sak
Leung,
Ka-Chun
Wong*,
Tak-Ming
Chan,
Man-Hon
Wong,
Kin-Hong
Lee,
Chi-Kong
Lau,
and
Stephen
K.
W.
Tsui:
Discovering
proteinDNA
binding
sequence
patterns
using
association
rule
mining
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
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
BioData Mining (2016-now) Computer Modeling in Engineering and Sciences (2019-now)
Journal Editorial Board Memberships
Applied Soft Computing (2016-now) Journal of Biomedical Informatics (2021-now) PeerJ Computer Science (2020-now) Artificial Intelligence Research (2015-now) Big Data Analytics (2015-now, BioMedCentral) Soft Computing (Guest Editorship, ISCMI 2016 Special Issue) Neural Computing and Applications (Guest Editorship, ISMSI/ISCMI 2017 Special Issue) Neural Computing and Applications (Guest Editorship, ISMSI/ISCMI 2018 Special Issue) Neural Computing and Applications (Guest Editorship, ISMSI/ISCMI 2019 Special Issue)
Conference Chairships
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) (3 keynote speeches from Hong Kong, Sinagpore, and Switzerland; 35 accepted papers for oral presentations from China, Germany, Hong Kong, India, Indonesia, Italy, Japan, Korea, South Africa, Singapore, Slovenia, Switzerland, Taiwan, and Thailand) 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)
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 Services (Sorted by Alphabet)
Advanced Science Aging Algorithms Algorithms for Molecular Biology Analytical Chemistry Annals of Translational Medicine Applied Soft Computing Artificial Intelligence Review Bioinformatics Bioinformatics and Biology Insights Biomedical Engineering and Computational Biology Biomedical Informatics Insights Biotechnology and Bioengineering BMC Bioinformatics BMC Genomics BioSystems Briefing in Bioinformatics Cancer Informatics Cell Regeneration Complex & Intelligent Systems Computational and Structural Biotechnology Journal Computational Biology and Chemistry Computer Modeling in Engineering & Sciences Computers Cybernetics and Systems Data eLife Energies Engineering Applications of Artificial Intelligence Engineering Computations Entropy Evolutionary Bioinformatics Evolutionary Computation Expert Systems With Applications Frontiers Gene Expression to Genetical Genomics Genomics Genomics, Proteomics & Bioinformatics Genomics Insights IEEE Access IEEE Journal of Biomedical and Health Informatics IEEE Transactions on Big Data 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 iScience 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 Metabolites Methods Microarrays NAR Cancer NAR Genomics and Bioinformatics Natural Computing Nature Communications Nature Methods Neural Computing and Applications Neural Processing Letters Nucleic Acids Research Oncogene Patterns PLoS Computational Biology PLoS Genetics PLoS ONE RNA Science Bulletin Scientific Reports Statistical Analysis and Data Mining Symmetry The Computer Journal Trends in Genetics
Funding Proposal Review: (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) 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)
