East Asian Bioinformatics and Computational Biology (Hong Kong)
東亞洲生物信息研究 (香港)

Department of Computer Science, City University of Hong Kong

Genome Informatics, Applied Machine Learning, Applied Data Mining, Computational Intelligence, and Natural Computing

Hong Kong, 香港, East Asian, Big Data Analytics, Probabilistic Graphical Models, Bayesian Networks, Factor Graphs, Hidden Markov Models, Asian, Asia, SNPs, Statistical Inference, Statistical Tests, Gene Regulation, Next Generation Sequencing, ChIP-seq, RNA-seq, Hi-C, Cancer Informatics, DNA Motifs, Transcription Factors, Transcription Factor Binding Sites, Protein-DNA Binding Interactions, Differential Evolution, Genetic Algorithm, Evolutioinary Computation, Feature Selection, Classification, Clustering, Optimization, Random Forest, Support Vectro Machine (SVM), Ensemble Learning, Association Rule Mining, Deep Learning, Artificial Neural Networks, Artificial Intelligence, Rule-based Learning, Cloud Computing, and Parallel Computing.

Since 1990s, the whole genomes of different species have been sequenced by their corresponding genome sequencing projects. In 1995, the first free-living organism Haemophilus influenzae was sequenced by the Institute for Genomic Research. In 1996, the first eukaryotic genome (Saccharomyces cerevisiase) was completely sequenced. In 2000, the first plant genome, Arabidopsis thaliana, was also sequenced by Arabidopsis Genome Initiative. In 2006, the Human Genome Project (HGP) announced its completion. Following the HGP, the Encyclopedia of DNA Elements (ENCODE) project was started, revealing massive functional elements on the human genome in 2011. The drastically decreasing cost of sequencing also enables the 1000 Genomes Project and Roadmap Epigenomics Project to be carried out. Their results have been published in 2012 and 2015 respectively. Nonetheless, the massive genomic data generated by those projects impose an unforeseen challenge for massive data analysis. In our group, we aim at tackling the challenges by scalable machine learning and data mining methods, paving the foundation of personalized medical research in the near future.

Group Leader: Ka-Chun Wong (PhD Toronto)
[Email] [Official Profile] [Google Scholar] [Toronto Profile]

Group Members: (*co-supervision; sorted by position and then surname)

Group Alumni: (sorted by year)

Courses:

MSc / Interns (sorted by year and surname)

Final Year Projects (sorted by year and surname)

Recommended Applied Machine Learning / Data Mining Websites:
scikit-learn(Python) Weka(Java) RStudio(R) rOpenSci(R) UCI OpenAI TensorFlow

Recommended Computing Services:
CityU(CS) CityU(Sci&Eng) GroupServers(Email)

Recommended Self-Learning Websites:
Coursera Quora OpenStax QuoraShot1 QuoraForPhDstudents PhD Comics

Recommended Bioinformatics Websites:
ToolRegistry OMICtools Biostars SEQanswers Bioconductor

Recommended English Language / LaTeX / BibTex Support Services:
CityU(ELSS) Pronounciation(Forvo) LaTeX WikiBook TeXstudio LyX TeXMed JabRef

*** PhD Student / PostDoc Recruitment ***

We always have self-financed/funded (i.e. with fully funded scholarships covering living costs and tuition fee) positions available for graduate students (PhD/Master) and postdoctorial scholars. Please send an email (with your CV and other supporting materials) to us if you are interested. Especially, PhD applicants are highly encouraged to apply for the Hong Kong PhD Fellowship Scheme (About USD$ 2600 per month (tax free)). If unsuccessful, your application will be considered for normal studentship (tax free). Please put down "Ka-Chun Wong" as your potential supervisor in your applications (i.e. please type "Ka-Chun Wong" in the question "If you have contact any CityU academic staff member, please provide his/her fullname." in the *Other Information* section in the CityU(HK) graduate school application system); otherwise, your applications may not reach us. (***Please click here to send an email to us***). More information can be found at Graduate School. You have to apply thorough the graduate school via this link. In the past 3 years (2015-2017), PhD offers have already been given to students from Hong Kong, Mainland China, Parkistan, India, Canada, France, and UK.

A suitable candidate should have ALL of the following good (not necessarily excellent) qualifications:

*** Intern Recruitment ***

For undergraduate students / interns, we have lesser requirement. Please send emails to us and apply through the following links: CSE Summer Exchange (for International Students) CityU CIS and CWS (for CityU Students)

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