Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: KWOH Chee Keong

 

Dr. Kwoh Chee Keong, PBM  

PhD, DIC, MSc(ISE), Beng(EE), PGDIG, Sr.MIES, M.ICAAS, M.AMBIS

 

AsC - Graduate Studies 

ACM - Service

PD MSc – Bioinformatics

 

School of Computing Science and Engineering

Block N4, Level 2, Section C, Room 73/74 Nanyang Avenue, Singapore 639798

Tel: (65) 6790 6057

Fax: (65) 6792 6559 |

Email: asckkwoh@ntu.edu.sg

Web: http://www.ntu.edu.sg/home/asckkwoh/

 

 

I think the nicest, most sincere compliments that I have received are those from my students and people I did not expect. 

Notes from Students and Friends

 

 HONORS AND AWARDS

National Day Awards

Public Service Medal (National Day Award)

National Day Awards 2008, The Public Service Medal (PBM) http://www.pmo.gov.sg/NationalHonoursandAwards/Pingat+Bakti+Masyarakat+(The+Public+Service+Medal).htm , conferred by the President of Singapore, Mr S R Nathan

 

Ministry of Education Long Service Medal (National Day Award) 2016

 

 

Other Awards (NTU)

Best Faculty Mentor Award form Temasek Foundation (TF) LEARN 2014

Best Faculty Mentor Award form Temasek Foundation (TF) LEARN 2013

 

OPPORTUNITY

I am looking for versatile, highly motivated Research Fellow/Pos-doc PhD candidates. The successful candidates will build on the ongoing research directed and will help define and explore this exciting area of research.

 

Applicants must have a strong background in Computer Science and/or closely related areas (e.g. Mathematics, Computer Science, Bioinformatics, Statistics and Physics) and excellent skills in both written and spoken English, as the working language of the Faculty is English.

 

 

For PhD application, please visit the Graduate Studies by Research at NTU before writing. Please note that Ph.D program is a very intensive program and applicant must have strong interest, strong analytical mind, technically sound in the area of data mining, learning theory, algorithms and computer programming. You must be highly independent with good initiatives and aspire to publish in top-tier journals. If you are interested and suitable,

 

Enquiries about these vacancies can be sent to asckkwoh@ntu.edu.sg (the deadlines are flexible) with with your CV, your proposed research area with at least 3 references (either your own publications or papers that inspired you to do research).

 

RESEARCH EXPERTISE

My main interests lie in our desire to making sense of big heterogeneous data for real application in engineering, life science, and medical.

Machine Learning and Statistical Inference

Machine Learning and statistical modeling techniques that can learn from data to enables the making of decision and simply classification, this has application in almost every area. There are many approaches and each has its own merits. The following have been heavily used in my group: support vector machines, decision tree learning, artificial neural networks, Bayesian networks, genetic and mimetic algorithms. Example include application in supertype-specific HLA Class I binding peptides, protein–ligand binding affinity.

Learning with Unlabeled Data

In the context of machine learning, PU learning is a collection of semi-supervised techniques for training binary classifiers on positive (P) and unlabeled (U) examples. To improve performance, it is important to partition U into four sets, namely, reliable negative set RN, likely positive set LP, likely negative set LN, and weak negative set WN. Such approach has been used to identifying disease genes from human genome is an important but challenging task in biomedical research.

Meta and Ensemble learning

Meta learning is where automatic learning algorithms are applied on meta-data about machine learning experiments. The main goal is to use meta-data to understand how automatic learning can become flexible in solving different kinds of learning problems and enrich the knowledge discovered. Coupled with ensemble methods that that integrates results of multiple predictive methods into one system, these approach has found to be instrumental in improve predictive performance. Application of this approach has been widely used in big data such as bioinformatics and medical informatics. Example includes multiple kernel learning for heterogeneous data fusion and sparse learning in genome wide association study (GWAS), and drug-target interaction prediction.

Ontology for Knowledge Representation

Ontology is a formal representation of a set of concepts within a domain and the relationships between those concepts. There have been major initiatives in medical and bioinformatics to standardize the representation of terminology and relationship across diseases, species and databases. The controlled vocabulary of terms and description of product characteristics are the main outcome to improve annotation for representation of meta concept that greatly enhance analysis. Specifically it has been extensively applied in complex mining, inferring gene-disease-phenotype association.

Computational Structural Biology

This is where Computational Science and Engineering finds its applications in understanding molecular structure of biological macromolecules. Dealing with computational models and simulations, the field makes use of high-performance computing to solve complex and expensive problems in biology. Result include the acceleration of docking and its application in understanding of influenza and other viruses.

SOFTWARE

CovalentDock Cloud: a web server for automated covalent docking

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online.

 

Software for Accelerating Autodock Vina

            Quickvina: This project aims at accelerating Autodock Vina, a program for protein-ligand docking. The main idea is to skip some of the local searches which is not promising in finding a better solution.

Quick Vina 2 is a fast and accurate molecular docking tool, attained at accurately accelerating AutoDock Vina. It was tested against 195 protein–ligand complexes that compose the core set of the 2014 release of the PDBbind using default exhaustiveness level of 8, QVina 2 successfully attained up to 20.49-fold acceleration over Vina.

Software for Learning with Unlabeled Data

1.      PUDI (2013) -  a Positive-Unalbeled (PU) learning based method aiming to address the problem of disease gene identification

Software – for complexes

1.      CACHET- Discovery of Protein Complexes with Core-Attachment Structures from TAP Data

2.      COACH- COre-AttaCHment based Complex Mining

 

Software – for Computational Structural Biology

1.      CovalentDock Cloud (2013) - This web server allows the researchers and scientists to perform protein-ligand covalent docking.

2.      CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constrains

3.      QuickVina: Accelerating AutoDock Vina Using Gradient-based Heuristics for Global Optimization

 

MY GRANTS

List of Research Grants

·         Computational Virulence Model with Functional Information for Influenza Viruses

·         Methodological Investigation for Automatic Detection of Primary Angle Closure Condition (PAC) and PAC induced Glaucoma

·         Bioinformatics Algorithms for Detecting Genetic and Epigenetic Determinants of Meiotic Recombination Hotspots from Genomic Data

·         Whole genome sequencing, single nucleotide polymorphisms, electron microscopy, Acinetobacter baumannii, lipopolysaccharide

·         Collaborative Research Programme On Bioinformatics Algorithms And Tools

·         Structural Analysis and Characterisation of Protein Complexes

·         Genomic analysis and development of a new multilocus variable-number tandem-repeat analysis - scheme for molecular epidemiological typing of Acinetobacter baumannii

·         Core-Attachment Based Mining For Protein Complexes & Small molecule

·         Interactions

·         Characterization of novel extracellular proteins produced by a newly-isolated strain of Bacillus subtillis.

·         Improved Design via Evolutionary Algorithms

·         Protein binding hotspots are water-free?

·         Analysis of Past DRG data for the study of LOS for better utilization of Hospital Resources

·         Data Warehousing and Data Mining Analysis on Staphylococcus Aureus

·         A novel approach for inter- to intra- network analysis of genetic diseases using high-throughput data

·         Neural Systems modeling with functional MRI

·         SCE incubator proposal for “Evolutionary and Complex Systems Lab”

·         The Application of ultrasound based augmented reality with the directional vacuum-assisted breast biopsy device in the treatment of breast cancer

·         Distributed Diagnosis and Home Healthcare (D2H2)

·         Development of a robotic semi-automated remote handling system for radioiodine dispensing

·         Functional MR Time-Series Analysis

·         Augmented Reality for Prosthesis Cup Placement

·         Robotic Skull Based Surgery

·         Cardiovascular and Respiratory Systems' Signal Simulation, Processing and Analysis for ICU, OR and Telemedicine Applications.

·         Strategic research: Interventive augmented reality for medical applications.

·         Surgeon Assistant Robot for Selected urological disorder.

 

MY GRADUATE STUDENTS

 

·         YIN RUI (PhD, 2016 -)

·         Aly Mohamed Alaa Eldin Aly Ezzat - Biological Network Mining and its application in healthcare (PhD, 2013-)

·         Tan Kuan Pern - N-body Statistical Force-Field for 3D Structure Modeling of Biomolecules (PhD, 2012 -)

·         Amr Ali Mokhtar Alhossary - Accelerating Drug Design Workflow (PhD, 2012 -)

·         Pan Hong – DNA methylation biomarkers of personal disease risk (PhD, 2012)

·         Luay Aswad - A molecular basis of the 5-gene breast tumor aggressiveness grading signature (AGS) and its network – PhD, (2012 -)

·         Han Xu - Constructing the Semantic Web for Biomedical Literature (PhD, 2011 - )

·         Ouyang Xuchang - Automated and Accelerated Covalent Docking and Covalent Virtual Screening (PhD, 2010–)

·         Thidathip Wongsurawat - Computational Analysis and Prediction of Specific Genomic Regions Forming R-loop Structure and Chromosomal Variations Associated with Cancer  - (PhD, 2015)

·         Zhang Zhou - Knowledge Discovery In Post Genome-Wide Association Study For Glaucoma (PhD, 2015)

·         Su Tran To Chinh - Improving the Discrimination of Near-Native Complexes for Protein Rigid Docking by Implementing Interfacial Water into Protein Interfaces (PhD, 2015)

·         Yang Peng - Computational Approaches for Disease Gene Identification (PhD, 2014)

·         Wu Min - Mining Protein Complexes From Protein Interaction Data (PhD, 2012)

·         Zhang Tianyou - Contact Network Based Framework For Infectious Disease Interventions (PhD, 2015)

·         Stephanus Daniel Handoko - Constrained-Oriented Refinement-Efficacious Memetic Algorithms for Efficient Optimization of Computationally-Expensive Problems (PhD, 2014)

·         Adrianto Wirawan - Whole-Genome Discovery Of Transcriptional Regulator Binding Sites (PhD, 2011)

·         Zhang Guanglan- Computational Epitope-Driven Vaccine Design (PhD, 2008)

·         Zheng Yun- Design Of Gene Expression Networks From Microarray Data (PhD, 2006)

·         Zhao Ying- Efficient Model And Feature Selection For SVM In Biomedical Data Analysis (M Eng, -2004)

·         Zhao Jianhui- Human Animation from Motion Recognition, Analysis and Optimisation ( PhD, 2003)

·         Chen Yintao - Image Processing For Ultrasound Guidance System In Breast Lump Operation (M Eng, 2002)

·         Wang Yan - Image-Based Indexing And Retrieval Of Trademark Logos, (M Eng, 2001)

·         Veena Mohan Bhajammanavar - Image Processing Of The Digital Mammogram For Segmentation And Characterization Of Microcalcifications, (M Eng, 2000)

·         Misra Sabita - Time Series Analysis Of ECG For Detection Of Premature Ventricular Contraction (M Eng, 2000)

·         Zou Qingsong - Object Based Volume Visualisation For Medical Imaging (PhD, 2001)

 

TEACHING

 

Planed and lectured subjects in

  1. CZ4032 Data Analytics and Mining (2014,15): Data Mining is an analytic process designed to explore big data in search of consistent patterns and/or systematic relationships between variables, and then to validate the findings by applying the algorithms to new data.
  2. CE7411 Bioinformatics (2015): This course covers basic bioinformatics concepts, databases, tools and applications. Introduction: cell biology's central dogma, biological technologies for collecting and storing genomic sequence data; databases that store these data and strategies to extract information from them; Pairwise sequence alignment for assessment of similarity to infer homology; Fundamental of Scoring matrices to understand the assigned scores when performing alignment; The popular heuristic search tool - Basic Local Alignment Search Tool (BLAST) and advanced database searching; Multiple sequence alignment and phylogenetic trees to complete the coverage from genomic sequences. Functional genomics with the introduction to gene expression. Processes for microarray data analysis; Feature selection and classification for microarray data analysis. Protein families & proteomics; Protein structure and structural genomics; and Molecular evolution and phylogeny.
  3. BI6123 Methods and Tools of Proteomics (2007): Proteomics study and identify protein structure, interactions of protein/protein and protein/DNA and biology of organisms. We will further introduce the newly developed technology for the quantitative analysis of protein expression and function on a genome-wide scale.
  4. BI1602 and SC448 Introductory Bioinformatics (2005,06): Basic bioinformatics concepts. Databases, tools and applications.
  5. BI1603 Computational Biology (2006) Introduce the applications of the techniques of computer science, applied mathematics, and statistics to address problems inspired by biology. Major computational techniques used in biology include: Bayes, HMM, MI etc.
  6. BG3011 Biocomputing (2005, 06): Introduction the new course of biocomputing for students in SCBE, the subject is first offered in July 2005; It covers Concepts; Bioinformatics databases; Sequence alignment; Phylogeny and protein structure prediction.
  7. BI6104 Biostatistics: First offered in July 2003, this course equipped the students in MSc with Knowledge of statistics, experimental design and statistical learning.
  8. Curriculum for MSc in Bioinformatics: From August 2001 to June 2002, I worked with Vice-Dean (Academic) SCE, Head, Natural Science of NIE, Vice-Dean (Academic) of SBS and Professor from MPE and EEE to structure the new MSc in Bioinformatics. 
  9. SC104 Mathematics I Fundamental of mathematics for Engineering include statistics and calculus
  10. CE307 Computer Peripherals: In 1996 ?2000, re-design the course to include start-of-the-art techniques such as PRML, USB and Bluetooth.
  11. M495 & M6524 Medical Assist Surgery (2000-2002): Co-planed and lectured the final year and MSc elective for Biomedical Engineering.
  12. Digital Signal Processing (1992): Planed and lectured the final year elective for the computer engineering.

 

MY PHD THESIS

GRADUATE ADVISORS:  Prof Duncan Fyfe Gillies - Professor of Biomedical Data Analysis, Department of Computing, Imperial College London

 

My PhD thesis Probabilistic Reasoning From Correlated Objective Data, University of London, Imperial College

 

PUBLICATIONS

Selected Journal Papers

 

2015

1.             Alhossary, A., S. D. Handoko, Y. Mu and C.-K. Kwoh (2015). "Fast, accurate, and reliable molecular docking with QuickVina 2." Bioinformatics: btv082. [PDF]

2.             Niwas, S. I., W. Lin, X. Bai, C. K. Kwoh, C. C. Sng, M. C. Aquino and P. Chew (2015). "Reliable Feature Selection for Automated Angle Closure Glaucoma Mechanism Detection." Journal of medical systems 39(3): 1-10.[URL]

3.             S Issac, N., W. Lin, C. Kwoh, M. Aquino, C. Sng and P. Chew (2015). "Cross-examination for Angle-Closure Glaucoma Feature Detection." IEEE Journal of Biomedical and Health Informatics. [PDF]

4.             Zhang, F., M. Wu, X. Li, X. Li, C. K. Kwoh and J. Zheng (2015). "Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates." Journal of bioinformatics and computational biology. [PDF]

2014

5.             Zhang, Z., R. Srivastava, H. Liu, X. Chen, L. Duan, D. W. K. Wong, C. K. Kwoh, T. Y. Wong and J. Liu (2014). "A survey on computer aided diagnosis for ocular diseases." BMC medical informatics and decision making 14(1): 80.[PDF]

6.             Yang, P., Wu, M., Guo, J., Kwoh, C. K., Przytycka, T. M., & Zheng, J. (2014). LDsplit: Screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms. BMC Bioinformatics, 15(1). [PDF]

7.             Yang, P., X. Li, H.-N. Chua, C.-K. Kwoh and S.-K. Ng (2014). "Ensemble positive unlabeled learning for disease gene identification." PloS one 9(5): e97079. [PDF]

8.             Wu, M., C.-K. Kwoh, X. Li and J. Zheng (2014). "Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast." BMC systems biology 8(1): 107.[PDF]

9.             Wu, M., X. Li, F. Zhang, X. Li, C.-K. Kwoh, J. Zheng, M. Wu, X. Li, F. Zhang, X. Li, C.-K. Kwoh and J. Zheng (2014). "In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer." Cancer Informatics(Supplementary Materials 14026): 71-80.

10.          Teh AL, Pan H, Chen L, Ong M-L, Dogra S, Wong J, MacIsaac JL, Mah SM, McEwen LM, Saw S-M, Godfrey KM, Chong Y-S, Kwek K, Kwoh C-K, Soh S-E, Chong MF, Barton S, Karnani N, Cheong CY, Buschdorf JP, Stunkel W, Kobor MS, Meaney MJ, Gluckman PD, Holbrook JD. The effect of genotype and in utero environment on inter-individual variation in neonate DNA methylomes: Evidence for interaction of genetic and environmental effects. Genome Research 2014;Accepted. [PDF]

11.          Nguyen TD, Schmidt B, Zheng Z, Kwoh CK. LargeScale Clustering of Short Reads for Metagenomics On GPUs. Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data 2014:1003-22.[URL]

12.          Patanaik, A., C. K. Kwoh, E. Chua, J. J. Gooley and M. Chee (2014). "Classifying Vulnerability to Sleep Deprivation Using Baseline Measures of Psychomotor Vigilance." Sleep.[URL]

13.          Patanaik, A., V. Zagorodnov, C. K. Kwoh and M. Chee (2014). "Predicting Vulnerability to Sleep Deprivation Using Diffusion Model Parameters." Journal of Sleep Research [PDF]

14.          Su, C. T.-T., T.-D. Nguyen, J. Zheng and C.-K. Kwoh (2014). "IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking." BMC bioinformatics 15(Suppl 16): S9.[PDF]

15.          Fong, S., O. Mohammed, J. Fiaidhi, S. Mohammed and C. K. Kwoh (2014). "Measuring Similarity by Prediction Class between Biomedical Datasets via Fuzzy Unordered Rule Induction." International Journal of Bio-Science and Bio-Technology 6(2): 159-168. [PDF]

16.          Liu, Q., S. C. Hoi, C. K. Kwoh, L. Wong and J. Li (2014). "Integrating water exclusion theory into ß contacts to predict binding free energy changes and binding hot spots." BMC bioinformatics 15(1): 57. [PDF]

 

2013

1.              Zheng Y, Kwoh CK. Improved Time Complexities for Learning Boolean Networks. Entropy2013;15(9):3762-95. [PDF]

2.              Zhang Z, Xu Y, Liu J, Wong DWK, Kwoh CK, Saw S-M, Wong TY. Automatic Diagnosis of Pathological Myopia from Heterogeneous Biomedical Data. PLOS ONE2013;8(6):e65736.[PDF]

3.              Wu M, Yu Q, Li X, Zheng J, Huang J, Kwoh C. Benchmarking Human Protein Complexes to Investigate Drug-Related Systems and Evaluate Predicted Protein Complexes. PLoS ONE 2013;8(2):e53197. [PDF]

4.              Wu M, Xie Z, Li X, Kwoh C-K, Zheng J. Identifying protein complexes from heterogeneous biological data. Proteins: Structure, Function, and Bioinformatics2013 [PDF]

5.              Su CT-T, Ouyang X, Zheng J, Kwoh C-K. Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. BMC Bioinformatics2013;14(Suppl 16):S7.[PDF]

6.              Su C, Schonbach C, Kwoh C-K. Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development. BMC Bioinformatics2013;14(Suppl 2):S21.[PDF]

7.              Ouyang X, Zhou S, Su CTT, Ge Z, Li R, Kwoh CK. CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constrains. Journal of Computational Chemistry2013;34(4):326-36. [PDF]

8.              Ouyang X, Zhou S, Ge Z, Li R, Kwoh CK. CovalentDock Cloud: a web server for automated covalent docking. Nucleic Acids Research2013 May 15, 2013.[PDF]

9.              Mei J-P, Kwoh C-K, Yang P, Li X-L, Zheng J. Drug-Target Interaction Prediction by Learning From Local Information and Neighbors. Bioinformatics2013 November 17, 2012;29(2):238-45.[PDF]

10.           Liu Q, Kwoh CK, Li J. Binding Affinity Prediction for Protein−Ligand Complexes Based on β Contacts and B Factor. Journal of Chemical Information and Modeling2013. [PDF]

11.           Liu Q, Kwoh CK, Hoi SCH. Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces. PLoS ONE2013;8(4):e59737. [PDF]

12.           Liu J, Zhang Z, Wong DWK, Xu Y, Yin F, Cheng J, Tan NM, Kwoh CK, Xu D, Tham YC, Aung T, Wong TY. Automatic glaucoma diagnosis through medical imaging informatics. Journal of the American Medical Informatics Association2013 March 28, 2013. [PDF]

13.           Lim KG, Kwoh CK, Hsu LY, Wirawan A. Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance. Briefings in Bioinformatics2013 May 29, 2012;14(1):67-81. [PDF]

14.           Li Z, He Y, Liu Q, Zhao L, Wong L, Kwoh CK, Nguyen H, Li J. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics2013;14(16):1-15.[PDF]

15.           Fong S, Mohammed S, Fiaidhi J, Kwoh CK. Using causality modeling and Fuzzy Lattice Reasoning algorithm for predicting blood glucose. Expert Systems With Applications2013;40(18):7354-66.[PDF]

16.           Ellabaan MMH, Ong YS, Handoko SD, Kwoh CK, Man H. Discovering Unique, Low-energy Transition States of Small, Non-cyclic Molecules Using Evolutionary Molecular Memetic Computing. IEEE Computational Intelligence Magazine2013;Accepted. [PDF]

17.           Choi H, Lin W, Loon S, Tan C, Wong W, See J, Gu Z, Kwoh C, Chew P. Facial Scanning With a Digital Camera: A Novel Way of Screening for Primary Angle Closure. Journal of  Glaucoma2013 2013 Oct 17. [PDF]

18.           Baskaran N, Kwoh CK, Hui KM. Comprehensive Detection of Cancer Gene Expression Profiles and Gene Networks are Impacted by the Choice of Pre-Processing Algorithm and Gene-Selection Method. Int J Data Mining and Bioinformatics2013;7(4):416-35. [PDF]

 

2012

1.              Zhang Z, Xu Y, Liu J, Kwoh CK. Identify Predictive SNP groups in Genome Wide Association Study: A Sparse Learning Approach. Procedia Computer Science2012;11:107-14.[PDF]

2.             Zhang Z, Kwoh C, Aung T, Wong T, Liu J. Automatic Glaucoma Diagnosis with mRMR-based Feature Selection. Journal of Biometrics & Biostatistics2012;S7:008.[PDF]

3.             Zhang T, Fu X, Ma S, Xiao G, Wong L, Kwoh CK, Lees M, Lee GKK, Hung T. Effects of Temporal Factors in Combined Intervention of School Closure and Workforce Shift for Mitigating the Spread of Influenza. PLoS ONE2012. [PDF]

4.             Yang P, Wu M, Kwoh CK, Khil PP, Camerini-Otero RD, Przytycka TM, Zheng J. Predicting DNA sequence motifs of recombination hotspots by integrative visualization and analysis. International Symposium on Integrative Bioinformatics; Hangzhou, China2012:52-8.[PDF]

5.             Yang P, Li X-L, Mei J-P, Kwoh C-K, Ng S-K. Positive-Unlabeled Learning for Disease Gene Identification. Bioinformatics2012 August 24, 2012. [PDF]

6.             Yang P, Kwoh C-K, Mei J. Neighbor-Based Bipartite Learning Model for Small Molecule-Target Interaction Identification. Journal of Medical Imaging and Health Informatics2012 Dec 2012;2(4).[PDF]

7.             Wu M, Kwoh C-K, Przytycka T, Li J, Zheng J. Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots. Proteome Science2012;10(Suppl 1):S11. [PDF]

8.              Wu M, Li X, Kwoh CK, Ng SK, Wong L. Discovery of Protein Complexes with Core-Attachment Structures from TAP Data. Journal of Computational Biology2012;19(9):1027-42.[PDF]

9.             Wu M, Kwoh C-K, Przytycka T, Li J, Zheng J. Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots. Proteome Science2012;10(Suppl 1):S11.[PDF]

10.         Wongsurawat T, Jenjaroenpun P, Kwoh CK, Kuznetsov V. Quantitative model of R-loop forming structures reveals a novel level of RNA–DNA interactome complexity. Nucleic Acids Research2012;40(2 e16). [PDF]

11.         Liu Q, Hoi SCH, Chinh STT, Li Z, Kwoh C-K, Wong L, Li J. Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding? Bioinformatics2012;28(5). [PDF]

12.         Handoko SD, Ouyang X, Su CTT, Kwoh CK, Ong YS. QuickVina: Accelerating AutoDock Vina Using Gradient-based Heuristics for Global Optimization IEEE/ACM Transactions on Computational Biology and Bioinformatics2012. [URL]

13.         Ellabaan MMH, Handoko SD, Ong YS, Kwoh CK, Bahnassy S, Elassawy F, Man HY. A Tree-structured Covalent-bond-driven Molecular Memetic Algorithm for Optimization of Ring-deficient Molecules. Computers and Mathematics with Applications2012.[PDF]

 

2011

1.                  Zheng Y, Kwoh CK. A Feature Subset Selection Method Based On High-Dimensional Mutual Information. Entropy2011;13(4):860-901. [PDF]

2.                  Zhang T, Fu X, Kwoh CK, Xiao G, Wong L, Ma S, Harold Sohe G, Lee KK, Hung T, Lees M. Temporal factors in school closure policy for mitigating the spread of influenza. Journal of Public Health Policy2011. [PDF]

3.                  Yang P, Li X, Wu M, Kwoh C-K, Ng S-K. Inferring Gene-Phenotype Associations via Global Protein Complex Network Propagation PLoS ONE2011 [URL]

4.                  Xie Z, Kwoh C-K, Li X-L, Wu M. Construction of Co-complex Score Matrix for Protein Complex Prediction from AP-MS Data. Bioinformatics2011 [PDF]

5.                  Wu M, Li X, Kwoh CK, Ng SK, Wong L. Discovery of Protein Complexes with Core-Attachment Structures from TAP Data. Journal of Computational Biology2011;18:1 - 16. [PDF]

6.                  Toh S, Prathipati P, Motakis E, Kwoh CK, Yenamandra S, Kuznetsov V. A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma. BMC Genomics2011;12(Suppl 3):S24.[PDF]

7.                  Ouyang X, Handoko SD, Kwoh CK. CScore: A Simple yet Effective Scoring Function for Protein–Ligand Binding Affinity Prediction Using Modified CMAC Learning Architecture. Journal of Bioinformatics and Computational Biology2011;9(1):1-14.[PDF]

8.                  Le T-V, Kwoh C-K, Lee K-H, Teo ES. Trend Analysis of Length of Stay Data via Phase-type Models. International Journal of Knowledge Discovery in Bioinformatics (IJKDB)2011. [PDF]

9.                  Zheng Y, Kwoh CK. A Feature Subset Selection Method Based On High-Dimensional Mutual Information. Entropy2011;13(4):860-901. [PDF]

10.              Zhang, T., Fu, X., Kwoh, C.K., Xiao, G., Wong, L., Ma, S., Harold Sohe, G., Lee, K.K., Hung, T. and Lees, M. (2011) Temporal factors in school closure policy for mitigating the spread of influenza. Journal of Public Health Policy. [URL]

 

2010 and Before (Selected)

1.                  Wu, M., Li, X., Chua, H. N., Kwoh, C.-K. & Ng, S.-K. Integrating diverse biological and computational sources for reliable protein-protein interactions. BMC Bioinformatics (2010). [PDF]

2.                  Wirawan A, Kwoh CK, Schmidt B. Multi Threaded Vectorized Distance Matrix Computation on the Cell/BE and x86/SSE2 Architectures. Bioinformatics2010 March 26, 2010. [PDF]

3.                  Li X, Wu M, Kwoh C-K, Ng S-K. Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics2010;11(Suppl 1):S3. [PDF]

4.                  Handoko SD, Kwoh CK, Ong YS. Feasibility Structure Modeling: An Effective Chaperon for Constrained Memetic Algorithms. IEEE Transactions on Evolutionary Computation2009. [PDF]

5.                  Eisenhaber F, Kwoh C-K, Ng S-K, Sung W-K, Wong. L. Brief Overview of Bioinformatics Activities in Singapore. PLoS Computational Biology2009. [URL]

6.                  Min Wu, Xiao-Li Li *, Chee-Keong Kwoh and See-Kiong Ng, “A Core-Attachment based Method to Detect Protein Complexes in PPI Networks”, BMC Bioinformatics, Vol 10:169.[PDF]

7.                  Wirawan, A., et al., High performance protein sequence database scanning on the Cell Broadband Engine. Scientific Programming, 2009. 17(1-2): p. 97-111. [PDF]

8.                  Zhou, D., Y. He, and C.K. Kwoh, Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model. International Journal of Bioinformatics Research and and Applications, 2008. [PDF]

9.                  Zhang, G.L., et al., Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics, 2008. [PDF]

10.              Wirawan, A., et al., CBESW: Sequence Alignment on the Playstation 3. BMC Bioinformatics, 2008. 9(1): p. 377. [PDF]

11.              Zhou, D., Y. He, and C.K. Kwoh, Semi-supervised learning of the hidden vector state model for extracting protein–protein ? Artificial Intelligence In Medicine, 2007. [PDF]

12.              Zhou, D., Y. He, and C. Kwoh, Semi-supervised learning of the hidden vector state model for Extracting Protein-Protein Interactions. International Journal Artificial Intelligence in Medicine, 2007. [PDF]

13.              Zhang, G.L., et al., Prediction of Supertype-Specific HLA Class I Binding Peptides Using Support Vector Machines. Journal of Immunological Methods, 2007. 320: p. 143-154. [PDF]

14.              Lim, C., et al., Special Report Biomedical & Pharmaceutical Engineering Week (BPE Week) 2006. Journal of Biomedical & Pharmaceutical Engineering, 2007. 1(1).  [PDF]

15.              KWOH, C.K. and P.Y. NG, Network Analysis Approach for Biology. Cellular and Molecular Life Sciences, 2007. [PDF]

16.              CHAN, C.F., et al., VOLUME VISUALIZATION FOR SURGICAL PLANNING SYSTEM Journal of Mechanics in Medicine and Biology, 2007. 7(1): p. 55-64. [PDF]

17.              Zheng, Y. and C.K. Kwoh, Cancer Classification With MicroRNA Expression Patterns Found By An Information Theory Approach. JOURNAL OF COMPUTERS (JCP), 2006. 1(5): p. 30-39. [PDF]

18.              Zheng, Y. and C.K. Kwoh, Informative microRNA expression patterns for cancer classification, in Data Mining for Biomedical Applications, Proceedings. 2006, Springer-Verlag Berlin: Berlin. p. 143-154. [PDF]

19.              Zheng, Y. and C.K. Kwoh, Dynamic Algorithm for Inferring Qualitative Models of Gene Regulatory Networks. The International Journal of Data Mining and Bioinformatics, 2006. 1(2). [PDF]

20.              Zhao, Y. and C.K. Kwoh, Fast Leave-one-out Evaluation Guided Dynamic Gene Selection for Microarray Data Analysis. Soft Computing, 2006. 10(4): p. 346-350. [PDF]

21.              Zhao, J., L. Li, and K.C. Keong, MOTION RECOVERY BASED ON FEATURE EXTRACTION FROM 2D IMAGES. COMPUTATIONAL IMAGING AND VISION, 2006. [PDF]

22.              Zhang, G.L., et al., PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Research, 2006. 2(1): p. 3. [PDF]

23.              Zhao, J., L. Ling, and C.K. Kwoh, 3D Posture Reconstruction and Human Animation from 2D Feature Points. Computer Graphics Forum (CGF), 2005. 24(4). [PDF]

24.              Zhou, Z.L. and C.K. Kwoh, The Nearest Feature Midpoint - A Novel Approach for Pattern Classification. International Journal of Information Technology (IJIT), 2005. 11(1): p. 1-15. [PDF]

25.              Zhao, J., L. Ling, and C.K. Kwoh, Human Posture Reconstruction and Animation from Monocular Images Based on Genetic Algorithms. International Journal of Image and Graphics, 2005. 5(2): p. 371-396. [PDF]

26.              Sakharkar, K.R., et al., u-Genome: A database on genome design in unicellular genomes. In Silico Biology, 2005. 5.[PDF]

27.              Teo, M.Y., et al., Development of a Robotic Dispensing System for Radioactive Iodine 131. SGH Proceedings, 2002. 11(1): p. 47-50. [PDF]

28.              Kassim, W.S.Ng, and C.K.Kwoh, Review of locomotion techniques for robotic colonoscopy. IEEE Engineering in Medicine and Biology Magazine, 2002. [PDF]

29.              Zou, Q., C.K. Kwoh, and W. Ng, Convex object based volume visualization: a formal proof and example. Computers & Graphics, 2001. 25(5): p. 857-873. [PDF]

30.              Yeo, S.J., et al., Augmented Reality wtih X-ray Localisation for Total Hip Replacement. SGH Proceedings, 2001. 9(4). [PDF]

31.              Ho, G., et al., Computer- Assisted Transurethral Laser Resection Resection of the Prostate (CALRP):Theoretical and Experimental Motion Plan. IEEE Transactions on Biomedical Engineering, 2001. 48(10): p. 1125-1135. [URL]

32.              Ho, G., et al., Fundamental studies of transurethral robotic laser resection of the prostate by means of continuous wave Nd:YAG laser using Lasertrode lightguide. Journal of Biomedical Optics, 2001. 6(2): p. 244-251. [URL]

33.              Ho, G., et al., Experimental study of transurethral robotic laser resection of the prostate using the LaserTrode lightguide. Journal of Biomedical Optics, 2001. 6(2): p. 244-251. [URL]

34.              Fei, B., et al., The safety issues of medical robotics. Reliability Engineering & System Safety, 2001. 73(2): p. 183-192. [PDF]

35.              Sabita, M., C.K. Kwoh, and S.M. Krishnan, A New Technique for Non-linear Time Series Analysis of ECG signal for Detection of Ventricular Premature Beats. Annals of Biomedical Engineering: The Journal of the Biomedical Engineering Society, 2000.

36.              Bhajamanavar, V.M., C.K. Kwoh, and S.M. Krishnan, Extraction of microcalcifications in a digital mammogram using regional watershed method. Journal of Digital Imaging, 2000. 13(2 Suppl 1): p. 127-130.

37.              Tang, S.L., et al., Augmented Reality Systems for Medical Applications. IEEE Transaction, Engineering in Medicine and Biology, 1998. 17(3): p. 49-58. [PDF]

38.              Kwoh, C.-K. and D.F. Gillies, Probabilistic reasoning and multiple-expert methodology for correlated objective data. Artificial Intelligence in Engineering, 1998. 12(1-2): p. 21-33. [PDF]

39.              Kwoh, C.K., et al., Outline of Prostate Boundary using Harmonics Method. Medical & Biological Engineering & Computing, 1998. 36(6): p. 768-771. [PDF]

40.              Chan, C., et al., Prostate biopsy using augmented reality 3D visualization. Critical Reviews in Biomedical Engineering, 1998. 26(5): p. 415-416. [PDF]

41.              Kwoh, C.-K. and D.F. Gillies, Using hidden nodes in Bayesian networks. Artificial Intelligence, 1996. 88(1-2): p. 1-38.[PDF]

 

Book Chapters

 

1          Zhang T, Fu X, Goh RSM, Kwoh CK, Lee GKK. A Integrated Approach to Speed up GA-SVM Feature Selection Model", Computational In: Yoel Tenne C-KG, editor. Computational Intelligence in Optimization: Applications and Implementations Springer; 2010.Intelligence in Optimization-Applications and Implementations

2          D. Zhou, Y. He, and C. Kwoh, "From Biomedical Literature to Knowledge: Mining Protein-Protein Interactions," in Computational Intelligence in Biomedicine and Bioinformatics Springer, 2008.

3          S. Krishnan, C. Kwoh, S. Yan, and K. Chan, "ECG Signal Conditioning by Morphological Filters," in Advances in Cardiac Signal Processing: Springer, 2007.

 

Selected Conferences papers and other publications

 

·         S Issac, N., W. Lin, C. Kwoh, M. Aquino, C. Sng and P. Chew (2015). "Cross-examination for Angle-Closure Glaucoma Feature Detection."

·         Guo, J., R. Jain, P. Yang, R. Fan, C. K. Kwoh and J. Zheng (2014). "Reliable and fast estimation of recombination rates by convergence diagnosis and parallel Markov Chain Monte Carlo." IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 11(1): 63-72.

·         Nguyen, T. D., B. Schmidt and C. K. Kwoh (2014). SparseHC: a memory-efficient online hierarchical clustering algorithm. International Conference on Computational Science 2014 (ICCS), Cairns, Australia.

·         Nguyen, T.-D., B. Schmidt and C.-K. Kwoh (2014). Fast dendrogram-based OTU clustering using sequence embedding. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM.

·         Patanaik, A., V. Zagorodnov and C. Kwoh (2014). Parameter estimation and simulation for one-choice Ratcliff diffusion model. Proceedings of the 29th Annual ACM Symposium on Applied Computing, ACM.

·         Zhang, F., C.-K. Kwoh, M. Wu and J. Zheng (2014). Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM.

·         Zhang, Z., C. Guan, T. E. Chan, J. Yu, A. K. Ng, H. Zhang and C. K. Kwoh (2014). Automatic sleep onset detection using single EEG sensor. Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE, IEEE.

·         Wu M, Li X, Zhang F, Li X, Kwoh C-K, Zheng J, editors. Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics; 2013: ACM.

·         Su CT-T, Ouyang X, Zheng J, Kwoh C-K, editors. Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. Twelfth International Conference on Bioinformatics (InCoB2013); 2013 20-22 September 2013; Taicang, China.

·         Su CTT, Schonbach C, Kwoh CK, editors. Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: Implications for TCR cross recognition and vaccine development. The Eleventh Asia Pacific Bioinformatics Conference (APBC 2013); 2013 21-24 January 2013; Vancouver, Canada.

·         Guo J, Jain R, Yang P, Fan R, Kwoh C, Zheng J. Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo. 2013.

·         Zhang Z, Xu Y, Liu J, Kwoh CK, editors. Identify Predictive SNP groups in Genome Wide Association Study: A Sparse Learning Approach. CSBio2012,  International Conference on Computational Systems and Bioinformatics 2012 3-5 Oct 2012; Bangkok, Thailand.

·         Zhang T, Fu X, Lee G, Lees M, Kwoh CK, editors. A CONTACT-NETWORK-BASED SIMULATION MODEL FOR EVALUATING INTERVENTIONS UNDER “WHAT-IF” SCENARIOS IN EPIDEMIC. Winter Simulation Conference; 2012 December 9-12, 2012.; Berlin, Germany.

·         Yang P, Wu M, Kwoh CK, Khil PP, Camerini-Otero RD, Przytycka TM, Zheng J. Predicting DNA Sequence Motifs of Recombination Hotspots by Integrative Visualization and Analysis. 2012 International Symposium on Integrative Bioinformatics; Hangzhou, China2012.

·         Wu M, Kwoh CK, Przytycka T, Li J, Zheng J. Integration of Genomic and Epigenomic Features to Predict Meiotic Recombination Hotspots in Human and Mouse. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB); Orlando, FL, USA2012.

·         Wu M, Kwoh CK, Li X-L, Zheng J. NetPipe: A Network-based Pipeline for Discovery of Genes and Protein Complexes Regulating Meiotic Recombination Hotspots, . ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB); Orlando, FL2012.

·         Mei J-P, Kwoh C-K, Yang P, Li X-L, Zheng J. Globalized Bipartite Local Learning Model for Drug-Target Interaction Prediction. The 11th International Workshop on Data Mining in Bioinformatics (BIO-KDD'12); Beijing, China2012.

·         Ezzat A, Kwoh CK, editors. Comparison of structure-based tools for the prediction of ligand binding site residues in apo-structures. CSBio2012,  International Conference on Computational Systems and Bioinformatics 2012; 2012 3 - 5 Oct 2012; Bangkok, Thailand.

·         Zheng Y, Kwoh CK. Improved time complexities for learning Boolean networks. The 4th RECOMB Conference on Regulatory Genomics, Systems Biology, and DREAM Challenges (IDIBELL); October 14-19; Barcelona2011.

·         Zhang Z, Kwoh CK, Liu J, Yin F, Wirawan A, Cheung C, Baskaran M, Aung T, Wong TY. MRMR Optimized Classification for Automatic Glaucoma Diagnosis. International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'11); August 30 - September 3, 2011.; Boston, USA2011.

·         Xie Z, Kwoh C-K, Li X-L, Wu M, editors. Construction of Co-complex Score Matrix for Protein Complex Prediction from AP-MS Data. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011); 2011; VIENNA, AUSTRIA.

·         Wu M, Kwoh C-K, Przytycka T, Li J, Zheng J. Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. IEEE International Conference on Bioinformatics & Biomedicine 12-15 November 2011 Atlanta, GA, USA: IEEE; 2011.

·         Toh SH, Prathipati P, Motakis E, Kwoh CK, Yenamandra SP, Thiery J-P, Kuznetsov VA. Discriminative microarray analysis reveals a global reprogramming of transcriptional profile in the human lung adenocarcinoma and predicts diagnostic and prognostic biomarkers. 4th Annual BioPharma IT World Asia 2011; 29-30 March; Singapore2011.

·         Tan Z, Zhang Z, Liu J, Kwoh C, Ong S, Teo Y, Khor C, Tai E, Aung T, Vithana E, Wong T. A hybrid framework for genome wide epistasis discovery. Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE; Aug. 30 2011-Sept. 3 20112011.

·         Le TV, Kwoh CK, Teo ES, Lee KH. Analyzing trends of hospital length of stay using Phase-type distributions. Workshop on Biological Data Mining and its Applications in Healthcare, Proc IEEE ICDM Workshop; Vancouver, Canada2011.

·         Kwoh CK, Chandrasekaran L, editors. Phylogenetic and mutational analysis of 2008, 2009 & 2010 neuraminidase of H1N1 influenza A. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011; 2011; Chicago, Illinois, USA.

·         Kwoh CK, Bharija N. Comparative Study of Protein Interaction Networks for Virulence Factors of Co-existing Bacteria responsible for Nosocomial Infections. IEEE Symposium Series in Computational Intelligence 2011; April 2011; Paris (France)2011.

·         Jain D, Kwoh CK, editors. A Ranking-based Method to Predict Protein Function in terms of Gene Ontology. ICBPE2011 / CSBio2011; 2011 August 2011; Singapore.

·         Handoko SD, Kwoh CK, Ong YS. Classification-assisted Memetic Algorithms for Equality-constrained Optimization Problems with Restricted Constraint Function Mapping. IEEE Congress on Evolutionary Computation 2011; June 5-8, 2011; New Orleans2011.

·         Zheng C, C K Kwoh, C. Aquino, J. See, A. Chia, W. Lin, F.C. Ng_Lee, S.H. Ong, T. Aung, Chew PTK. Comparing Machine Learning Classifier for Diagnosing Different Angle Closure Mechanisms from Anterior Segment Optical Coherence Tomography Imaging. ARVO (Association for Research in Vision and Ophthalmology) Annual Meeting; May 2010; USA2010.

·         Zhang Z, Liu J, Kwoh CK, Sim X, Tay WT, Tan Y, Yin F, Wong TY, editors. Learning in Glaucoma Genetic Risk Assessment. Engineering in Medicine and Biology Society (EMBC), 2010 Annual International Conference of the IEEE 2010 Aug. 31 2010-Sept. 4 2010 Buenos Aires

·         Wu M, Li X, Chua H, Kwoh CK, Ng SK. Integrating Diverse Biological and Computational Sources for Reliable Protein-Protein Interactions. Ninth International Conference of Bioinformatics (InCoB2010); 26-28 Sept 2010; Tokyo, Japan2010.

·         Wirawan A, Kwoh CK, Schmidt B. Comparison of Sequence Alignment Tools on Accelerator Technologies. BIRC symposium Singapore2010.

·         Wirawan A, Kwoh CK, Hsu LY, Koh TH. INVERTER: INtegrated Variable numbER Tandem rEpeat findeR. CSBio 2010 : 1st International Conference on Computational Systems and Bioinformatics; Bangkok, Thailand: Springer; 2010. p. 151-64.

·         Toh SH, Yenamandra PS, Prathipati P, Kwoh CK, Kuznetsov VA. DISCRIMINATIVE MICROARRAY ANALYSIS IN PAIRED SAMPLES REVEALS A GLOBAL REPROGRAMMING OF TRANSCRIPTIONAL PROFILE IN THE HUMAN LUNG ADENOCARCINOMA AND PREDICTS EARLY DIAGNOSTICS BIOMARKERS. InCob; Tokyo, Japan2010.

·         Ramadoss R, Kwoh CK. A vaccine strategy for plant allergy by RNA interference - an in silico approach. CSBio 2010 : 1st International Conference on Computational Systems and Bioinformatics; Bangkok, Thailand: Communication in Computer and Information Science; 2010. p. 193-207.

·         Ong AL, Kwoh CK. Bioinformatics Approaches in Tuberculosis Vaccination Strategies by Whole Genome Sequence. IEEE International Conference on Bioinformatics & Biomedicine 18-21 Dec; Hong Kong2010.

·         Handoko SD, Kwoh CK, Ong YS. Feasibility structure modeling: an effective chaperone for constrained memetic algorithms. Evolutionary Computation, IEEE Transactions on2010;14(5):740-58.

·         Handoko SD, Chinh STT, Kwoh CK, Ong YS. Structural Analysis of (TCR–)HLA/peptide Complexes: An Initial Study. IEEE International Conference on Bioinformatics & Biomedicine 18-21 Dec; Hong Kong2010.

·         Chinh STT, Handoko SD, Schoenbach C, Li X, Kwoh CK. A Possible Mutation that Enables H1N1 Influenza A Virus to Escape Antibody Recognition. IEEE International Conference on Bioinformatics & Biomedicine 18-21 Dec; Hong Kong2010.

·         Bharija N, Kwoh CK. Comparative Study of Protein Interaction Networks for Virulence Factors of Co-existing Bacteria responsible for Nosocomial Infections. IEEE Symposium Series in Computational Intelligence 2011; April 11-15, 2011; Paris, France2010.

·         Baskaran N, Kwoh CK, Hui KM. Outcomes of Gene Association Analysis of Cancer Microarray Data are Impacted by Preprocessing Algorithms. IEEE International Conference on Bioinformatics & Biomedicine 18-21 Dec; Hong Kong2010.

·         Otto CN, Handoko SD, Kwoh CK. Identifying Patterns of Conformational Changes in HLA-A*0201-related Immunological Activities. International Conference on Biomedical and Pharmaceutical Engineering (ICBPE2009); Dec 2-4; Singapore2009

·         Kwoh C-K, Lee K-H, Le T-V. Using Survival Models to Analyze the Effects of Social Attributes on Length of Stay of Stroke Patients. International Conference on Biomedical and Pharmaceutical Engineering (ICBPE2009); Dec 2-4; Singapore2009

·         Zhang T, Soh SH, Fu X, Lee KK, Wong L, Ma S, Xiao G, Kwoh CK. HPCgen – A Fast Generator of Contact Networks of Large Urban Cities for Epidemiological Studies. International Conference on Computer Modelling and Simulation (CSSim 2009 - EUROSIM / CSSS); 7 - 9 September 2009; Brno, Czech Republic2009.

·         Zhang T, Fu X, Goh RSM, Kwoh CK, Lee GKK. A GA-SVM Feature Selection Model Based on High Performance Computing Techniques. SMC 2009; 2009.

·         Wirawan A, Schmidt B, Kwoh CK. Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. The International Conference on Computational Science 2009 (ICCS 2009); Baton Rouge, Louisiana, USA2009.

·         Lee K, Le T, Chee T, Kwoh C. Effects of Social Attributes on the Length of Stay of Stroke Patients in a Hospital. WONCA 2009 Asia Pacific Regional Conference; 4-7 June; Hong Kong2009.

·         Handoko SD, Kwoh CK, Ong YS. Classification-assisted Memetic Algorithms for Equality-constrained Optimization Problems. The 22nd Australasian Joint Conference on Artificial Intelligence; 1 - 6 June, 2008; Australia2009.

·         Wu M, Li X-L, Kwoh C-K. Algorithms for Detecting Protein Complexes in PPI Networks: An Evaluation Study. Proceedings of Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008); Oct 20082008.

·         Wu M, Li X, Kwoh C-K, Ng S-K. Semantic labeling to identify reliable interactions in the protein interaction network. The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008); May 16-18, 2008 Shanghai,China2008.

·         Nim TH, Kwoh CK, Wirawan A, Schmidt B. Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search. The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2008); May 16-18, 2008 Shanghai,China: IEEE Press; 2008. p. 5-8.

·         Nikhil Prasanna Jayan, Devasia Arun George, Keong KC. A Database for Analysis of SNP-Protein Structure Relationship and Predictive SNP-Metabolic Pathway Interaction for Disease Eradication. . A-Star UK-Spore Joint Symposium; 12 sept 2008; Singaproe2008.

·         Handoko SD, Kwoh CK, Ong YS, Lim MH. A Study on Constrained MA Using GA and SQP: Analytical vs. Finite-Difference Gradients. 2008 IEEE World Congress on Computational Intelligence (WCCI 2008); 1 - 6 June, 2008; Hong Kong2008.

·         Handoko SD, Kwoh CK, Ong YS. Using Classification for Constrained Memetic Algorithm: A New Paradigm. IEEE International Conference on Systems, Man, and Cybernetics 2008; 2008.

·         George DA, Kwoh CK, Jayan NP. PHOSPHORYLATION SITE PREDICTION TOOL FOR. CHANNEL PROTEINS USING STATISTICAL MACHINE. LEARNING TECHNIQUES. GIW; Australia2008.

·         Zhou, D., Y. He, and C.K. Kwoh, Training the Hidden Vector State Model from Un-annotated Corpus. LECTURE NOTES IN COMPUTER SCIENCE, 2007.

·         Zhou, D., Y. He, and C.K. Kwoh. Effective Reranking for Extracting Protein-protein Interactions from Biomedical Literature. in InCoB - Sixth International Conference on Bioinformatics 2007. 2007. Hong Kong.

·         Zhou, D., et al., Ant-MST: An Ant-Based Minimum Spanning Tree for Gene Expression Data Clustering, in Pattern Recognition in Bioinformatics. 2007. p. 198-205.

·         Zhang, T.Y., C.K. Kwoh, and C.S. Lim. A Comparison of Methods for Detection of Horizontal Gene Transfer, with Reference to Resistance Determinant Genes in Staphylococcus aureus in Pattern Recognition for Bioinformatics PRIB 2007. 2007. Singapore.

·         Zhang, G.L., et al. Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. in InCoB - Sixth International Conference on Bioinformatics 2007. 2007. Hong Kong.

·         Wirawan, A., C.K. Kwoh, and S. B. Parallel DNA Sequence Alignment on the Cell Broadband Engine. in Parallel Processing and Applied Mathematics. 2007. 2007. Gdansk, Poland: Lecture Notes of Computer Science.

·         Zhou, D., Y. He, and C.K. Kwoh. Validating Text Mining Results on Protein-Protein Interactions using Gene Expression Profiles. in The International Conference on Biomedical and Pharmaceutical Engineering 2006 (ICBPE2006) 2006. Singapore.

·         Zhou, D., Y. He, and C.K. Kwoh. Extracting Protein-Protein Interactions from the Literature using the Hidden Vector State. in International Conference on Computational Science 2006 (ICCS 2006). 2006. University of Reading, UK: Lecture Notes in Computer Science (LNCS).

·         Zheng, Y. and C.K. Kwoh. Informative MicroRNA Expression Patterns For Cancer Classification. in PAKDD2006 BioDM Workshop. 2006.

·         Zhang, T., C.K. Kwoh, and C. Lim. Studying Genetic Diversity by Mutations for Identification of Methicillin-resistant S.aureus. in The First International Conference on Computational Systems Biology. 2006. Shanghai, China.

·         Zhang, G.L., et al. Computational Models for Identifying Promiscuous HLA-B7 Binders based on Information Theory and Support Vector Machine. in The International Conference on Biomedical and Pharmaceutical Engineering 2006 (ICBPE2006) 2006. Singapore.

·         Zhang, G.L., et al. Performance Evaluation of MULTIEPD1 on Prediction of MHC Class I Binders. in The International Conference on Biomedical and Pharmaceutical Engineering 2006 (ICBPE2006) 2006. Singapore.

·         SEAH, S.H., et al. Functional Prediction of Snake Neurotoxins in ICARCV 2006. 2006. Singapore.

·         Kwoh, C.K. and C.H. Tan. Predition of Shared Regulatory Motifs from Upstream DNA Database for Gallus Gallus. in The International Conference on Biomedical and Pharmaceutical Engineering 2006 (ICBPE2006) 2006. Singapore.

·         Handoko, S.D., et al. Extreme Learning Machine for Predicting Hla-peptide Binding. in Third International Symposium on Neural Networks (ISNN 2006). 2006. China: Springer.

·         Zheng, Y.K., Chee Keong. A Feature Vector Selection Method for Cancer Classification. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Zheng, Y. and C.K. Kwoh. Classifying Eukaryotes With The Discrete Function Learning Algorithm. in 3rd Asia-Pacific Bioinformatics Conference, APBC 2005. 2005.

·         Zheng, Y. and C.K. Kwoh. Identifying Simple Discriminatory Gene Vectors with an Information Theory Approach. in IEEE Computational Systems Bioinformatics Conference CSB2005. 2005: IEEE Computer Society Press.

·         Tan, S.K., Chee Keong. Cytokine Information System and Pathway Visualization. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Ong, Z.X., J.C. Tay, and C.K. Kwoh. Applying the Clonal Selection Principle to find Flexible Job-Shop Schedules. in International Conference for Artificial Immune Systems (ICARIS 2005). 2005. Banff, Alberta, Canada.

·         Kwoh, C.K.K., Wui Lim. A Genome-Specific PCR Primer Design Program for Open Reading Frames. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Kwoh, C.K.H., Jing Ming; Loh, Kok Keong. HaBDiT: a Handy Biological Data Integration Tools. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Devi, S.S.K., Chee Keong; Kolatkar, Prasanna R. Comparison of Protein-Protein Interaction from Geometry and Biochemistry View with Computation-Driven Data. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Chan, C.F.I.K.C.L.K., Chee Keong;Ivan Ng, VOLUME VISUALISATION FOR SURGICAL PLANNING SYSTEM. 7TH NTU-SGH SYMPOSIUM 2005, 2005.

·         Adi, M.Z., Yun; Kwoh, Chee Keong. Development of Correlation Based Feature Selection Method by Predicting the Markov Blanket for Gene Selection Analysis. in International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005). 2005. Pusan, Korea.

·         Zhou, Z., J. Li, and C.K. Kwoh. The SVM classification of light regulated Arabidopsis genome expression profiles. in Proc. of Biotech China 2004 - An International Conference. 2004. Beijing, China.

·         Zhou, Z. and C.K. Kwoh. AN EVOLUTIONARY LINEAGE FOR INTRON LOSS/GAIN IN FIVE EUKAYOTIC GENOMES. in The Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004). 2004. [PDF]

·         Zhou, Z. and C.K.Kwoh. The Pattern Classification Based on the Nearest Feature Midpoints. in International Conference on Pattern Recognition (ICPR). 2004. [PDF]

·         Zheng, Y. and C.K. Kwoh. Dynamic Algorithm For Inferring Qualitative Models of Gene Regulatory Networks. in IEEE Computational Systems Bioinformatics Conference, CSB2004. 2004. [PDF]

·         Zheng, Y. and C.K. Kwoh. Reconstructing Boolean Networks from Noisy Gene Expression Data. in Eighth International Conference on Control, Automation, Robotics and Vision, ICARCV 2004. 2004. [PDF]

·         Zheng, Y. and C.K. Kwoh. IMPROVED MDL SCORE FOR LEARNING OF BAYESIAN NETWORKS. in AISAT 2004 - International Conference on Artificial Intelligence in Science and Technology. 2004. [PDF]

·         Zheng, Y. and C.K. Kwoh. IDENTIFYING DECISION LISTS WITH THE DISCRETE FUNCTION LEARNING ALGORITHM. in AISAT 2004 - International Conference on Artificial Intelligence in Science and Technology. 2004. Australia. [PDF]

·         Zhao, Y. and C.K. Kwoh. Fast Leave-one-out Evaluation and Improvement on Inference for LS-SVMs. in International Conference on Pattern Recognition (ICPR). 2004. [PDF]

·         Zhao, J., L. Li, and C.K. Kwoh. A Model-based Approach for Human Motion Reconstruction from Monocular Images. in 2nd International Conference on Information Technology for Application (ICITA 2004). 2004. [PDF]

·         Zhao, J., L. Li, and C.K. Kwoh. Human Motion Recovery Based on Extraction of Feature Points from Monocular Images. in ICCVG 2004 - International Conference on Computer Vision and Graphics. 2004. [PDF]

·         Zhang, Y., et al. The sensitivity and rationality of pairwise linkage disequilibrium measures - a practical analysis. in Genomic Signal Processing and Statistics (GENSIPS). 2004. [PDF]

·         Zhang, Y., et al. Comparison of four algorithms for haplotype inference problem. in 2nd RECOMB satellite workshop on computational methods for SNPs and Haplotypes. 2004.

·         Zhang, Y., et al. Application Comparison and Analysis of Computational Methods for Haplotype Inference Problem. in RECOMB2004 workshop. 2004. USA.

·         Shi, D.M., et al. Augmented Reality Assisted Sinus Surgery. in 1st International Bioengineering Conference. 2004. [PDF]

·         Jia, Y., et al. INTRON/EXON: Which One Tells Us More About Coding Of Life? ?Evidence From Statistical Analysis Of Length Distribution. in Genomic Signal Processing and Statistics (GENSIPS 2004). 2004.

·         Jia, Y., et al. Length Distributions Of Exons And Introns Imply The Evolutionary Constraints For Exon/Intron Length. in Conference on Research in Computational Molecular Biology (RECOMB 2004). 2004.

·         Eng, Y., C.K. Kwoh, and Z. Zhou. ON THE TWO-LEVEL HYBRID CLUSTERING ALGORITHM. in AISAT 2004 - International Conference on Artificial Intelligence in Science and Technology. 2004. [PDF]

·         Zhou, Z., et al. The SVM classification of light regulated Arabidopsis genome expression profiles. in Joint Singapore-Canada Workshop on "The Interface of Biology with Information Technology". 2003.

·         Jia, Y., et al. Statistical analysis of symmetric exon sets in eukaryotic genes. in International Conference on Genome Informatics (GIW 2003). 2003.

·         Zhao, J.H., L. Li, and C.K. Kwoh. Human Posture Reconstruction from Monocular Images. in IASTED international Conference Computer, Graphics and Imaging (CGIM2002). 2002.

·         Li, L., J.H. Zhao, and C.K. Kwoh. HIERARCHICAL APPROACH FOR HUMAN ANIMATION. in Visualization, Imaging, and Image Processing (VIIP 2002). 2002.

·         Kwoh, C.K. Life Science Initiatives and Milestones of NTU. in Bioscience Asia 2002. 2002.

·         Agusanto, K., et al. Photorealistic rendering for augmented reality. in The First IEEE International Augmented Reality Toolkit Workshop (ART02). 2002.

·         Zou, Q.S., et al. An Internet Based Collaborative Surgical Planning System. in 4th annual NTU-SGH Biomedical Engineering Symposium. 2001.

·         Zou, Q.S., et al. MRI Head Segmentation for Object Based Volume Visualization. in The Seventh Australian and New Zealand Intelligent Information Systems Conference. 2001.

·         Zou, Q.S., C.K. Kwoh, and W.S. Ng. A Web Based Collaborative Volume Visualization System. in Proceedings of 15th European Simulation Multiconference. 2001.

·         Zou, Q.S., C.K. Kwoh, and W.S. Ng. Interactive Surgical Planning Using Context Based Volume Visualization Techniques. in Proceedings of International Workshop on Medical Imaging and Augmented Reality. 2001. [PDF]

·         Yang, K.Y., et al. Use of augmented reality in acetabular fixation in total hip arthroplasty. in 5th Computer Adided Orthopaedic Surgery (CAOS). 2001.

·         Xiao, d., et al. Rectal wall structure delineation and broken layer recognition by multigradient field active contour. in The Seventh Australian and New Zealand Intelligent Information Systems Conference (ANZIIS). 2001.

·         Chen, Y.T., et al. Adaptive Expanding BSnake Model For Extracting Ultrasound Breast Lump Boundary. in The Seventh Australian and New Zealand Intelligent Information Systems Conference (ANZIIS). 2001.

·         Zou, Q.S., C.K. Kwoh, and W.S. Ng. A Collaborative 3D Volume Visualization Pipeline. in IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Wang, Y., et al. Boundary Description for Trademark. in Sixth International Conference on Control, Automation, Robotics and Vision (ICARCV2000). 2000.

·         Veena and C.K. Kwoh. Mathematical Morphology based Feature Extraction Technique for Classification of Microcalcifications in a Digital Mammogram. in IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Tan, E.C., D. Xiao, and C.K. Kwoh. Area calculation of medical image onscreen. in Proceedings of IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Tan, E.C. and C.K. Kwoh. Group-access control of E-medicine records. in Proceedings of IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Sabita, M., C.K. Kwoh, and S.M. Krishnan. Complexity measures of ECG signal for detecting a life threatening cardiac arrhythmia. in 10th International Conference on Biomedical Engineering (10 ICBME) Biomedical Engineering in the New Millennium: Integration and Breakthroughs. 2000. Singapore.

·         Sabita, M., C.K. Kwoh, and S.M. Krishnan. A New Approach for Detecting and Delineation of QRS complex for PVC Detection. in IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Sabita, M., C.K. Kwoh, and S.M. Krishnan. A New Technique for Non-linear Time Series Analysis of ECG signal. in 2000 Annual Fall Meeting of the Biomedical Engineering Society. 2000.

·         Kwoh, C.K., S.J. Yeo, and S.W. Yung. X-RAY LOCALIZATION FOR TOTAL HIP REPLACEMENT. in 3rd NTU-SGH Annual Scientific Symposium. 2000.

·         Khan, L.A., et al. The image intensifier (II) distortion calibration method in X-ray localization for total hip replacement (THR). in Conference of Society for Computer Applications in Radiology (SCAR). 2000. Philadelphia, Pennsylvania.

·         Ho, G., et al. Perspectives of transurethral robotic laser resection of the prostate; Vaporization and coagulation effects with the Nd:YAG laser. in Proceedings of SPIE - The International Society for Optical Engineering. 2000. San Jose, CA, USA: Society of Photo-Optical Instrumentation Engineers.

·         Fei, B.W., C.K. Kwoh, and W.S. Ng. The hazard identification and safety insurance control (HISIC) for medical robot. in World Congress on Medial Physics and Biomedical  Engineering, 22nd Annual International Conf. Of IEEE EMBS. 2000.

·         Chen, Y.T. and C.K. Kwoh. Lesion Boundary Enhancement using Threshold Directed. in IEEE-EMBS Asia-Pacific Conference on Biomedical Engineering. 2000.

·         Chan, K.L., et al. Nonlinear Techniques for Processing and Analysis of ECG Signals. in Third Annual SGH-NTU Biomedical Engineering Symposium. 2000.

·         Bhajamanavar, V.M., C.K. Kwoh, and S.M. Krishnan. Extraction of microcalcifications in a digital mammogram using regional watershed method. in Society for Computer Applications in Radiology (SCAR 2000). 2000.

·         Bhajamanavar, V.M., C.K. Kwoh, and S.M. Krishnan. Entropy-based thresholding for detection of microcalcifications in a digital Mammogram. in 14th international congress and Exhibition Computer Assisted Radiology and Surgery (CARS 2000). 2000.

·         Sabita, M., C.K. Kwoh, and S.M. Krishnan. A quantitative method for ECG analysis for PVC detection. in The International Conference on Medical Diagnostic Techniques & Procedures. 1999.

·         Kwoh, C.K., G.N. Khan, and D.F. Gillies. Automated Endoscope Navigation and Advisory System from Medical Image. in SPIE's Int. Conf. on Physiology and Function from Multidimensional Images (Medical Imaging 1999). 1999. San Diego, California. [PDF]

·         Khan, L.A., et al. X-ray localization technique for total hip replacement operation in augmented reality for therapy (ART). in 21st IEEE EMBS, 1st EMBS-BMES joint Conference. 1999.

·         Fei, B.W., C.K. Kwoh, and W.S. Ng. Software design method for medical robot. in 21st IEEE EMBS, 1st EMBS-BMES joint Conference. 1999.

·         Chee, C.F., et al. Prostate Biopsy using Augmented Reality 3D visualisation. in 18th Southern Biomedical Conference and the 2nd International Conference on Ethical Issues in Biomedical Engineering. 1999.

·         Chan, C.F., et al. Tessellated surface reconstruction from 2D contours. in Medical Image Computation and Computer-Assisted Intervention (MACCAI), 2nd International Conference. 1999.

·         Chan, C., et al., Tessellated Surface Reconstruction from 2D Contours, in Medical Image Computing and Computer-Assisted Intervention ?MICCAI?9. 1999. p. 297-307.

·         Kwoh, C.K., et al. Augmented Reality for Therapy. in Inaugural Biomedical Engineering Symposium of NTU and SGH: Partnering for Healthcare Solutions. 1998. Auditorium, College of Medicine Building, Singapore General Hospital.

·         Kwoh, C.K., M.Y. Teo, and W.S. Ng. Evalutation of computerised prostate boundary estimation in ultrasound images. in 4th Asian Congress in Urology by Singapore Urological Association and Urological Association of Asia. 1998.

·         Kwoh, C.K., et al. Safety guidelines for medical robots. in 4th Asian Congress in Urology by Singapore Urological Association and Urological Association of Asia. 1998.

·         Kwoh, C.K., W.S. Ng, and M.Y. Teo. Computer assisted prostate treatment ?past, present and future. in 4th Asian Congress in Urology by Singapore Urological Association and Urological Association of Asia. 1998.

·         Kwoh, C.K. Radial Bas-relief (RBR) and Parametrically Deformable Model for Ultrasound Contour Determination. in 4th Asian congress in Urology, organised by Singapore Urological Association and Urological Association of Asia. 1998. Mandarin, Singapore.

·         Teo, T.T., E.C. Tan, and C.K. Kwoh. Implementation of a 4.8 Kbps CELP Speech Coder on a TMS320C44 Processor Board. in Proceedings of 1st International Conference on Information, Communications & Signal Processing (ICICS '97). 1997.

·         Kwoh, C.K., et al. ROBOTIC TURP AND TREATMENTS OF BPH. in International College of Surgeons and New Changi Hospital Combined Scientific Meeting. 1997.

·         Kwoh, C.K., et al. Image guidance for robotic TURP using ultrasound. in International College of Surgeons and New Changi Hospital Combined Scientific Meeting. 1997.

·         Kwoh, C.K., et al. Interventive Augmented Reality. in International College of Surgeons and New Changi Hospital Combined Scientific Meeting. 1997.

·         Kwoh, C.K. and D.F. Gillies. Choice of error cost function for training unobservable nodes in Bayesian networks. in Proceedings of 1st International Conference on Knowledge-based Intelligent Electronic Systems. 1997. [PDF]

·         Kwoh, C.K. and D.F. Gillies. Estimating the Initial Values of Unobservable Variables in Visual Probabilitic Networks. in Proceedings of the 6th International Conference, CAIP 95. 1995. Prague.

·         Kwoh, C.K. and D.F. Gillies. Using Fourier Information for the Detection of the Lumaen in Endoscope Images. in Proceedings of the IEEE TENCON '94. 1994. [PDF]

MASTER OF SCIENCE IN BIOINFORMATICS

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