Jacky Lee (a.k.a. Hongjian Li 李宏健)

• BEng (SYSU), MPhil (CUHK), PhD Pre-Candidate (CUHK)

• Department of Computer Science and Engineering

Foshan 2009

Guangzhou 2009

Introduction

I received B.Eng. degree in network engineering from Sun Yat-sen University, Guangzhou, China in 2009 and M.Phil. degree in computer science and engineering from Chinese University of Hong Kong, Hong Kong, China in 2011.

I'm currently working on a Ph.D. degree at CUHK under the supervisions of Prof. Kwong Sak Leung and Prof. Man Hon Wong.

Research Interests

Bioinformatics, Cheminformatics, GPU Computing, Web 2.0

My major research interest is CUDA/OpenCL/multithreaded applications in computational drug discovery in terms of in silico protein-ligand docking and drug design.

Publications

1. Hongjian Li, Bing Ni, Man-Hon Wong, and Kwong-Sak Leung. A Fast CUDA Implementation of Agrep Algorithm for Approximate Nucleotide Sequence Matching. 9th IEEE Symposium on Application Specific Processors (SASP), pp.74-77, San Diego, United States, 5-6 June 2011. DOI: 10.1109/SASP.2011.5941082

2. Ching-Man Tse, Hongjian Li, Kwong-Sak Leung, Kin-Hong Lee, and Man-Hon Wong. Interative Drug Design in Virtual Reality. 15th International Conference on Information Visualisation (IV), pp.226-231, London, United Kingdom, 13-15 July 2011. DOI: 10.1109/IV.2011.72

3. Hongjian Li, Kwong-Sak Leung, and Man-Hon Wong. idock: A Multithreaded Virtual Screening Tool for Flexible Ligand Docking. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), San Diego, United States, 9-12 May 2012. Accepted manuscript.

Tools

CUDAagrep http://agrep.cse.cuhk.edu.hk

CUDAagrep is a fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching

idock https://github.com/HongjianLi/idock

idock is a multithreaded virtual screening tool for flexible ligand docking for computational drug discovery

igrow https://github.com/HongjianLi/igrow

igrow is a multithreaded ligand growing tool for structure-based molecule design for computational drug discovery

ichem https://github.com/HongjianLi/ichem

ichem is an integrated platform for protein-protein and protein-chemical interaction query with neo4j and node.js.

Presentations in 2009

• Latest Generation of GPUs
• Fast N-Body Simulation with CUDA
• GPU Applications in Bioinformatics

Presentations in 2010

• Parallelizing Agrep Using CUDA
• Introducing XScore
• Side Effects of Tenofovir Disoproxil Fumarate
• Bioinformatics Database Selection Fuzzy Project Report
• Introduction to Expert System Shell
• Reviewing AutoGrow
• Introduction to AutoGrow
• Computer-Aided Drug Design
• Computer-Aided Drug Discovery with GPU Acceleration
• SmartGrow: A Smart Algorithm for Potent Ligand Construction
• Computational Synthesis of Potent Ligands
• Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
• Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications
• SmartGrow: An Efficient Tool for Computational Synthesis of Potent Ligands for Drug Discovery

Presentations in 2011

• PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements
• A Fast CUDA Implementation of Agrep Algorithm for Approximate Nucleotide Sequence Matching
• A Computational Framework for Structure-Based Drug Discovery with GPU Acceleration
• idock: A Multithreaded Virtual Screening Tool for Flexible Ligand Docking
• Accelerate Conformational Space Sampling for Protein-DNA Docking using GPUs
• Computational Drug Discovery Tutorial
• Evaluation of Multilayer Perceptron, Naive Bayes, K Nearest Neighbors and C4.5 on Classifying Native Ligand Conformations out of a Large Pool of Decoys

Presentations in 2012

• Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction
• Roadmap in 2012
• Efficiently Answering Reachability Queries on Very Large Directed Graphs
• 3-HOP: A High-Compression Indexing Scheme for Reachability Query
• Gene-Drug Interactions
• idock: A Multithreaded Virtual Screening Tool for Flexible Ligand Docking
• ichem: An Integrated Platform for Protein-Protein and Protein-Chemical Interaction Query with Neo4j and Node.js

Teaching Assistantship

• 2009/10 Term 1: CSC 3170 Introduction to Database Systems
• 2009/10 Term 2: CSC 1030 Hands-on Introduction to Java
• 2010/11 Term 1: CSCI2510 Computer Organization
• 2010/11 Term 2: CSCI1140 Programming Laboratory
• 2011/12 Term 1: CSCI3220 Algorithms for Bioinformatics
• 2011/12 Term 2: CSCI1140 Programming Laboratory

Excellent TA

Teaching Merit

Contact

• Email

  JackyLeeHongJian@Gmail.com

• QQ

  445225711

• Address

  Room 1013, Ho Sin-Hang Engineering Building

  Chinese University of Hong Kong

  Shatin, New Territories, Hong Kong

• Galleries

  https://picasaweb.google.com/JackyLeeHongJian/JackyLee

Computer System Explained in Washroom