[Photo of Prof Chin] Francis Y.L. Chin

B.A.Sc.(Toronto); M.Sc., M.A., Ph.D.(Princeton); FIEEE, FHKIE, FHKACE (Hon.)

Chair of Computer Science; Taikoo Professor of Engineering; Associate Dean of Engineering 


Email: chin@cs.hku.hk
Office: CB301A, Chow Yei Ching Building, The University of Hong Kong, Pokfulam Road, Hong Kong
Telephone: (+852) 2859 2178
Fax: (+852) 2858 4141

Keynote and Invited Talks (since 2008):

Publications (since 2008):

Book Chapter

Refereed Journal Papers

  • Stanley Fung, Feifeng Zheng, W.T. Chan, Francis Y.L. Chin, C.K.Poon and Prudence W.H. Wong, "Improved on-line broadcast scheduling with deadlines", Journal of Scheduling 11(4): 299-308 (2008) - preliminary version appeared in COCOON'06
  • Henry Leung and Francis Chin, "DNA Motif Representation with Nucleotide Dependency," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(1): 110-119 (January-March 2008) - preliminary version appeared in BIBE06
  • Wun-Tat Chan, Francis Y. L. Chin, Deshi Ye, Guochuan Zhang, Yong Zhang, "On-Line Scheduling of Parallel Jobs on Two Machines", Journal of Discrete Algorithms, 6(1): 3-10 (March 2008) - preliminary version appeared in AWOCA 2005
  • Francis Y.L. Chin, Henry C.M. Leung, Wei-Lin Li and Siu-Ming Yiu, "Finding Optimal Threshold for Correction Error Reads in DNA Assembling", BMC Bioinformatics 2009, 10(Suppl 1): S15 (January 2009) - also presented at APBC2009
  • Henry C.M. Leung, Qian Xiang, S.M. Yiu and Francis Y.L. Chin, "Predicting Protein Complexes from PPI Data: A Core-Attachment Approach", Journal of Computational Biology, 16(2): 133-144, 2009 - preliminary version also presented in RECOMB Satellite Conference on Systems Biology and DREAM, MIT (October-November 2008)
  • Yong Zhang, Francis Chin and Hong Zhu, "A 1-local 13/9-competitive Algorithm for Multicoloring Hexagonal Graphs", Algorithmica 54: 557–567 (August 2009) - preliminary version appeared in the COCOON'07
  • Mee Yee Chan, Wun-Tat Chan, Francis Y.L.Chin, Stanley P.Y.Fung, and Ming-Yang Kao, "Linear-time Haplotype Inference on Pedigrees without Recombinations and Mating Loops" SIAM Journal of Computing, 38(6): 2179-2197 (2009) - preliminary version appeared in WABI2006
  • Francis Chin, Hing Fung Ting and Yong Zhang, "A Constant-Competitive Algorithm for Online OVSF Code Assignment", Algorithmica, 56(1): 89-104 (January 2010) - preliminary version appeared in ISAAC 2007
  • Bin Yang, Yu Peng, Henry C.M. Leung, S.M. Yiu, J.C. Chen and Francis Y.L. Chin, "Unsupervised Binning of Environmental Genomic Fragments based on an Error Robust Selection of l-mers", BMC Bioinformatics 2010, 11(Suppl 2):S5 - also presented in DTMBIO 09
  • Francis Y. L. Chin, Hingfung Ting, Yong Zhang, "One-Space Bounded Algorithms for Two-Dimensional Bin Packing", International Journal of Foundations of Computer Science, 21(6): 875-891 (December 2010) - preliminary version appeared in ISAAC 2009
  • Keqiu Li, Takashi Nanya, Hong Shen, Francis Y. L. Chin and Weishi Zhang, " An Efficient Cache Replacement Algorithm for Multimedia Object Caching", International Journal of Computer Systems Science and Engineering
  • Yongkai Liu, Defu Zhang and Francis Y.L. Chin, "A Clique-based Algorithm for Constructing Feasible Timetables", Optimization Methods and Software, 1029-4937 (electronic) 1055-6788 (paper), 2010
  • Francis Y. L. Chin, Zeyu Guo and He Sun, "Minimum Manhattan Network is NP-Complete", Discrete and Computational Geometry (2011) 45:701-722- preliminary version appeared in ACM SoCG 2009
  • Henry C.M. Leung, S.M. Yiu, Bin Yang, Yu Peng, Yi Wang, Zhihua Liu, Jingchi Chen, Junjie Qin, Ruiqiang Li, Francis Y.L. Chin, "A Robust and Accurate Binning Algorithm for Metagenomic Sequences with Arbitrary Species Abundance Ratio," Bioinformatics, 27(11):1489-95, Jun 2011. also presented in HiTSeq 2011.
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "Meta-IDBA: "A de Novo Assembler for Metagenomic Data," Bioinformatics, 27(13):i94-101, July 2011, also presented in ISMB/ECCB 2011
  • Yong Zhang, Zhuo Chang, Francis Y.L. Chin, Hing-Fung Ting and Yung H. Tsin, "Online Uniformly Inserting Points on Grid", Information Processing Letters. 111(2011):773-779 - preliminary version appeared in AAIM 2010
  • Yong Zhang, Francis Y.L. Chin, Hing-Fung Ting, Joseph Wun-Tat Chan, Xin Han, Ka-Cheong Lam, "Online Call Control in Cellular Networks Revisited", Information Processing Letters. 112(2012):21-25 - preliminary version appeared in FAW 2010
  • Xin Han, Francis Y. L. Chin, Hing-Fung Ting, Guochuan Zhang, Yong Zhang, "A new upper bound 2.5545 on 2D Online Bin Packing". ACM Transactions on Algorithms 7(4): 50 (2011)
  • Francis Chin, Henry C.M. Leung and S.M. Yiu. "Non-Adaptive Complex Group Testing with Multiple Positive Sets", Theoretical Computer Science, - preliminary version appeared in TAMC 2011 (to appear)
  • Yi Wang, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin, "MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species" Journal of Computational Biology 19(2): 241-249, also presented in RECOMB Regulatory Genomics 2011
  • Yong Zhang, Yuxin Wang, Francis Y.L. Chin, Hing-Fung Ting, "Competitive Algorithms for Online Pricing", Discrete Mathematics, Algorithms and Applications (DMAA),4(2): (2012)- preliminary version appeared in COCOON 2011
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin,"IDBA-UD: A de Novo Assembler for Single-Cell and Metagenomic Sequencing Data with Highly Uneven Depth," Bioinformatics 28(11): 1420-1428, May 2012, also presented in HiTSeq 2012
  • Francis Chin, Marek Chrobak and Li Yan, "Algorithms for Placing Monitors in a Flow Network", Algorithmica, June 2012, Preliminary version appeared in AAIM 2009.
  • Yi Wang, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "MetaCluster 5.0: A two-round Binning Approach for Metagenomic Data for Low-abundance Species in a Noisy Sample," Bioinformatics, 28(18): i356-i362, Sept 2012, also presented in ECCB 2012
  • Henry C.M. Leung, S.M. Yiu, John Parkinson and Francis Y.L. Chin, "IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating" Journal of Computational Biology, 20(7), 540-550, 2013, also presented in RECOMB System Biology/Regulatory Genomics/DREAM 2012
  • Yu Peng, Henry C.M. Leung, S.M. Yiu, Xin-Guang Zhu, Ming-Ju Lv and Francis Y.L. Chin, "IDBA-Tran: A More Robust de novo de Bruijn Graph Assembler for Transcriptomes with Uneven Expression Levels", Bioinformatics Vol. 29 ISMB/ECCB 2013, pages i326–i334.
  • Yong Zhang, Francis Y.L. Chin, Hing-FungTing, "Online Pricing for Bundles of Multiple Items", Journal of Global Optimization (2013): 1-11 , February 24, 2013, preliminary version also presented in FAW and AAIM 2012.
  • Yong Zhang, Francis Chin, Hingfung Ting, Xin Han and Zhuo Chang, "Online Algorithm for 1-Space Bounded Multi-Dimensional Bin Packing," Journal of Combinatorial Optimization, 26(2): 223-236 (2013)-preliminary version appeared in FAW and AAIM 2011
  • Yong Zhang, Francis Y.L. Chin, Hing-Fung Ting, "Constant-Competitive Tree Node Assignment", Theoretical Computer Science, available online 16 May 2013
  • Hari K.Yalamanchili1, Bin Yan, Mulin J. Li, Jing Qin, Zhongying Zhao, Francis Y.L. Chin and Junwen Wang, "DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment", Bioinformatics, 30(3):377-83, Feb 2014
  • Yong Zhang, Francis Y. L. Chin, Hing-Fung Ting, Xin Han, Chung Keung Poon, Yung H. Tsin, Deshi Ye: "Online Algorithms for 1-Space Bounded 2-Dimensional Bin Packing and Square Packing". Theortical Computer Science (2014), also presented in COCOON'13 (to appear)
  • Jie Yang, Henry C.M. Leung, S.M. Yiu, Yunpeng Cai, and Francis Y.L. Chin,"Intra- and Inter-sparse Multiple Output Regression with Application on Environmental Microbial Community Study", BMC Bioinformatics, also presented in BIBM13
  • Refereed Conference Papers

  • Francis Y.L. Chin, Henry C.M. Leung, M.H. Siu and S.M. Yiu, "Optimal Algorithm for Finding DNA Motifs with Nucleotide Adjacent Dependency," The 6th Asia-Pacific Bioinformatics Conference (APBC2008), Kyoto, Japan, 343-352 (January 2008)
  • Wun-Tat Chan, Francis Y. L. Chin, Xiangyu Hong and HingFung Ting, "Dynamic Offline Conflict-Free Coloring for Unit Disks", The 6th Workshop on Approximation and Online Algorithms (WAOA 2008), Universitat Karlsruhe, Germany, (September 2008)
  • Henry C.M. Leung, Qian Xiang, S.M. Yiu and Francis Y.L. Chin, "Predicting Protein Complexes from PPI Data: A Core-Attachment Approach", The Annual RECOMB Satellite Conference on Regulatory Genomics, Systems Biology and DREAM (Recomb-Sat/DREAM 08), MIT, Boston, USA (October-November 2008) - final version appears in Journal of Computational Biology 2009
  • Francis Y.L. Chin, Henry C.M. Leung, Wei-Lin Li and Siu-Ming Yiu, "Finding Optimal Threshold for Correction Error Reads in DNA Assembling", The 7th Asia-Pacific Bioinformatics Conference (APBC2009), Beijing, China, 153-161 (January 2009) - final version appears in BMC Bioinformatics 2009
  • Francis Y. L. Chin, Hingfung Ting, Yong Zhang, "1-Space Bounded Algorithms for 2-Dimensional Bin Packing", The 2nd Annual Meeting of Asian Association for Algorithms and Computation (AAAC 2009), Hangzhou, China (April 1009)
  • Francis Y. L. Chin, Zeyu Guo and He Sun, "Minimum Manhattan Network is NP-Complete", The 25th Annual ACM Symposium on Computational Geometry (SoCG 2009), 393-402, Denmark (June 2009) - final version appears in Discrete and Computational Geometry
  • Francis Y.L. Chin, Hing-Fung Ting, and Yong Zhang, "Variable-size Rectangle Covering", The 3rd Annual International Conference on Combinatorial Optimization and Applications (COCOA'09), Huangshan, China, 145-154 (June 2009)
  • Francis Chin, Marek Chrobak and Li Yan, "Algorithms for Placing Monitors in a Flow Network", The 5th International Conference on Algorithmic Aspects in Information and Management (AAIM 2009), San Francisco, USA (June 2009) - complete version appeared in Algorithmica 2012
  • Joseph Wun-Tat Chan, Francis Y.L. Chin, Hing-Fung Ting, and Yong Zhang, "Online Tree Node Assignment with Resource Augmentation", The 15th International Computing and Combinatorics Conference (COCOON'2009), Niagara Falls, New York, U.S.A.,  358-367 (July 2009)
  • Henry C.M. Leung, S.Y. Leung, S. M. Yiu, Francis Y. L. Chin, "Predicting Conserved Metabolic Pathways Leading to an Important Final Product", The 8th Annual International Conference on Computational Systems Bioinformatics Conference (CSB2009) (poster), Stanford University, USA (August 2009)
  • Yu Peng, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin and Ruiqiang Li, "Assembling Short Reads with Much Less Memory", The 11th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV2009), Tallinn, Estonia (September 2009)
  • Bin Yang, Yu Peng, Henry C.M. Leung, S.M. Yiu, J.C. Chen and Francis Y.L. Chin, "Unsupervised Binning of Environmental Genomic Fragments based on an Error Robust Selection of l-mers",The 3rd International Workshop on Data and Text Mining in Bioinformatics (DTMBIO 09) in the 18th ACM Conference on Information and Knowledge Management, Hong Kong (November 2009) - complete version appears in BMC Bioinformatics 2010
  • Francis Y. L. Chin, Hingfung Ting, Yong Zhang, "1-Bounded Space Algorithms for 2-Dimensional Bin Packing", The 20th International Symposium on Algorithms and Computation (ISAAC 2009), Hawaii, USA, 321-330 (December 2009) - complete version appears in International Journal of Foundations of Computer Science 2010
  • Yong Zhang, Francis Y.L. Chin and Hing-Fung Ting, "Approximated Distributed Minimum Vertex Cover Algorithms for Bounded Degree Graphs", The 16th Annual International Computing and Combinatorics Conference (COCOON 2010), Nha Trang, Vietnam (July 2010)
  • Joseph Wun-Tat Chan, Francis Y.L. Chin, Xin Han, Ka-Cheong Lam, Hing-Fung Ting, and Yong Zhang, "Deterministic Online Call Control in Cellular Networks and Triangle-Free Cellular Networks" The Fourth International Frontiers of Algorithmics Workshop (FAW 2010), Wuhan, China (August 2010)
  • Bin Yang, Yu Peng, Henry C.M. Leung, S.M. Yiu, Junjie Qin, Ruiqiang Li and Francis Y.L. Chin, "MetaCluster: Unsupervised Binning of Environmental Genomic Fragments and Taxonomic Annotation", The ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), Niagra Falls, New York, USA, 358-367 (August 2010)
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler", The Fourteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal (August 2010)
  • S.Y. Leung, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "Predicting Metabolic Pathways from Metabolic Networks with Limited Biological Knowledge", International Workshop on Graph Theoretic Analysis of Biological Networks, IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong (December 2010)
  • Yong Zhang, Jingchi Chen, Francis Y.L. Chin, Xin Han, Hing-Fung Ting, and Yung H. Tsin, "Improved Online Algorithms for 1-Space Bounded 2-Dimensional Bin Packing", The 21st International Symposium on Algorithms and Computation (ISAAC 2010), Jeju Island, Korea (December 2010)
  • Henry C.M. Leung, S.Y. Leung, Carlos Xiang, S.M. Yiu and Francis Y.L. Chin, "DMPFinder - Finding Differentiating Pathways with Gaps from Two Groups of Metabolic Networks", The 3rd International Conference on Bioinformatics and Computational Biology (BICoB), New Orleans USA (March 2011)
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome", The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), Vancouver (March 2011)
  • Francis Chin, Henry C.M. Leung and S.M. Yiu. "Non-Adaptive Complex Group Testing with Multiple Positive Sets", The 8th Annual Conference on Theory and Applications of Models of Computation (TAMC 2011), Tokyo Japan (May 2011), complete version appeared in Theoretical Computer Science
  • Yong Zhang, Francis Chin, Hingfung Ting, Xin Han and Zhuo Chang, "Online Algorithm for 1-Space Bounded Multi-Dimensional Bin Packing," The Joint Conference of FAW and AAIM 2011, Jinhua China (May 2011), to appear in Journal of Combinatorial Optimization.
  • Henry C.M. Leung, S.M. Yiu, Bin Yang, Yu Peng, Yi Wang, Zhihua Liu, Jingchi Chen, Junjie Qin, Ruiqiang Li, Francis Y.L. Chin, "A Robust and Accurate Binning Algorithm for Metagenomic Sequences with Arbitrary Species Abundance Ratio," HiTSeq: Conference on High Throughput Sequencing Analysis and Algorithms, Vienna, July 2011, appeared in Bioinformatics, 27(11):1489-95, Jun 2011.
  • Yong Zhang, Francis Y.L. Chin, Hing-Fung Ting, "Competitive Algorithms for Online Pricing", The 17th Annual International Computing and Combinatorics Conference (COCOON 2011), Dallas, Texas, 391-401 (August 2011), to appear in Discrete Mathematics, Algorithms and Applications (DMAA)
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "Meta-IDBA: "A de Novo Assembler for Metagenomic Data," The 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Vienna, July 2011, appeared in Bioinformatics, 27(13):i94-101, July 2011
  • Henry C.M. Leung, S.M. Yiu, John Parkinson and Francis Y.L. Chin, "IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating" RECOMB Conference on Regulatory and Systems Genomics November 12 - 15, 2012, also appeared in Journal of Computational Biology
  • Francis Y.L. Chin, Henry C.M. Leung and Siu-Ming Yiu, "Adaptive Phenotype Testing for AND/OR Items", The 22th International Symposium on Algorithms and Computation (ISAAC 2011), Yokohama, Japan, 754-763 (December 2011)
  • Junjie Yu, Henry C.M. Leung, S. M. Yiu, Yong Zhang, Francis Y.L. Chin, Nathan Hobbs, and Amy Y.X. Wang, "Phylogenetic Tree Reconstruction with Protein Linkage" International Symposium on Bioinformatics Research and Applications (ISBRA), Dallas, USA, LNBI 7292, pp. 315--327. May 2012
  • Yong Zhang, Francis Y.L. Chin, and Hing-Fung Ting, "Online Pricing for Multi Type of Items," Proceedings of the Joint Conference of FAW and AAIM 2012, Beijing China, 82-92, May 2012, complete paper appeared in Journal of Global Optimization.
  • Yu Peng, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "IDBA-UD: A de Novo Assembler for Single-Cell and Metagenomic Sequencing Data with Highly Uneven Depth," HiTSeq 2012, Long Beach CA, July 2012, also appeared Bioinformatics 28(11): 1420-1428, May 2012
  • S.M. Yiu and Francis Y.L. Chin, "Algorithms for constructing k-articulated network: a more powerful classification of phylogenetic networks", First RECOMB Satellite Conference Open Problem in Algorithmic Biology (RECOMB-AB), Petersburgh, Russia, August 2012.
  • Francis Chin and S. M. Yiu, "Phylogenetic tree reconstruction with protein linkage", First RECOMB Satellite Conference Open Problem in Algorithmic Biology (RECOMB-AB), Petersburgh, Russia, August 2012 (to appear).
  • Yi Wang, Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "MetaCluster 5.0: A two-round Binning Approach for Metagenomic Data for Low-abundance Species in a Noisy Sample," ECCB 2012, Bali, Switzerland, also appeared in Bioinformatics, 28(18): i356-i362, Sept 2012.
  • Henry C.M. Leung, S.M. Yiu, John Parkinson and Francis Y.L. Chin, "IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating"RECOMB System Biology/Regulatory Genomics/DREAM, San Francisco, Nov 2012, to appear in Journal of Computational Biology.
  • Yu Peng, Henry C.M. Leung, S.M. Yiu, Xin-Guang Zhu, Ming-Ju Lv and Francis Y.L. Chin, "IDBA-Tran: A More Robust de novo de Bruijn Graph Assembler for Transcriptomes with Uneven Expression Levels",  The 21th Annual International Conference on Intelligent Systems for Molecular Biology and 12th European Conference on Computational Biology (ISMB/ECCB 2013), Berlin, July 2013, also appeared in Bioinformatics, Vol. 29 ISMB/ECCB 2013, pages i326–i334.
  • Hoa Vu, Chin F.Y.L., Hon W.K., Leung H.C.M., Sadakane K., Sung W.K. and Yiu S.M., "Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees", The 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, North Carolina, May 2013
  • Yong Zhang, Francis Y. L. Chin, Hing-Fung Ting, Xin Han, Chung Keung Poon, Yung H. Tsin, Deshi Ye: "Online Algorithms for 1-Space Bounded 2-Dimensional Bin Packing and Square Packing". The 19th Annual International Computing and Combinatorics Conference (COCOON'13): 506-517, Hangzhou, China, June 2013, complete version to be appeared in Theoretical Computer Science
  • Xiao Zhu, Henry C.M. Leung, FrancisY.L. Chin, S.M.Yiu and Yadong Wang, "PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach", ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB), Washington DC, September 2013
  • Jie Yang, Henry C.M. Leung, S.M. Yiu, Yunpeng Cai, and Francis Y.L. Chin,"Intra- and Inter-sparse Multiple Output Regression with Application on Environmental Microbial Community Study", The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shanghai, December 2013, complete version to be appeared in BMC Bioinformatics
  • Yi Wang, Henry C.M. Leung, S.M.Yiu, Francis Y.L.Chin, "MetaCluster-TA: Taxonomic Annotation for Metagenomic Data Based on Assembly-assisted Binning", The 12th Asia-Pacific Bioinformatics Conference (APBC), Shanghai, January 2014
  • Henry C.M. Leung, S.M. Yiu and Francis Y.L. Chin, "IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information", The Eighteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2014), Pittsburgh, US (April 2014)

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    Research Grants:

    Hong Kong Industrial Support Fund/ITF:


    Last updated : January 2011