Chunmei Liu, Ph.D.

Associate Professor
Department of Systems and Computer Science
Howard University
Washington, DC 20059
Office: (202) 865-0056
Email: chunmei AT scs.howard.edu

Research Interests

• Computational Biology
• Algorithms
• Graph Theory
• Combinatorial Complexity

Students who are interested in Algorithms and Computational Biology are welcome to talk to me. Colleagues and visiting scholars are welcome to talk to me on potential collaborations.

Projects

• Emerging Frontier of Information (NSF STC award from Purdue University)
• Protein Identification via Graph Algorithms (2009 NSF Faculty Early CAREER Award)
• Genome-based Protein Structure Prediction (with Dr. Legand Burge, funded by Howard University, the Mordecai Wyatt Johnson Program)

Workshop Chair

• International Workshop on Applications of Machine Learning in Bioinformatics, 2009 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2009)

Teaching

• SYCS Computational Biology Track
• SYCS 572: Computability and Complexity
• SYCS 574: Computational Biology
• SYCS 341: Theory of Computation
• SYCS 570: Advanced Algorithms
• SYCS 354: CS III
• SYCS 652: Special Topics
• SYCS 599: Masters' Project
• SYCS 699: Masters' Thesis

Selected Publications

REFEREED JOURNAL PUBLICATONS

1. Peng Chen, Chunmei Liu, Legand Burge, Muhammad Mahmood, William Southerland, and Clay Gloster, "Protein Fold Recognition Using Genetic Algorithms and Feature Selection", Journal of Bioinformtics and Computational Biology, accepted.

2. Chunmei Liu, Legand Burge, and Ajoni Blake, "Algorithms and Complexity of the Request-Service Problem", Journal of Combinatorial Optimization, accepted.

3. Chunmei Liu, Yinglei Song, and Moses Garuba, "An Improved Upper Bound for Computing the Minimum Feedback Vertex Cover", Journal of Scientific and Practical Computing, accepted.

4. Chunmei Liu, Moses Garuba, and Yinglei Song, "Exact Algorithms for Finding the Minimum Independent Dominating Set in Graphs", Journal of Scientific and Practical Computing, accepted.

5. Jia Song, Chunmei Liu, Yinglei Song, Junfeng Qu, and Gurdeep Hura, "Alignment of Multiple Proteins with An Ensemble of Hidden Markov Models", International Journal of Data Mining and Bioinformatics, in press.

6. Chunmei Liu and Yinglei Song, "Parameterized Dominating Set Problem in Chordal Graphs: Complexity and Lower Bound", Journal of Combinatorial Optimization, Springer, in press.

7. Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai, "Graph Tree Decomposition Based Fast Peptide Sequencing and Spectral Alignment", International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, Vol. 2, No. 5, pp. 632 - 645, 2008.

8. Chunmei Liu, Ajoni Blake, and Legand Burge, "The Identification of Ion Types in Tandem Mass Spectra Based on a Graph Algorithm", Journal of Scientific and Practical Computing, Vol. 2, No. 1, 46-60, 2008.

9. Yinglei Song, Jia Song, Junfeng Qu, Chunmei Liu, Alberta Chi, and Yi Lu, "Single Node and Efficient Communications in Complex Networks", International Journal of Computational Science, Vol. 2, No. 2, pp. 250-260, 2008.

10. Chunmei Liu, Yinglei Song, Jiang Li, Moses Garuba, and Legand Burge, "An Asymptotic Upper Bound for Tree Widths of Graphs of Bounded Degree", International Journal of Computational Science, Vol. 2, No. 4, pp. 460-474, 2008.

11. Chunmei Liu, Yinglei Song, and Legand Burge, "Parameterized Lower Bound and Inapproximability of Polylogarithmic String Barcoding", Journal of Combinatorial Optimization, Vol. 16, No.1, 39-49, July 2008.

12. Liming Cai, Xiuzhen Huang, Chunmei Liu, Francis Rosamond, and Yinglei Song, "Parameterized Complexity and Biopolymer Sequence Comparison", invited paper to The Computer Journal, Special Issue in Parameterized Complexity, Oxford University Press, 51(3): 270-291, May 2008.

13. Chunmei Liu and Louis Shapiro, "The Combinatorics of M' = 3MT", Congressus Numernatium, 186 (2007), 185-192.

14. Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, and Liming Cai, "Peptide Sequence Tag-Based Blind Identification of Post-Translational Modifications with Point Process Model", Bioinformatics, Vol. 22, No. 14, 307-313, Oxford University Press, 2006.

15. Yinglei Song, Chunmei Liu, Russell Malmberg, Congzhou He, and Liming Cai, "Memory Efficient Alignment between RNA Sequences and Stochastic Grammar Models of Pseudoknots", International Journal of Bioinformatics Research and Applications, Vol. 2, No. 3, 289-304, Inderscience Publishers, 2006.

16. Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell Malmberg, Ying Xu, and Liming Cai, "Efficient Biopolymer Structure-Sequence Alignment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 3, No. 4, 423-431, IEEE Computer Society, 2006.

17. Chunmei Liu, Yinglei Song, Russell Malmberg, and Liming Cai, "Profiling and Searching for RNA Pseudoknot Structures in Genomes", Transactions on Computational Systems Biology 2: 37-47, Springer-Verlag, 2005.

18. Yinglei Song, Jizhen Zhao, Chunmei Liu, Kan Liu, Russell Malmberg, and Liming Cai, "RNA Structural Homology Search with a Succinct Stochastic Grammar Model", Journal of Computer Science and Technology, Special Issue in Bioinformatics, 20 (4): 454-464, Springer-Verlag, 2005.

19. Chunmei Liu, Yinglei Song, Moses Garuba, and Legand Burge, "HMMF: An Hidden Markov Model Based Approach for Motif Finding", The 3^rd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2009), June 2009.

20. Peng Chen, Chunmei Liu, Legand Burge, Muhammad Mahmood, William Southerland, and Clay Gloster, "DomSVR: Domain Boundary Prediction with Support Vector Regression and Evolutionary Information", The 3^rd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2009), June 2009.

21. Peng Chen, Chunmei Liu, Legand Burge, Mohammad Mahmood, William Southerland, Clay Gloster, and Bing Wang, "IRCDB: A Database of Inter-residues Contacts in Protein Chains", The First International Conference of Databases, Knowledge, and Data Applications (DBKDA 2009), March 1-6, 2009, Cancun, Mexico.

22. Jia Song, Chunmei Liu, Yinglei Song, and Junfeng Qu, "Clustering for DNA Microarray Data analysis with a Graph Cut Based Algorithm", The Seventh International Conference on Machine Learning and Applications (ICLMA 2008), IEEE, pp. 595-598, December 2008.

23. Peng Chen, Chunmei Liu, Legand Burge, Muhammad Mahmood, Bill Southerland, and Clay Gloster, "Prediction of Inter-residue Contact Clusters from Hydrophobic Cores", The Seventh International Conference on Machine Learning and Applications (ICLMA 2008), IEEE, pp. 703-708, December 2008.

24. Moses Garuba, Chunmei Liu, and D. Fraites, "Intrusion Techniques: Comparative Study of Network Intrusion Detection Systems", Proceedings of the 5^th International Conference on Information Technology - New Generations (ITNG 2008), 794-798, IEEE Computer Society, April 2008.

25. Moses Garuba, Chunmei Liu, and Alicia N. Washington, "Comparative Analysis of Anti-Malware Software, Patch Management, and Host-Based Firewalls in Preventing Malware Infections on Client Computers", Proceedings of the 5^th International Conference on Information Technology - New Generations (ITNG 2008), 794-798, IEEE Computer Society, April 2008.

26. Hui Guo, Jiang Li, Alicia N. Washington, Chunmei Liu, Marcus Alfred, Rajni Goel, Legand Burge, and Peter Keiller, "Performance Analysis of Homing Pigeon Based Delay Tolerant Networks", Proceedings of 2007 Military Communications Conference (MILCOM 2007), Oct., 2007, Orlando, FL.

27. Jia Song, Chunmei Liu, Yinglei Song, Junfeng Qu, and Gurdeep Hura, "Alignment of Multiple Proteins with An Ensemble of Hidden Markov Models", Proceedings of the Sixth International Conference on Machine Learning and Applications (ICLMA 2007), IEEE, p. 594-599, 2007.

28. Chunmei Liu, Yinglei Song, and Louis Shapiro, "RNA Folding Including Pseudoknots: A new Parameterized Algorithm and Improved Upper Bound", The 7^th International Workshop on Algorithms in Bioinformatics (WABI 2007), Lecture Notes in Bioinformatics, 4645: 310-322, 2007.

29. Rajni Goel, Moses Garuba, Chunmei Liu, and Trang Nguyen, "The Security Threat Posed by Steganographic Content on the Internet", Proceedings of the 4^th International Conference on Information Technoloy - New Generations (ITNG 2007), 794-798, IEEE Computer Society, 2007.

30. Chunmei Liu and Yinglei Song, "Exact Algorithms for Finding the Minimum Independent Dominating Set in Graphs", The 17^th International Symposium on Algorithms and Computation (ISAAC 2006), Kolkata, India; Lecture Notes in Computer Science, 4288: 439-448, Springer-Verlag, 2007.

31. Chunmei Liu, Yinglei Song, Ping Hu, Russell Malmberg, and Liming Cai, "Efficient Annotation of Non-coding RNA Structures Including Pseudoknots via Automated Filters", Proceedings of 2006 LSS International Computational Systems Bioinformatics Conference (CSB 2006), Stanford, CA, 99-110, Imperial College Press, 2006.

32. Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, and Liming Cai, "Peptide Sequence Tag-Based Blind Identification of Post-Translational Modifications with Point Process Model", The 14^th International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil (acceptance rate: 16%), 2006.

33. Yinglei Song, Chunmei Liu, Russell Malmberg, and Liming Cai, "hylogenetic network inference through efficient haplotyping", The 6^th International Workshop on Algorithms in Bioinformatics (WABI 2006), Zurich, Switzerland; Lecture notes in Computer Science, 4175: 68-79, Springer-Verlag, 2006.

34. Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, and Liming Cai, "Fast de novo peptide sequencing and spectral alignment via tree decomposition" Proceedings of the 11^th International Pacific Symposium on Biocomputing (PSB 2006), 255-266, World Scientific Publisher Co, 2006.

35. Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell Malmberg, Ying Xu, and Liming Cai, "Efficient Parameterized Algorithm for Biopolymer Structural-Sequence Alignment", The 5^th International Workshop on Algorithms in Bioinformatics (WABI 2005), Mallorca, Spain; Lecture Notes in Bioinformatics, 3692: 376-388, Springer-Verlag, 2006.

36. Yinglei Song, Chunmei Liu, Russell Malmberg, Fangfang Pan, and Liming Cai, "Tree Decomposition Based Fast Search of RNA Secondary Structures in Genomes", Proceedings of 2005 IEEE International Computational Systems Bioinformatics Conference (CSB 2005), 223-234 (acceptance rate: 13%), IEEE Computer Society, 2005.

37. Chunmei Liu, Yinglei Song, Russell Malmberg, and Liming Cai, "Profiling and Searching for RNA Pseudoknot Structures in Genomes? the 1^st International Workshop on Bioinformatics Research and Application (IWBRA 2005); Lecture Notes in Computer Science, 3515: 968-975, Springer-Verlag, 2005.