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


News

  1. Dr. Hui Li will start to work in the team as a postdoc research fellow from Oct. 1, 2013
  2. Our paper "Intensity-Based Skeletonization of CryoEM Grayscale Images Using a True Segmentation-Free Algorithm” was accepted by IEEE/ACM Transactions on Computational Biology and Bioinformatics in September.

Research Interests

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


Workshop Organization


Teaching


Selected Publications

REFEREED JOURNAL PUBLICATONS

  1. Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He, “Intensity-Based Skeletonization of CryoEM Grayscale Images Using a True Segmentation-Free Algorithm”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted.

  2. Hui Li, Chunmei Liu+, Legand Burge, and William Southerland, “Classification of Protein 3D Structures Using Artificial Neural Network”, International Journal of Machine Learning and Computing, vol. 2, no. 6, pp. 791-793 (2012).
  3. Hui Li, Jean-Claude Tounkara*, and Chunmei Liu+, “Prediction of Protein-Protein Docking Sites Based on a Cloud-Computing Pipeline”, International Journal of Machine Learning and Computing, vol. 2, no. 6, pp. 798-801 (2012).
  4. Hui Li, Chunmei Liu+, and Legand Burge, “Predicting Protein-Protein Interactions Based on PPI Networks”, International Journal of Machine Learning and Computing, vol. 2, no. 6, pp. 794-797 (2012).
  5. Hui Li, Chunmei Liu+, Legand Burge, William M. Southerland, “Identification of Two Post-Translational Modifications via Tandem Mass Spectrometry”, International Journal of Computational Biology and Drug Design, 5(3/4): 314-324 (9/2012).
  6. Hui Li, Chunmei Liu+, “Peptide Sequence Tag Generation for Tandem Mass Spectra Containing Post-translational Modifications”, International Journal of Computational Biology and Drug Design, 5(3/4): 325-334 (9/2012).
  7. Hui Li, Chunmei Liu+, “Biomarker Identification Using Text Mining”, Computational and Mathematical Methods in Medicine, doi:10.1155/2012/135780, Oct. 2012.
  8. Hui Li, Chunmei Liu+, “A Dynamic Data-Driven Framework for Biological Data Using 2D Barcodes”, Computational and Mathematical Methods in Medicine, doi:10.1155/2012/892098, Oct. 2012.
  9. Chunmei Liu+ and Yinglei Song, “Parameterized Complexity and Inapproximability of Dominating Set Problem in Chordal and near Chordal Graphs”, Journal of Combinatorial Optimization, 22(4): 684-698 (11/2011).
  10. Peng Chen, Chunmei Liu+, Legand Burge, Muhammad Mahmood, William Southerland, and Clay Gloster, “Prediction of Inter-Residue Contact Clusters from Hydrophobic Cores”, International Journal of Data Mining and Bioinformatics, Vol. 4, No. 6: 720-732, (2010).
  11. Peng Chen, Chunmei Liu+, Legand Burge, Jinyan Li, Muhammad Mahmood, William Southerland, and Clay Gloster, “DomSVRa: Domain Boundary Prediction with Support Vector Regression Using Amino Acid Alone”, Amino Acids, 39(3): 713-726, (2010).
  12. Chunmei Liu+, Legand Burge, and Ajoni Blake‡ , “Algorithms and Complexity of the Request-Service Problem”, Journal of Combinatorial Optimization, Vol. 20, No. 2: 180-193, (8/2010).
  13. 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, 4(1): 60-71 (2010).
  14. 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, Vol. 7, No. 5, 2009, pp. 773-788, Oct. 2009.
  15. Chunmei Liu+ and Yinglei Song, “Parameterized Dominating Set Problem in Chordal Graphs: Complexity and Lower Bound”, Journal of Combinatorial Optimization, Springer, Vol. 18, No. 1, pp. 87-97, July 2009.
  16. 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.
  17. 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, June 2008.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. Chunmei Liu+ and Louis Shapiro, “The Combinatorics of  M'=3M^3T and T'=T^3M”, Congressus Numernatium, 186 (2007), 185-192.
  23. Chunmei Liu+, Bo Yan, Yinglei Song, Ying Xu, Liming Cai+, “Peptide Sequence Tag Based Blind Identification of Post-Translational Modifications with Point Process Model”, The 14th International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Bioinformatics, 2006: 307-313.
  24. Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai, “Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment”, IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4): 423-432.
  25. Yinglei Song, Chunmei Liu, Russell L. Malmberg, Congzhou He, Liming Cai, “Memory Efficient Alignment between RNA Sequences and Stochastic Grammar Models of Pseudoknots”, International Journal of Bioinformatics Research Applications 2(3): 289-304 (2006).
  26. Yinglei Song, Jizhen Zhao, Chunmei Liu, Kan Liu, Russell L. Malmberg, Liming Cai, “RNA Structural Homology Search with a Succinct Stochastic Grammar Model”, Special Issue in Bioinformatics, Journal of Computational Science and Technology, 20(4): 454-464 (2005).
  27. Chunmei Liu+, Yinglei Song, Russell L. Malmberg, Liming Cai+, “Profiling and Searching for RNA Pseudoknot Structures in Genomes”, Transactions on Computational Systems Biology 2: 37-47 (2005).

REFEREED CONFERENCE PUBLICATIONS

  1. Xumin Liu, Rajendra Raj, Tom ReiChlmayr, Chunmei Liu, Alex Pantaleev, “Work in Progress: Incorporating Service-Oriented Programming Techniques into Undergraduate CS and SE Curricula”, The 43rd IEEE Frontiers in Education, Oct. 2013, accepted.
  2. Kamal Al Nasr, Chunmei Liu+, Mugizi Rwebangira, Legand Burge, “A Graph Approach to Bridge the Gaps in the Volumetric Electron Cryo-Microscopy Skeletons”, The 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC, May 2013, Lecture Notes in Computer Science, 7875: 211-223.
  3. Hui Li, Chunmei Liu+, “Prediction of Protein Structures Using GPU Based Simulated Annealing”, The 11th IEEE International Conference on Machine Learning and Applications (ICMLA 2012): 630-633, December 2012, Boca Raton, FL.
  4. Hui Li, Chunmei Liu+, Legand Burge, William Southerland, “Classification of Protein 3D Structures Using Artificial Neural Network”, The 1st International Conference on Information and Intelligent Computing (ICIIC 2012), December 2012, Chengdu, China.
  5. Hui Li, Jean-Claude Tounkara*, Chunmei Liu+, “Prediction of Protein-Protein Docking Sites Based on a Cloud-Computing Pipeline”, The 1st International Conference on Information and Intelligent Computing (ICIIC 2012), December 2012, Chengdu, China.
  6. Hui Li, Chunmei Liu+, and Legand Burge, "Predicting Protein-Protein Interactions Based on PPI Networks", The 1st International Conference on Information and Intelligent Computing (ICIIC 2012), December 2012, Chengdu, China.
  7. Hui Li, Chunmei Liu+, Legand Burge, William M. Southerland, “Spatial Index and Visualization of Protein Structure”, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2012): 540-543, Philadelphia, PA, October 2012.
  8. Hui Li, Chunmei Liu+, Legand Burge, Kyung Dae Ko, William M. Southerland, “Predicting Protein-Protein Interactions Using Full Bayesian Network”, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2012): 544-550, Philadelphia, PA, October 2012.
  9. Hui Li, Jean-Claude Tounkara*, Legand Burge, Chunmei Liu+, "A Rapid 3D protein Structural Classification using Pseudo 2D HMMs", 2012 IEEE International Conference on Granular Computing (GrC 2012), August 2012, 742-745, Hangzhou, China.
  10. Hui Li, Chunmei Liu+, Xumin Liu, "Collaboration Visualization on Large Dataset for Protein-Protein Interaction Network", 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), May 2012, pp. 177-183, San Diego, CA.
  11. Hui Li, Chunmei Liu+, William Southerland, "Blind Identification of Post-translational Modifications via Dynamic Time Warping Model", 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), May 2012, pp. 192-197, San Diego, CA.
  12. Kyung Dae Ko, Chunmei Liu+, Amen Ra Mashariki, Legand Burge, "SMISB : A System for Managing Minimum Information from omics’ Studies in Systems Biology", 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), May 2012, pp. 164-168, San Diego, CA.
  13. Hui Li, Chunmei Liu+, Mugizi Rwebangira, Legand Burge, and William Southerland, “Rapid Identification of Multi-PTMs Peptide Sequence Tags with a Graph Search Approach”, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011), November 2011, pp. 247-250, Atlanta, GA.
  14. Hui Li, Chunmei Liu+, Mugizi Rwebangira, Legand Burge, and William Southerland, “Rapid generation of peptide sequence tags with a graph search algorithm”, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011), November 2011, pp. 251-254, Atlanta, GA.
  15. Kyung Dae Ko, Chunmei Liu+, Mugizi Rwebangira, Legand Burge, and William Southerland, “The Development of a Proteomic Analyzing Pipeline for Identifying Proteins with Multiple RRMs and Predicting their Domain Boundaries”, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011), November 2011: 374-381, Atlanta, GA.
  16. Hui Li, Lauren Scott*, Chunmei Liu+, Mugizi Rwebangira, Legand Burge, and William Southerland, “ Rapid and Accurate Generation of Peptide Sequence Tags with a Graph Search Approach”, The 7th International Symposium on Bioinformatics Research and Applications (ISBRA 2011), May 2011, Lecture Notes in Bioinformatics, 2011, Volume 6674/2011, 253-261, Changsha, China.
  17. Hui Li, Chunmei Liu+, Xumin Liu, Macire Diakite*, Legand Burge, Abdul-Aziz Yakubu, and Williams Southerland, “Peptide Sequence Tag-based Blind Protein Identification-based SVM Model”, Proceedings of The Ninth IEEE International Conference on Machine Learning and Applications (ICMLA 2010): 979-984, Dec. 2010.
  18. Chunmei Liu+, Hui Li, Alison Leonce, Legand Burge, John Trimble, Peter Keiller, and Abdul-Aziz Yakubu, “A Heuristic Algorithm for Finding the Longest Pathways in a Biochemical Network”, Proceedings of the Ninth IEEE International Conference on Machine Learning and Applications (ICMLA 2010): 515-522, Dec. 2010.
  19. Xumin Liu, Chunmei Liu, Manjeet Rege, and Athman Bouguettaya, “Semantic Support for Adaptive Long Term Composed Services”, The 8th IEEE International Conference on Web Services (ICWS 2010), pp. 267-274, Miami, Florida, July, 2010.
  20. Chunmei Liu+, Yinglei Song, Junfeng Qu, and Anietie Andy* , “A Graph Algorithm for Extracting Features from Transcription Factor Binding Sites”, IEEE International Workshop on Applications of Machine Learning in Bioinformatics, pp. 68-72, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Nov. 2009, Washington, DC.
  21. Yinglei Song, Chunmei Liu, and Junfeng Qu, “Learning Parameters for Non-coding RNA Sequence-Structure Alignment”, IEEE International Workshop on Applications of Machine Learning in Bioinformatics, pp. 73-78, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009), Washington, DC, Nov. 2009.
  22. Chunmei Liu+, Yinglei Song, Moses Garuba, and Legand Burge, “HMMF: An Hidden Markov Model Based Approach for Motif Finding”, The 3rd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2009), June 2009.
  23. 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 3rd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2009), June 2009.
  24. 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), pp. 1-6, March 1-6, 2009, Cancun, Mexico.
  25. 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 (ICMLA 2008), IEEE, pp. 595-598, December 2008.
  26. 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 (ICMLA 2008), IEEE, pp. 703-708, December 2008.
  27. Moses Garuba, Chunmei Liu, and D. Fraites, “Intrusion Techniques: Comparative Study of Network Intrusion Detection Systems”, Proceedings of the 5th International Conference on Information Technology - New Generations (ITNG 2008), 794-798, IEEE Computer Society, April 2008.
  28. Moses Garuba, Chunmei Liu, and Alicia N. Washington, “A Comparative Analysis of Anti-Malware Software, Patch Management, and Host-Based Firewalls in Preventing Malware Infections on Client Computers”, Proceedings of the 5th International Conference on Information Technology - New Generations (ITNG 2008), 794-798, IEEE Computer Society, April 2008.
  29. 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 (ICMLA 2007), IEEE, p. 594-599, Dec. 2007.
  30. 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.
  31. Chunmei Liu+, Yinglei Song, and Louis Shapiro, “RNA Folding Including Pseudoknots: A new Parameterized Algorithm and Improved Upper Bound”, the 7th International Workshop on Algorithms in Bioinformatics (WABI 2007), September 2007, PA; Lecture Notes in Bioinformatics, 4645: 310-322, 2007.
  32. Rajni Goel, Moses Garuba, Chunmei Liu, and Trang Nguyen, “The Security Threat Posed by Steganographic Content on the Internet”, Proceedings of the 4th International Conference on Information Technology - New Generations (ITNG 2007), 794-798, IEEE Computer Society, April 2007.
  33. Chunmei Liu+ and Yinglei Song, “Exact Algorithms for Finding the Minimum Independent Dominating Set in Graphs”, The 17th International Symposium on Algorithms and Computation (ISAAC 2006), Dec. 18-20, Kolkata, India; Lecture Notes in Computer Science, 4288: 439-448, Springer-Verlag, 2007.
  34. Chunmei Liu+, Yinglei Song, Ping Hu, Russell L. Malmberg, Liming Cai+, “Efficient annotation of non-coding RNA structures including pseudoknots via automated filters”, Proceedings of Life Science Society Computational Systems Biology Conference (CSB 2006), Palo Alto, California, 99-110.
  35. Chunmei Liu+, Yinglei Song, Bo Yan, Ying Xu, Liming Cai+, “Fast De Novo Peptide Sequencing and Spectral Alignment via Tree Decomposition”, Pacific Symposium on Biocomputing (PSB 2006): 255-266.
  36. Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai, “Phylogenetic Network Inferences through Efficient Haplotyping”, The 6th International Workshop on Algorithms in Bioinformatics (WABI 2006): 68-79.
  37. Yinglei Song, Chunmei Liu, Russell L. Malmberg, Fangfang Pan, Liming Cai, “Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes, IEEE Computer Society Computational Systems Bioinformatics Conference (CSB 2005): 223-234.
  38. Chunmei Liu+, Yinglei Song, Russell L. Malmberg, Liming Cai+, “Profiling and Searching for RNA Pseudoknot Structures in Genomes”, International Workshop in Bioinformatics Research and Applications (IWBRA 2005), Lecture Notes in Computer Science 3515: 968-975.
  39. Yinglei Song, Chunmei Liu+, Xiuzhen Huang, Russell L. Malmberg, Liming Cai+, “Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment”, The 5th International Workshop on Algorithms in Bioinformatics (WABI 2005), Mallorca, Spain, Lecture Notes in Bioinformatics 3692: 376-388.

BOOK CHAPTERS

  1. Chunmei Liu+ and Hui Li, “In Silico Prediction of Post-Translational Modifications”, In Silico Tools for Gene Discovery, Series of Methods in Molecular Biology, 2011; 760: 325-40.

CONFERENCE ABSTRACTS

  1. Kamal Al Nasr, Geremew Begna*, Chunmei Liu, Mugizi Rwebangira, Legand Burge, “A Graph Approach to Bridge the Gaps in Volumetric Electron Cryo-Microscopy Skeletons”, The First Annual Howard University Research Day, the highest score in Computation & Biology Modeling, poster, Howard Univ., April 1, 2013.
  2. Oluwaseun Ademuwagun*, Mugizi Rwebangira, Chunmei Liu, Legand Burge, “Predicting Marked Code-switching in African Languages”, 2012 The 84th National Technical Association Conference (NTA 2012), Sep. 2012, Baltimore, MD.
  3. David Harris*, Mugizi Rwebangira, Chunmei Liu, Legand Burge, “Empirical Evaluation of Strategy-Proofness of Majority Judgment”, 2012 The 84th National Technical Association Conference (NTA 2012), Sep. 2012, Baltimore, MD.
  4. W ardell Samotshozo*, Mugizi Robert Rwebangira, Chunmei Liu, Legand Burge, Rhonda Davis†, Ronald Doku†, and William Southerland, “Pairing Algorithm for De Novo Sequencing of Tandem Mass Spectra”, The 83rd National Technical Association NTA Conference (NTA 2011), September 2011, Howard University, Washington, DC.
  5. Rhonda Davis*, Ronald Doku*, Wardell Samotshozo*, Mugizi Rwebangira, Chunmei Liu, Legand Burge, “De Novo Peptide Sequencing from Mass Spectrometry Data”, 2011 Symposium on Computing at Minority Institutions (ADMI 2011), poster, April 2011, Clemson, SC.
  6. Chunmei Liu+ and Legand Burge, “A Graph-based Approach for Protein Identification”, in the 4th Annual US HUPO Conference (US HUPO), March 16-19, 2008, Bethesda, MD.
  7. Chunmei Liu+ and Louis Shapiro, “The Combinatorics of  M'=3M^3T and T'=T^3M”, in the 38th Southeastern International Conference on Combinatorics, Graph Theory, and Computing (CGTC 38), March 5-9, 2007, Florida Atlantic University, Boca Raton, FL.

Post-doctoral Researcher Position Available for Application

A post-doctoral researcher position is available in Computational Biology in the Department of Systems Computer Science at Howard University, Washington, DC, USA. Applicants must have strong experience and desire to work in the field of computational biology. The specific research subject is in Computational Proteomics, especially in peptide sequencing and spectral alignment. Applicants with strong algorithmic and theoretical background are particularly sought. Independent research in any other area of computational biology is encouraged as well. Qualifications: a PhD in Computer Science or a related field and extensive experience in algorithm design and computer programming. To apply, please send a complete CV with the names and contact information of three references via email to Dr. Chunmei Liu at chunmei AT scs DOT howard DOT edu.