Papers |
2008 |
E. Zeng, C. Ding, G. Narasimhan, S. Holbrook Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction, LSS Computational Systems Bioinformatics Conference (CSB2008) , To Appear, 2008. |
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| PNAS Website |
K. Mathee, Giri Narasimhan, C. Valdes, X. Qiu, J. Matewish,
M. Koehrsen, A. Rokas, C. Yandava, R. Engels, E. Zeng,
R. Olavarietta, M. Doud, R. Smith, P. Montgomery, J. White,
P. Godfrey, C. Kodira, B. Birren, J. Galagan, S. Lory, Dynamics of Pseudomonas aeruginosa genome evolution, Proceedings of the National Academy of Sciences (PNAS), 105(8):3100-05, 2008. |
| IJBRA Website |
Patricia Buendia and Giri Narasimhan, The Role of Internal Node Sequences and the Molecular Clock in the Analysis of Serially-Sampled Data, International Journal of Bioinformatics Research and Applications (IJBRA), 4(1):107-121, 2008. |
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Vagelis Hristidis, Fernando Farfan, Redmond Burke, Anthony Rossi,
Jeffrey White, Challenges for Information Discovery on Electronic Records, Book chapter in Next generation of data mining Eds. Hillol Kargupta, Jiawei Han, Philip Yu, Rajeev Motwani, Vipin Kumar, CRC - Taylor and Francis 2008. |
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Fernando Farfan, Vagelis Hristidis, Anand Ranganathan, Redmond Burke, Search on XML-based Electronic Medical Records, IEEE ICDE, 2008. |
2007 |
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Vagelis Hristidis, Fernando Farfan, Redmond Burke, Anthony Rossi,
Jeffrey White, Information Discovery on Electronic Records, National Science Foundation Symposium on Next Generation of Data Mining and Cyber-Enabled Discovery for Innovation (NGDM), 2007. |
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Patricia Buendia and Giri Narasimhan, Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach, Bioinformatics, 23(22):2993-3000, 2007; doi: 10.1093/bioinformatics/btm413 |
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T. Milledge, G. Zheng, T. Mullins, and Giri Narasimhan, SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing IEEE Conference on Bioinformatics and Bioengineering (BIBE2007) , 1343-47, 2007. |
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E. Zeng, C. Yang, T. Li, and Giri Narasimhan, On the Effectiveness of Constraints Sets in Clustering Genes IEEE Conference on Bioinformatics and Bioengineering (BIBE2007) , 79-86, 2007. |
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E. Zeng, K. Mathee, and Giri Narasimhan, IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data, LSS Computational Systems Bioinformatics Conference (CSB2007) , 227-35, 2007. |
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H. Alvarez, D. Chatfield, D. Cox, E. Crumpler, C. D'Cunha,
R. Gutierrez, J. Ibarra, E. Johnson, K. Kumar, Tom
Milledge, Giri Narasimhan, M. Sadjadi,
C. Zhang CyberBridges: A model collaboration infrastructure for e-Science, Proceedings of the IEEE CCGrid Conference, 65-72, 2007. |
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Patricia Buendia and Giri Narasimhan, Searching for recombinant donors in a phylogenetic network of serial samples, Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA), 109-20, 2007. |
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Erliang Zeng and Giri Narasimhan, Enhancing Motif Discovery using Comparative Genomics Data, Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA), 329-37, 2007. |
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| Book Info |
C. Yang, E. Zeng, K. Mathee, G. Narasimhan PlasmoTFBM: An intelligent queriable database for predicted transcription factor binding motifs in Plasmodium falciparum , In Methods of Microarray Data Analysis V , McConnell, Lin, Hurban (Eds.), Springer, p121-136, 2007. |
2006 |
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Vagelis Hristidis, Peter Clarke, Nagarajan Prabakar, Yi Deng,
Jeffrey White, Redmond Burke, A flexible approach for electronic medical records exhcange, International Workshop on Helath Information and Knowledge Management (HIKM), 2006. |
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W. Peng, Tao Li, and Giri Narasimhan, Mining the Database of Transcription Binding Sites, Proceedings of the 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE), p61-64, 2006. |
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| Abstract |
Patricia Buendia, and Giri Narasimhan, Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network, Bioinformatics, 22(18):2313-2314, 2006. |
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D. N. Kuhn, G. Narasimhan, K. Nakamura, J. S. Brown,
R. J. Schnell, A. W. Meerow, Identification of Cacao TIR NBS-LRR resistance gene analogs and their use as genetic markers, Journal of American Society for Horticultural Science, 131(6):806-813, 2006. |
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S. Ghandeharizadeh, G. Narasimhan, Challenges of a "What"-Oriented Framework for On-the-fly Integration of Biomedical Data, White Paper in response to National Library of Medicine Request for Information (RFI) on "Advanced Informatics for Biomedicine", February 2006. |
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C. Yang, D. Mills, K. Mathee, Y. Wang, K. Jayachandran,
M. Sikaroodi, P. Gillevet, J. Entry, G. Narasimhan, An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA, Journal of Microbiological Methods, 65(1):49-62, 2006. |
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Gaolin Zheng, Tom Milledge, E. Olusegun George,
and Giri Narasimhan, Pooling Evidence to Identify Cell Cycle-Regulated Genes, Proceedings of the International Workshop on Bioinformatics Research and Applications (IWBRA), Lecture Notes in Computer Science, Vol. 3992, Springer Verlag, p694-701, 2006. |
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Tom Milledge, Gaolin Zheng,
and Giri Narasimhan, Discovering Sequence-Structure Patterns in Proteins with Variable Secondary Structure, Proceedings of the International Workshop on Bioinformatics Research and Applications (IWBRA), Lecture Notes in Computer Science, Vol. 3992, Springer Verlag, p702-709, 2006. |
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Patricia Buendia, Tim Collins,
and Giri Narasimhan, Reconstructing ancestor-descendant lineages from serially-sampled data: a comparison study, Proceedings of the International Workshop on Bioinformatics Research and Applications (IWBRA), Lecture Notes in Computer Science, Vol. 3992, Springer Verlag, p807-814, 2006. |
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| Springer Website |
V. Renugopalakrishnan, X. Wei, G. Narasimhan,
C. S. Verma, P. Li, and A. Anumanthan, Enhancement of Protein Thermal Stability: Toward the design of robust proteins for bionanotechnological applications, chapter 8 Bionanotechnology: Proteins to Nanodevices, p117-139, Springer, 2006. |
2005 |
| Publisher Website |
V. Renugopalakrishnan, R. Garduno-Juarez, G. Narasimhan,
C. S. Verma, X. Wei, and P. Li, Rational Design of Thermally Stable Proteins: Relevance to Bionanotechnology, Journal of Nanoscience and Nanotechnology, 5(11), p1759-1767, 2005. |
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C. Yang, E. Zeng, T. Li,
G. Narasimhan A Knowledge-Driven Method to Evaluate Multi-Source Clustering, Proceedings of the International Symposium on Parallel and Distributed Processing and Applications (ISPA'05), Lecture Notes in Computer Science, Vol. 3759, Springer Verlag, p196-202, 2005. |
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C. Yang, E. Zeng, T. Li,
G. Narasimhan Clustering genes using gene expression and text literature data, Proceedings of CSB'05, p329-340, August 2005. |
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T. Milledge, S. Khuri, X. Wei, C. Yang,
G. Zheng, G. Narasimhan Sequence Structure Patterns: Discovery and Applications, Proceedings of the 6th Atlantic Symposium on Computational Biology and Genome Informatics (CBG), p1282-1285, July 2005. |
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Y. Wang, C. Yang, K. Mathee,
G. Narasimhan Clustering using Adaptive Self-Organizing Maps (ASOM) and Applications, Proceedings of the International Workshop on Bioinformatics Research and Applications (IWBRA), Lecture Notes in Computer Science, Vol. 3515, Springer Verlag, p944-951, 2005. |
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M. He, G. Narasimhan S. Petoukhov, (Editors) Advances in Bioinformatics and its Applications, (Series in Mathematical Biology and Medicine), World Scientific Press, June 2005. [ISBN: 981256148X] |
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M. Handfield, J. Mans, G. Zheng, M.C. Lopez, A. Progulske-Fox,
G. Narasimhan, H.V. Baker, R.J. Lamont, Distinct Expression Profiles Characterize Oral Epithelium-Microbiota Interactions, Cellular Microbiology, 7(6):811-823, 2005. Electronic version of the article published in Cellular Microbiology is provided: complete citation information for the final version of the paper, as published in the print edition of Cellular Microbiology, is available on the Blackwell Synergy online delivery service, accessible via the journal's website at http://www.blackwellpublishing.com/cmi or http://www.blackwell-synergy.com. |
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G. Zheng, E. O. George, G. Narasimhan Microarray Data Analysis Using Neural Network Classifiers and Gene Selection Methods, In Methods of Microarray Data Analysis IV, Shoemaker, J. S., Lin, S. M. (Eds.) Springer, p207-222, 2005 [ISBN: 0-387-23074-2]. |
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J. Ye, T. Li, T. Xiong, R. Janardan. Using Uncorrelated Discriminant Analysis for Tissue Classification with Gene Expression Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics., In Press, 2005. |
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T. Li,
C. Zhang, M. Ogihara. A Comparative Study of Feature Selection and Multiclass Classification Methods for Tissue Classification Based on Gene Expression, Bioinformatics, In Press, 2005 |
2004 |
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L. Bobadilla, F. Nino, G. Narasimhan Predicting and Characterizing Metal-Binding Sites Using Support Vector Machines, Proceedings of ICBA'04, p307-318, December 2004. |
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C. Yang, E. Zeng, K. Mathee, G. Narasimhan Querying a Database of Regulatory Elements, Proceedings of ICBA'04, p81-92, December 2004. |
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T. Milledge, G. Zheng, G. Narasimhan Applications of Data Mining in Epitope Prediction, Proceedings of ICBA'04, p390-401, December 2004. |
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Y. Sun, Z. Deng, K. Mathee, G. Narasimhan Training Set Design for Pattern Discovery with Applications to Protein Motif Detection, Proceedings of ICBA'04, p240-251, December 2004. |
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G. Zheng, R. Capocasale, B. Amegadzie, P. Bugelski, J. Lu Analysis of the Effects of Recombinant Human Erythropoietin (EPO) on Murine Bone Marrow Populations using Mixture Modeling Techniques, Proceedings of ICBA'04, p285-296, December 2004. |
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C. Yang, E. Zeng, K. Mathee, G. Narasimhan Mining Regulatory Elements in the Plasmodium falciparum Genome Using Gene Expression Data, Proceedings of CAMDA'04: Critical Assessment of Microarray Data Analysis, Durham, NC, p16-20, November 2004. |
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P. Buendia, G. Narasimhan MinPD: Distance-based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies, Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford, CA, p110-119, 2004. |
| Abstract |
A. Plata, G. Narasimhan, D. Ohman, J. Barakat, M. Hentzer,
S. Molin, A. Kharazmi, N. Hoiby, K. Mathee, Detection of Alginate production affects Pseudomonas aeruginosa biofilm development and architecture, but is not essential for biofilm formation, Journal of Medical Microbiology, Vol. 53(7):679-690, 2004. |
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D. Cazalis, T.Milledge, G. Narasimhan Probe Selection Algorithms, Proceedings of the SCI Conference, Orlando, July 2004. |
2003 |
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G. Zheng, E. O. George, G. Narasimhan Neural Network Classifiers and Gene Selection Methods for Microarray Data on Human Lung Adenocarcinoma, Proceedings of CAMDA'03: Critical Assessment of Microarray Data Analysis, Durham, NC, 63-67, November 2003. |
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X. Wei, D. Kuhn, G. Narasimhan Degenerate primer design via clustering, Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford, CA, p75-83, August 2003. |
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K. Mathee, G. Narasimhan, Detection of DNA_binding helix-turn-helix motifs in proteins using the pattern dictionary method, Methods in Enzymology, Vol. 370, Chapter 22, 250-264, 2003. |
2002 |
| Abstract |
T. R. Sutter, X.-R. He, P. Dimitrov, L. Xu, G. Narasimhan,
E. O. George, C. H. Sutter, C. Grubbs,
R. Savory,M. Stephan-Gueldner, D. Kreder, M. J. Taylor,
R. Lubet, T. A. Patterson, T. W. Kensler, Multiple comparisons model-based clustering and ternary pattern tree numerical display of gene response to treatment: Procedure and application to the preclinical evaluation of chemopreventive agents, Molecular Cancer Therapeutics, 1(14):1283-1292, 2002. |
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G. Narasimhan, C. Bu, Y. Gao, X. Wang, N. Xu, K. Mathee, Mining Protein Sequences for Motifs, Journal of Computational Biology, 9(5):707-720, 2002. |
2000 and earlier |
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Yuan Gao, Isidore Rigoutsos, Aris Floratos, Laxmi Parida, and G.
Narasimhan Unsupervised Building and Exploitation of Composite Descriptors for Collection of Proteins and Protein Fragments, IBM Technical Report , 2000. |
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Yuan Gao, Kalai Mathee, G. Narasimhan, and Xuning Wang Motif Detection in Protein Sequences, Proceedings of SPIRE'99 , pages 63-72, Cancun, September 1999. |
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G. Hernandez, G. Narasimhan, and L. F. Nino, Evolutionary Set Matching Smart Engineering Systems: Neural Networks, Fuzzy Logic, Evolutionary Programming, Data Mining, and Rough Sets , Volume 8, Eds.: C. H. Dagli, M. Akay, A. L. Buczak, O. Ersoy, B. R. Fernandez, pages 265-272, 1998. |
Posters |
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Daniel Cazalis, Tom Milledge, G. Narasimhan, Probe Selection Problem: Structure and Algorithms, In Silico Conference, Atlanta, November 2003. |
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Gaolin Zheng, Erliang Zeng, E.O. George, G. Narasimhan, " Integrating Information from Different Microarray Data Sets, In Silico Conference, Atlanta, November 2003. |
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Tom Milledge, Chengyong Yang, G. Narasimhan, Seqeunce-Structure Patterns in Proteins, In Silico Conference, Atlanta, November 2003. |
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Nestor A. Parra, G. Narasimhan, Sanjiv S. Samant, An optmized point-based multimodality image registration algorithm, AAPM, 2003. |
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Y. Wang, C. Yang, D. Mills, K. Mathee, P. Gillevet, J. Entry,
K. Jayachandran, G. Narasimhan, Ecoinformatics Tools: unsupervised clustering and classification of microbial communities using ALH profile data from 16S rRNA, ASM 2003. |
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C. Yang, Y. Wang, D. Mills, K. Mathee, P. Gillevet, J. Entry,
K. Jayachandran, G. Narasimhan, An Ecoinformatics tool for microbial diversity studies: supervised classification of ALH profile of 16S rRNA, ASM 2003. |
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G. Narasimhan, Changsong Bu, Yuan Gao, Tom Milledge, Xuning Wang, Ning Xu,
Gaolin Zheng, and Kalai Mathee, Helix-Turn-Helix Motif Detection in Protein Sequences , ACT 2002. |
 [BIP] |
Zhou Ji, Qichang Li, Arne Heydorn, Soren Molin, Kalai Mathee, and
G. Narasimhan Quantitative Analysis of Pseudomonas aeruginosa Biofilm Images using Fractal Dimensions, ASM Biofilms 2000 , Big Sky, MT, July 16-20, 2000. SOFTWARE: Trial Version Available for download. [Software: BIP] |
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[Poster ps Version] [Abstract ps Version] |
Yuan Gao, Mu Yang, Xingqiang Wang, Kalai Mathee, and G. Narasimhan Detection of HTH Motifs via Data Mining Poster at Int'l Conference on Bioinformatics , Atlanta, Nov 6-9, 1997. SOFTWARE: Go to GYM Home Page. |
Recent Talks |
| G. Narasimhan, Pattern Discovery and its Applications to Bioinformatics, Tutorial Session, International Conference on Intelligent Sensing and Information Processing, Chennai, India, January 4, 2004. | G. Narasimhan, Applications of Pattern Discovery in Bioinformatics, Invited Speaker, International Conference on Intelligent Sensing and Information Processing, Chennai, India, January 4, 2004. | G. Narasimhan, Applications of Pattern Discovery in Bioinformatics, Invited Speaker, Fourth International Conference on Information Technology, Gopalpur-on-Sea, India, December 21, 2001. |
[6.5MB] |
G. Narasimhan, "Bioinformatics Research at FIU", Department Seminar, October 10, 2003. |
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G. Narasimhan, "What is Bioinformatics? Why Bioinformatics?", Survey Talk at Student ACM Seminar, April 10, 2002. |
Software |
| DePiCt (Web Version 2.0) | C. Archer, J. Farrow & G. Narasimhan | Web Version of Software for designing degenerate primers. | DePiCt 1.0 | X. Wei & G. Narasimhan | Software for designing degenerate primers. | GYM 2.0 | C. Bu, K. Mathee, & G. Narasimhan | Improved Software for Detecting HTH motif in Proteins. |
| GYM 1.0 | Y. Gao, X. Wang, K. Mathee, & G. Narasimhan | Software for Detecting HTH motif in Proteins. | BIP | Q. Li, J. Zhou, K. Mathee, & G. Narasimhan | Software for Biofilm Image Processing. | m-NP | G. Zheng & G. Narasimhan | Java software to analyze replicate microarray data using non-parametric statistics. | ProteinAlign | G. Zheng & G. Narasimhan | MATLAB software to align two protein molecules. |
Theses/Dissertations |
| Gaolin Zheng | PhD Dissertation, 2006, | FIU | Microarray Data Analysis |
| Patricia Buendia | PhD Dissertation, 2006, | FIU | Phylogenetic Analysis of Within-host Serially-sampled Data |
| Chengyong Yang | PhD Dissertation, 2006, | FIU | Knowledge Discovery Using Multiple Sources of Biological Data |
| Minchi Hu | Masters Thesis, 2004, | FIU | Geometric Hashing |
| Xintao Wei | Masters Thesis, 2003, | FIU | Degenerate Primer Design via Clustering |
| Yong Wang | Masters Thesis, 2003, | FIU | Unsupervised Clustering Techniques and its Application to Ecoinformatics Data |
| Zongying Xi | Masters Thesis, 2002, | UoM | Microarray Data Analysis |
| Meera Krishnan | Masters Thesis, 2002, | UoM | Pattern Discovery in anti-DNA Antibodies |
| Gaolin Zheng | Masters Thesis, 2001, | UoM | Software Tools for Bioinformatics Applications |
| Yuan Gao | PhD, 2001, | UoM | Motif-Based Protein Strcuture and Function Prediction |
| Xiao-rui He | Masters Thesis, 2001, | UoM | Gene Expression Patterns and Clusters |
| Junmin Liu | Masters Thesis, 2001, | UoM | DNA Microarray Data Management and Analysis |
| Ning Xu | Masters Thesis, 2000, | UoM | GYM 3.0: Improved Motif Detection in Protein Sequences |
| Zhou Ji | Masters Thesis, 2000, | UoM | Quantitative Analysis of Biofilm Images Using Fractal Dimensions |
| Changsong Bu | Masters Thesis, 1999, | UoM | Detecting Helix-Turn-Helix Motifs in Proteins |
| Yuan Gao | Masters Thesis, 1997, | UoM | Detection of Helix-Turn-Helix Motifs in Proteins |