JOURNAL ARTICLES PUBLISHED (Peer Reviewed)

Munoz, S.*, Guerrero, F.D., Kellogg, A.*, Heekin, A.M., Leung, M.-Y. (2017). Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis. PLOS ONE. Available at http://dx.doi.org/10.1371/journal.pone.0172326.


Guerrero, F., Kellogg, A.*, Ogrey, A. N.*, Heekin, A. M., Barrero, R., Bellgard, M. I., Dowd, S. E., Leung, M.-Y., (2016). Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus. Ticks and Tick-borne Diseases, 7(5),670-677. Available at dx.doi.org/10.1016/j.ttbdis.2016.02.014.


Zhang, B.*, Yehdego, D. T.*, Johnson, K. L., Leung, M.-Y., Taufer, M., (2013). Enhancement of Accuracy and Efficiency for RNA Secondary Structure Prediction by Sequence Segmentation and MapReduce. BMC Structural Biology, 13 (Suppl. 1)(S3), 1-24. www.biomedcentral.com/1472-6807/13/S1/S3

 

Cruz-Cano, R., Lee, M.-L. T., Leung, M.-Y., (2012). Logic Minimization and Rule Extraction for Identification of Functional Sites in Molecular Sequences. BioData Mining, 5(10), 1-21. www.biodatamining.org/content/5/1/10

 

Cruz-Cano, R.*, Chew, D.S.H.*, Choi, K.P., Leung, M.-Y., (2010). Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction. INFORMS J. Computing, 22(3), 457-470.

 

Schaubert, K. L., Price, D. A., Salkowitz, J. R., Sewell, A. K., Sydney, J., Asher, T. E., Blondelle, S. E., Adams, S., Marincola, F. M., Joseph, A., Sette, A., Douek, D. C., Ayyavoo, V., Storkus, W., Leung, M.-Y., Ng, H. L., Yang, O. O., Goldstein, H., Wilson, D. B., Kan-Mitchell, J., (2010). Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes. European Journal Immunology, 40(7), 1950-1962. onlinelibrary.wiley.com/doi/10.1002/eji.200940079/full

 

Rosskopf, J. J.*, Upton, III, J. H.*, Rodarte, L.*, Romero, T. A.*, Leung, M.-Y., Taufer, M., Johnson, K. L., (2010). A 3’ terminal stem-loop structure directs initiation of Nodamura virus RNA2 negative strand synthesis. Virus Res./Elsevier B.V., 150(1-2), 12-21. www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20176063

 

Greenberg, H., Holder, A.G., Leung, M.-Y., Schwartz, R., (2009). Computational Biology and Medical Applications: Opportunities for Operations Research. ORMS Today, 36(3), 34-39. viewer.zmags.com/publication/ec30fb3c#/ec30fb3c/36

 

Taufer, M., Licon, A.*, Araiza, R.*, Mireles, D.*, Gultyaev, A., Van Batenburg, F.H.D., Leung, M.-Y., (2009). PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots. Nucleic Acids Research, 37((Database Issue) D), 127-135.

 

Grosu, D.*, Chronopoulos, A.T., Leung, M.-Y., (2008). Cooperative Load Balancing in Distributed Systems. Concurrency and Computation: Practice and Experience, 20, 1953-1976.

 

Taufer, M., Leung, M.-Y., Solorio, T., Licon, A., Mireles, D., Johnson, K.L., (2008). RNAVLab: A Virtual Laboratory for Studying RNA Secondary Structures Based on Grid Computing Technology. Parallel Computing, 34, 661-680.

 

Chew, D. S.H.*, Leung, M.-Y., Choi, K.-P., (2007). AT Excursion: a New Approach to Predict Replication Origins in Viral Genomes by Locating AT-rich Regions, BMC Bioinformatics, 8:. BMC Bioinformatics, 8, 163.

 

McMullin, B.T.*, Leung, M.-Y., Shanbag, A.S., McNulty, D., Mabrey, J.D., Agrawal, C.M., (2006). Correlating Subjective and Objective Descriptors of Ultra High Molecular Weight Wear Particles from Total Joint Prostheses. Biomaterials, 27, 752-757.

 

Leung, M.-Y., Choi, K.P., Xia, A., Chen, L.H.Y., (2005). Nonrandom Clusters of Palindromes in Herpesvirus Genomes. J. Computational Biology. J. Computational Biology, 12(3), 331-354.

 

Chew, D. S.H.*, Choi, K.-P., Leung, M.-Y., (2005). Scoring Schemes of Palindrome Clusters for More Sensitive Prediction of Replication Origins in Herpesviruses. Nucleic Acid Research, 33(15), e134.

 

Chew, D. S.H.*, Choi, K. P., Heidner, H., Leung, M.-Y., (2004). Palindromes in SARS and Other Coronaviruses, INFORMS J. Comp.. INFORMS Journal of Computing, 16(4), 331-34.

 

Leung, M.-Y., Marsh, G.M.*, Speed, T.P., (1996). Over and under representation of short oligonucleotides in herpes virus genomes, J. Computational Biology,. J. Computational Biology, 3(3), 345-360.

 

Leung, M.-Y., Schachtel, G., Yu, H.S., (1994). Scan statistics and DNA sequence analysis: The search for an origin of replication in a virus, Nonlinear World. Nonlinear World, 1, 445-471.

 

Leung, M.-Y., Burge,, C., Blaisdell, B.E., Karlin, S., (1991). An efficient algorithm for identifying matches with errors in multiple long molecular sequences, J. Mol. Biol. 221, -. J. Mol. Biol., 221, 1367-1378.

Karlin, S., Leung, M.-Y.*, (1991). Some Limit Theorems on Distributional Patterns of Balls in Urns, Ann. Appl. Prob... Ann. Appl. Prob., 1(4), 513-538.

 

Leung, M.-Y., (1988). Karlin, S., Morris, M., and Ghandor, G. and Leung, M.Y., Efficient algorithms for molecular sequence analysis, Proc. Natl. Acad. Sci. USA,. Proc. Natl. Acad. Sci. USA, 85, 841-845.

Karlin, S., Morris, M., Ghandor, G., Leung, M.-Y., (1988). Algorithms for identifying local molecular sequence features, Comp. Appl. Biosci.,. Comp. Appl. Biosci.,, 4(1), 41-51.

 

Lam, K., Leung, M.-Y., Siu, M.K., (1984). Self-organizing files with dependent accesses. J. Appl. Prob., 21, 343-359.

 

Lam, K., Leung, M.-Y.*, Siu, M.K., (1983). Self-organizing files. Undergraduate Mathematics and its Application Module Unit 612, Education Development Center, Massachusetts.. Education Development Center, Undergraduate Mathematics and its Application Module Unit(612).

 

Lam, K., Leung, M.-Y.*, Siu, M.K., (1982). A problem on processors.. Chinese J. Math., 10(1), 9-13.

 

 

BOOK CHAPTER PUBLISHED (Peer Reviewed)

Leung, M.-Y (2017) Scan Statistics Applications in Genomics. In: Handbook of Scan Statistics, Glaz, J. and Koutras, M.V. (Eds.); Springer, New York (To appear).

 

Leung, M.-Y., Knapka, J. A.*, Wagler, A. E., Rodriguez, G., Kirken, R. A., (2016). OncoMiner: A pipeline for bioinformatics analysis of exonic sequence variants in cancer. In: Big Data Analytics in Genomics, Wong, K.C. (Ed.), pp. 373-398, Springer, New York. Available at http://link.springer.com/chapter/10.1007/978-3-319-41279-5_12.

 

Zheng, J.*, Fuentes, O., Leung, M.-Y., Jackson, E.*, (2010). Mammogram Compression Using Super-Resolution. In Joan Martí, Arnau Oliver, Jordi Freixenet, and Robert Martí (Ed.), (vol. 6136, pp. 46-53). Springer-Verlag, Berlin: Lecture Notes in Computer Science. www.springerlink.com/content/a63k52581wp84631/

 

Leung, M.-Y., (2006). Scan Statistics for Detecting Clusters. In Salkind, N.J. (Ed.), (ed., vol. Encyclopedia of Measurement and Statistics, pp. 11-14). Thousand Oaks: SAGE Publications.

 

Leung, M.-Y., Yamashita, T.E. (1999). Applications of the scan statistic in DNA sequence analysis. In Recent Developments in Scan Statistics and Applications; Balakrishnan, N. and Glaz, J., Ed., pp. 269-286. Birkhauser, Boston. Available at http://link.springer.com/chapter/10.1007%2F978-1-4612-1578-3_12.

 

 

CONFERENCE PAPERS PUBLISHED (Peer Reviewed)

Yehdego, D. T.*, Zhang, B.*, Kodimala, V. K.R.*, Johnson, K. L., Taufer, M., Leung, M.-Y., (2013). Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce. (pp. 1-10). Boston, MA: Proceedings of the 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2013). www.hicomb.org/HiCOMB2013/papers/HICOMB2013-03.pdf

 

Aguilar-Bonavides, C.*, Cardenas, G. A.*, Nakayasu, E. S., Lopes, F. G.*, Almeida, I. C., Leung, M.-Y., (2013). Automatic Annotation of GPI Structures Using Grid Computing. (pp. 1-6). Honolulu, Hawaii: Proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013). toc.proceedings.com/17515webtoc.pdf

 

Zhang, B.*, Yehdego, D. T.*, Johnson, K. L., Leung, M.-Y., Taufer, M., (2012). A Modularized MapReduce Framework to Support RNA Secondary Structure. (pp. 1-8). IEEE: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). www.cs.odu.edu/~lchen/CSBW/programFinal.pdf

 

Aguilar-Bonavides, C.*, Leung, M.-Y., Nakayasu, E. S., Lopes, F. G.*, Almeida, I. C., (2012). Computational tool for large-scale GPIomic analysis. (pp. 585-587). ACM, New York, New York: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. doi.acm.org/10.1145/2382936.2383029

 

Yehdego, D. T.*, Kodimala, V. K.*, Viswakula, S.*, Zhang, B.*, Vegesna, R.*, Johnson, K. L., Taufer, M., Leung, M.-Y., (2012). Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results. (pp. 545-547). ACM, New York, NY: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. doi.acm.org/10.1145/2382936.2383016

 

Zheng, J.*, Fuentes, O., Leung, M.-Y., (2010). Super-resolution of Mammograms. (pp. 1-7). Montreal, QC: Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) 2010 IEEE Symposium. ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5510384

 

Licon, A.*, Taufer, M., Leung, M.-Y., Johnson, K. L., (2010). A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Secondary Structure Prediction. In Al-Mubaid, H. (Ed.), (pp. 165-170). Red Hook, N.Y.: 2nd International Conference on Bioinformatics and Computational Biology (BICoB)/Curran Associates, Inc..

 

Cruz-Cano, R.*, Leung, M.-Y., (2009). Comparison of Feature Selection Techniques for Viral DNA Replication Origin Prediction. (pp. 128-134). Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

 

Leung, M.-Y., Taufer, M., Solorio, T., Licon, A., Mireles, D., (2008). On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks.. Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB'08).

 

Araiza, R.*, Taufer, M., Leung, M.-Y., (2007). Towards Optimal Scheduling for Global Computing under Probabilistic, Interval, and Fuzzy Uncertainty, with Potential Applications to Bioinformatics. (pp. 520-525). Proceedings of the 2007 Annual Meeting of the North American Fuzzy Information Processing Society.

 

 

ONLINE MODULES, SOFTWARE RELEASED ELECTRONICALLY, AND OTHER PUBLICATIONS

Leung, M.-Y., Cardenas, G. A.*, Almeida, I. C., Gerken, T. A., (2014). Isoform Specific O-Glycosylation Prediction (ISOGlyP), Version 1.2.. Available at http://isoglyp.utep.edu. Accessed 10/31/2014.

 

Leung, M.-Y., Mohl, J.*, Licon, A.*, Viswakula, S.*, Kelley, P.*, Araiza, R.*, Kodimala, V.*, Vegesna, R.*, Saldivar, L.*, Yehadego, D.*, Cardenas, G.*, Vest, E.*, Fuentes, O., Taufer, M., Johnson, K. L., (2012). RNASSA 2.0: RNA Secondary Structure Analysis (Version 2.0.121208)... rnavlab.utep.edu/rnavlab/downloads.php

 

Leung, M.-Y., Viswakula, S.*, Kodimala, V., Yehadego, D., Vegesna, R., Taufer, M., Johnson, K. L., (2012). Segmenta 2.0: A Bioinformatics Tool for RNA Segmentation (Version 2.0.121208)... rnavlab.utep.edu/rnavlab/downloads.php

 

Leung, M.-Y., Kelley, P.*, Fuentes, O., Taufer, M., Johnson, K. L., (2012). InversFinder 2.0: A Bioinformatics Tool for Finding Inversions (Version 2.0.120908)... rnavlab.utep.edu/rnavlab/downloads.php

 

Chew, D.S.H.*, Choi, K.P., Leung, M.-Y., (2008). Stochastic Approaches to Predict Replication Origins in DNA Viral Genomes.. Proceedings of the 2008 International Workshop for Applied Probability.

 

Cruz-Cano, R.*, Chandran, D.*, Leung, M.-Y., (2007). Computational Prediction of Replication Origins in Herpesviruses.. Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

 

Taufer, M., Leung, M.-Y., Johnson, K., Licon, A., (2007). RNAVLab: A Unified Environment for Computational RNA Structure Analysis Based on Grid Computing Technology.. Proceedings of the Sixth IEEE International Workshop on High Performance Computational Biology.

 

Leung, M.-Y., (2004). An Update of Bioinformatics Information Modules for Education and Research. Available at http://www.math.utep.edu/Faculty/mleung/BIMER... www.bioinformatics.utep.edu/BIMER

 

Leung, M.-Y., (2003). An Update of Probability Research Information and Statistics Education Modules. Available at http://www.math.utep.edu/Faculty/mleung/PRISEM... www.math.utep.edu/Faculty/PRESEM

 

Grosu, D.*, Chronopoulos, A.T., Leung, M.-Y., (2002). Load Balancing in Distributed Systems: An Approach Using Cooperative Games Proceedings of the 16th IEEE International Parallel and Distributed Processing Symposium, April, 22,. (pp. 52-61). Fort Lauderdale, Florida, IEEE Computer Science Press,: Proceedings of the 16th IEEE International Parallel and Distributed Processing Symposium.

 

Leung, M.-Y., Garnett, K.*, (2001). Bioinformatics Information Modules for Education and Research. Interactive modules online or on CD for a project on web-based education funded by NSF Course, Curriculum, and Laboratory Improvement Grant.... www.bioinformatics.utep.edu/BIMER

 

Leung, M.-Y., (2000). Probability Research Information and Statistics Education Modules. Interactive modules online or on CD for a project on web-based education funded by NSF Course, Curriculum, and Laboratory Improvement Grant....

 

Leung, M.-Y., (1998). An Update of the Unix-Based Molecular Package (MOLPAC).. Austin: GenToolsTM distributed by the High Performance Computing Facility.

 

Leung, M.-Y., (1996). Billakanti, S.R., St. Julien, S.A., and Leung, M.Y. A graphics tool for visualizing genomic sequence features, Proc. First World Congress of Computational Medicine,....

 

Leung, M.-Y., (1996). Schachtel, G., Leung, M.Y., and Yu, H.S., Approximationsformeln der scan-statistik zur analyse langer DNA-Sequenzen, in Biometrische Berichte Band 4 - Biometrie der Genomanalyse,.. (pp. 41-68)..

 

Leung, M.-Y., (1995). Leung, M.Y. A tool for identifying nonrandom clusters of point markers on DNA sequences, Proceedings of the Third International Conference on Bioinformatics and Genome Research,.. (pp. 351-364).

 

Leung, M.-Y., (1993). Barron, S., Leung, M.Y., Witten, M., and Wu, C.H., GenTools TM: , Integrated Sequence Analysis Tools for Distributed High Performance Platform, distributed by the High Performance Computing Facility, University of Texas at Austin.