Sequence Analysis and Gene Silencing

URL: https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/

Contact: Lenwood Heath

This laboratory houses the Computational Modeling of Gene Silencing (CMGS) project. This project is constructing computational models of the gene silencing phenomenon for the microscopic worm Caenorhabditis elegans. One product of the project is a comprehensive database of information about gene silencing in C. elegans, CMGSDB. Data mining techniques play a large role in the computational modeling. This laboratory also features research in biological sequence analysis. One topic in that area is genomic signatures, mathematical structures that can be computed from genomic sequences and used to identify the original organism.
2016
Eid, F. - E., M. Elhefnawi, and L. S. Heath, "DeNovo: Virus-Host Sequence-Based Protein-Protein Interaction Prediction", Bioinformatics, vol. 32, pp. 1144-1150, 2016.
2010
Heath, L. S., A. -ping Hou, H. Xia, and L. Zhang, "A Genome Compression Algorithm Supporting Manipulation", 9th Annual International Conference on Computational Systems Bioinformatics (CSB 2010), Stanford, California, pp. 38-49, 2010.
2008
Pati, A., Y. Jin, K. Klage, R. Helm, L. S. Heath, and N. Ramakrishnan, "CMGSDB: Integrating Heterogeneous Caenorhabditis elegans Data Sources Using Compositional Data Mining", Nucleic Acids Research, vol. 36, pp. D69-76, 2008.
2007
Mane, S. P., C. Vasquez-Robinet, A. A. Sioson, L. S. Heath, and R. Grene, "Early PLD$\alpha$-Mediated Events in Response to Progressive Drought Stress in Arabidopsis: A Transcriptome Analysis", Journal of Experimental Botany, vol. 58, pp. pp. 241-252, 2007.
Heath, L. S., and A. A. Sioson, "Multimodal Networks: Structure and Operations", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
Heath, L. S., and A. A. Sioson, "Semantics of Multimodal Network Models,", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007.
Heath, L. S., and A. Pati, "Predicting Markov Chain Order in Genomic Sequences", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM): IEEE Computer Society Press, 2007.
Heath, L. S., and A. Pati, "Genomic Signatures in de Bruijn Chains", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), vol. 4645, pp. pp. 216-227. , 2007.
Heath, L. S., and A. Pati, "Genomic Signatures from DNA Word Graphs", Proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA , vol. 4463, pp. pp. 317-328., 2007.
Pati, A., and L. S. Heath, "Genomic signatures from DNA word graphs (poster)", Grace Hopper Celebration of Women in Computing, , 10/2007.
2006
Li, P., A. Sioson, S. P. Mane, A. Ulanov, G. Grothaus, L. S. Heath, T. M. Murali, H. J. Bohnert, and R. Grene, "Response diversity of Arabidopsis thaliana ecotypes in elevated CO/2 in the field.", Plant Mol Biol, vol. 62, no. 4-5, pp. 593-609, 2006. Abstract
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali, "XcisClique: Analysis of regulatory bicliques.", BMC Bioinformatics, vol. 7, no. 1, pp. 218, 2006. Abstract
Watkinson, J. I., L. Hendricks, A. A. Sioson, C. Vasquez-Robinet, L. S. Heath, M. Schuler, and H. J. Bohnert, "Accessions of Solanum tuberosum ssp. andigena Show Differences in Photosynthetic Recovery After Drought Stress as Reflected in Gene Expression Profiles", Plant Science , vol. 171, pp. pp. 745-758. , 2006.
Li, P. H., S. P. Mane, A. A. Sioson, C. V. Robinet, L. S. Heath, H. J. Bohnert, and R. Grene, "Effects of Chronic Ozone Exposure on Gene Expression in Arabidopsis thaliana Ecotypes and in Thellungielia halophila", Plant Cell and Environment , vol. 29, pp. pp. 854-868. , 2006.
Li, P. H., A. Sioson, S. P. Mane, A. Ulanov, G. Grothaus, L. S. Heath, T. M. Murali, H. J. Bohnert, and R. Grene, "Response Diversity of Arabidopsis thaliana Ecotypes in Elevated [Co2] in the Field", Plant Molecular Biology, vol. 62, pp. pp. 593-609, 2006.
Sioson, A. A., and L. S. Heath, "Some Fundamental Operations on Multimodal Networks in Biology", Philippine Computing Journal , vol. 1, pp. pp. 13-22. , 2006.
Sioson, A. A., S. P. Mane, P. Li, W. Sha, L. S. Heath, H. J. Bohnert, and R. Grene, "The Statistics of Identifying Differentially Expressed Genes in Expresso and TM4: A Comparison", BMC Bioinformatics , vol. 7, pp. 15 pages in main article; plus 5 pages in 2 additional files. , 2006.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali, "XcisClique: Analysis of Regulatory Bicliques", BMC Bioinformatics, vol. 7, pp. 14 pages in main article; plus 16 pages in 7 additional files, 2006.
2005
Brueni, D. J., and L. S. Heath, "The PMU Placement Problem", SIAM Journal on Discrete Mathematics, vol. 19, pp. pp. 744-761. , 2005.
John C. Gordon, J. B. Myers, T. Folta, V. Shoja, L. S. Heath, and A. Onufriev, "H++: A Server for Estimating pK(a)s and Adding Missing Hydrogens to Macromolecules", Nucleic Acids Research , vol. 33, no. 2, pp. pp. W368-W371, 2005.
Mane, S., C. Vasquez-Robinet, A. A. Sioson, L. S. Heath, and R. Grene, "Effects of Drought Stress on Phospholipid Signaling in Arabidopsis (Poster)", InterDrought-II, The Second International Conference on Integrated Approaches to Sustain and Improve Plant Production Under Drought Stress, Rome, Italy, 09/2005.
Pati, A., C. Vasquez-Robinet, L. S. Heath, R. Grene, and T. M. Murali, "XcisClique: Analyzing Regulatory Bicliques in Arabidopsis thaliana (Poster)", 8th Annual Conference on Computational Genomics , Cambridge, MA,, 11/2005.
2004
Heath, L. S., C. J. Ribbens, and S. V. Pemmaraju, "Processor-Efficient Sparse Matrix-Vector Multiplication", Computers and Mathematics with Applications , vol. 48, pp. pp. 589-608. , 2004.
Heath, L. S., and N. A. Loehr, "Efficient Algorithms for Finding Conway Polynomials,", Journal of Symbolic Computation , vol. 38, pp. pp. 1003-1024. , 2004.
2003
Watkinson, J. I., A. A. Sioson, C. Vasquez-Robinet, M. Shukla, D. Kumar, M. Ellis, L. S. Heath, N. Ramakrishnan, B. I. Chevone, L. T. Watson, et al., "Photosynthetic Acclimation is Reflected in Specific Patterns of Gene Expression in Drought-Stressed Loblolly Pine", Plant Physiology , vol. 133, no. 4, pp. pp. 1702-1716, 2003.
Heath, L. S., and J. P. C. Vergara, "Sorting by Short Swaps", Journal of Computational Biology, vol. 10, no. 5, pp. pp. 775-789. , 2003.
Slotta, D. J., L. S. Heath, N. Ramakrishnan, R. Helm, and M. Potts, "Clustering Mass Spectrometry Data using Order Statistics", Proteomics, vol. 3, no. 9, pp. pp. 1687-1691. , 2003.
Sioson, A. A., J. I. Watkinson, C. Vasquez-Robinet, M. Ellis, M. Shukla, D. Kumar, N. Ramakrishnan, L. S. Heath, R. Grene, B. I. Chevone, et al., "Expresso and Chips: Creating a Next Generation Microarray Experiment Management Systems", Proceedings of the Next Generation Software Workshop, 17th International Parallel and Distributed Processing Symposium (IPDPS'03),, Nice, France, IEEE Computer Society, 2003.
2002
Heath, L. S., N. Ramakrishnan, R. R. Sederoff, R. W. Whetten, B. I. Chevone, C. A. Struble, V. Y. Jouenn, D. Chen, L. M. van Zyl, and R. Grene, "Studying the Functional Genomics of Stress Responses in Loblolly Pine using the Expresso Microarray Management System", Comparative and Functional Genomics , vol. 3, pp. pp. 226-243. , 2002.
Grene, R., Neval Erturk, and L. S. Heath, "Role of Superoxide Dismutase (SODs) in Controlling Oxidative Stress in Plants", Journal of Experimental Botany, vol. 53, pp. pp. 1331-1341. , 2002.
Heath, L. S., "Networks in Bioinformatics", Proceedings of the 2002 International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN 2002), pp. pp. 141-150. , 2002.
Slotta, D. J., L. S. Heath, N. Ramakrishnan, R. Helm, and M. Potts, "Computational Approaches to Combining Predictive Biological Models", Advanced Simulation Technologies Conference (HPC 2002), 2002, , pp. pp. 75-80. , 2002.
Slotta, D. J., L. S. Heath, and N. Ramakrishnan, "Clustering Mass Spectrometry Data using Order Statistics (Abstract)", First Annual Proteomics Data Mining Conference, Duke University, Durham, NC, 09/2002.
Watkinson, J. I., A. A. Sioson, M. Shukla, L. S. Heath, N. Ramakrishnan, B. I. Chevone, L. T. Watson, J. W. Weller, R. R. Sederoff, L. M. van Zyl, et al., "Identifying Changes in Gene Expression During Drought Stress Using Expresso (Poster)", ASPB (American Society of Plant Biologists) Plant Biology 2002, Denver, CO, 08/2002.
Heath, L. S., and N. Ramakrishnan, "The Emerging Landscape of Bioinformatics Software Systems", IEEE Computer , vol. 35, pp. pp. 41-45. , 07/2002.
2001
Green, E. L., L. S. Heath, and C. A. Struble, "Constructing Homomorphism Spaces and Endomorphism Rings,", Journal of Symbolic Computation , vol. 32, pp. pp. 101-117. , 2001.
Ganley, J. L., and L. S. Heath, "The Pagenumber of $k$-Trees is $O(k)$", Discrete Applied Mathematics , vol. 109, pp. pp. 215-221. , 2001.
Alscher, R. G., B. I. Chevone, L. S. Heath, and N. Ramakrishnan, "Expresso -- A Problem Solving Environment for Bioinformatics: Finding Answers With Microarray Technology", Advanced Simulation Technologies Conference (HPC 2001), 2001, , pp. pp. 64-69., 2001.
Green, E. L., L. S. Heath, and C. A. Struble, "Constructing Endomorphism Rings Via Duals", International Symposium on Symbolic and Algebraic Computation (ISSAC 2000), 2001.
Rosenberg, A. L., and L. S. Heath, Graph Separators, with Applications, , Norwell, Massachusetts, Kluwer Academic Publishers, pp. 264 pp, 2001.
2000
Heath, L. S., and J. P. C. Vergara, "Sorting by Short Block-Moves", Algorithmica , vol. 28, pp. pp. 323-352. , 2000.
Heath, L. S., N. Ramakrishnan, R. R. Sederoff, L. M. van Zyl, D. Chen, Y. - H. Sun, B. I. Chevone, S. - H. Li, K. Ye, R. Whetten, et al., "Effects of Drought Stress on Gene Expression Patterns in the Needles of Loblolly Pine Trees: Towards a PSE for the Analysis of Microarray Data (Poster)", Gordon Conference on Biological Regulatory Mechanisms, Holderness, NH, 07/2000.
1999
Heath, L. S., S. V. Pemmaraju, and A. Trenk, "Stack and Queue Layouts of Directed Acyclic Graphs: Part I,", SIAM Journal on Computing , vol. 28, pp. pp. 1510-1539. , 1999.
Heath, L. S., and S. V. Pemmaraju, "Stack and Queue Layouts of Directed Acyclic Graphs: Part II", SIAM Journal on Computing , vol. 28, pp. pp. 1588-1626, 1999.
Brunick, G. P., E. L. Green, L. S. Heath, and C. A. Struble, "Efficient Construction of Drinfel'd Doubles,", International Symposium on Symbolic and Algebraic Computation (ISSAC'99),, 1999.
Heath, L. S., and N. A. Loehr, "New Algorithms for Generating Conway Polynomials over Finite Fields", Tenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 1999.
1998
Heath, L. S., and J. P. C. Vergara, "Sorting by Bounded Block-Moves", Discrete Applied Mathematics , vol. 88, no. 2, pp. pp. 181-206. , 1998.
Heath, L. S., and J. P. C. Vergara, "Edge-Packing in Planar Graphs", Theory of Computing Systems , vol. 31, pp. pp. 629-662. , 1998.
Ganley, J. L., and L. S. Heath, "An Experimental Evaluation of Local Search Heuristics for Graph Partitioning,", Computing , vol. 60, pp. pp. 121-132. , 1998.
Heath, L. S., and J. P. C. Vergara, "Edge-Packing Planar Graphs by Cyclic Graphs", Discrete Applied Mathematics , vol. 81, pp. pp. 169-180. , 1998.
1997
Heath, L. S., and S. V. Pemmaraju, "Stack and Queue Layouts of Posets,", SIAM Journal on Discrete Mathematics , vol. 10, pp. pp. 599-625. , 1997.
Heath, L. S., "Graph Embeddings and Simplicial Maps", Theory of Computing Systems , vol. 30, pp. pp 51-65., 1997.
Heath, L. S., D. Hix, L. T. Nowell, W. C. Wake, G. A. Averboch, E. Labow, S. A. Guyer, D. J. Brueni, R. K. France, K. Dalal, et al., "Envision: A User-Centered Database of Computer Science Literature", Communications of the ACM , vol. 38, pp. pp. 52-53, 1997.
Ganley, J. L., and L. S. Heath, "Optimal and Random Partitions of Random Graphs", The Computer Journal , vol. 37, pp. pp. 641-643. , 1997.
Green, E. A., L. S. Heath, and B. J. Keller, "Opal: A System for Computing Noncommutative Gröbner Bases (System Description)", Eighth International Conference on Rewriting Techniques and Applications (RTA-97), 1997.
1996
Shaffer, C. A., L. S. Heath, and J. Yang, "Using the Swan data structure visualization system for computer science education", SIGCSE '96: Proceedings of the twenty-seventh SIGCSE technical symposium on Computer science education, New York, NY, USA, ACM, pp. 140–144, 1996.
Nowell, L. T., R. K. France, D. Hix, L. S. Heath, and E. A. Fox, "Visualizing Search Results: Some Alternatives to Query-Document Similarity", 19th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, , pp. pp. 67-75. , 1996.
1995
Jun, Y., C. A. Shaffer, and L. S. Heath, The Swan User''s Manual, Version 1.1, , Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1995.
Heath, L. S., and S. V. Pemmaraju, "Recognizing Leveled-Planar Dags in Linear Time", Proceedings of Graph Drawing '95, vol. 1027: Springer, pp. pp. 300-311. , 1995.
1994
Heath, L. S., and S. V. Pemmaraju, "New Results for the Minimum Weight Triangulation Problem", Algorithmica , vol. 12, pp. pp. 533-552. , 1994.
Ganley, J. L., and L. S. Heath, "Heuristics for Laying Out Information Graphs", Computing , vol. 52, pp. pp. 389-405. , 1994.
1993
Heath, L. S., P. K. Paripati, and J. W. Roach, "Representing Polyhedra: Faces are Better than Vertices", Computational Geometry: Theory and Applications, vol. 3, pp. pp. 327-351. , 1993.
Fox, E. A., D. Hix, L. T. Nowell, D. J. Brueni, W. C. Wake, L. S. Heath, and D. Rao, "Users, User Interfaces, and Objects: Envision, a Digital Library", Journal of the American Society for Information Science , vol. 44, pp. pp. 480-491. , 1993.
Heath, L. S., Lower Bounds for Graph Embeddings Via Algebraic Topology (Extended Abstract), , pp. pp. 311-317. , 1993.
Fox, E. A., L. S. Heath, and D. Hix, "A User-Centered Database from the Computer Science Literature", AAAS Workshop on Advances in Data Management for the Scientist and Engineer, Boston, Massachusetts, 02/1993.
Brueni, D. J., B. Cross, E. A. Fox, L. S. Heath, D. Hix, L. T. Nowell, and W. C. Wake, What If There Were Desktop Access to the Computer Science Literature?, , pp. pp. 15-22. , 1993.
Heath, L. S., S. V. Pemmaraju, and A. Trenk, "Stack and Queue Layouts of Directed Acyclic Graphs", Planar Graphs , Providence, Rhode Island, American Mathematical Society, pp. pp. 5-1, 1993.
1992
Heath, L. S., and A. L. Rosenberg, "Laying Out Graphs Using Queues", SIAM Journal on Computing , vol. 21, pp. pp. 927-958. , 1992.
Heath, L. S., and S. Istrail, "The Pagenumber of Genus $g$ Graphs is $O(g),$", Journal of the Association for Computing Machinery , vol. 39, pp. pp. 479-501. , 1992.
Heath, L. S., F. T. Leighton, and A. L. Rosenberg, "Comparing Queues and Stacks as Mechanisms for Laying Out Graphs", SIAM Journal on Discrete Mathematics, vol. 5, pp. pp. 398-412. , 1992.
Fox, E. A., L. S. Heath, Q. F. Chen, and A. M. Daoud, "Practical Minimal Perfect Hash Functions for Large Databases", Communications of the ACM , vol. 35, pp. pp. 105-121. , 1992.
Fox, E. A., Q. F. Chen, and L. S. Heath, "A Faster Algorithm for Constructing Minimal Perfect Hash Functions", 15th Annual International Conference on Research and Development in Information Retrieval, 1992, , pp. pp. 266-273. , 1992.
Wartik, S., E. A. Fox, L. S. Heath, and Q. F. Chen, "Hashing", Information Retrieval: Data Structures and Algorithms, Engelwood Cliffs, NJ, Prentice-Hall, pp. pp. 293-362. , 1992.
1991
Fox, E. A., Q. F. Chen, A. M. Daoud, and L. S. Heath, "Order-Preserving Minimal Perfect Hash Functions and Information Retrieval,", ACM Transactions on Information Systems , vol. 9, pp. pp. 281-308. , 1991.
Heath, L. S., Edge Coloring Planar Graphs with Two Outerplanar Subgraphs, , pp. pp. 195-202. , 1991.
1990
Heath, L. S., "Covering a Set with Arithmetic Progressions is NP-Complete", Information Processing Letters , vol. 34, pp. 293-298. , 1990.
Heath, L. S., F. T. Leighton, and A. L. Rosenberg, Graph Layout Using Queues (Extended Abstract), , pp. pp. 305-314. , 1990.
Heath, L. S., P. K. Paripati, and J. W. Roach, Polyhedra: Faces are Better than Vertices (Extended Abstract), , pp. pp. 191-199. , 1990.
1989
Fox, E. A., Q. F. Chen, L. S. Heath, and S. Datta, "A More Cost Effective Algorithm for Finding Minimal Perfect Hash Functions", Seventeenth Annual ACM Computer Science Conference, 1989,, pp. pp. 114-122. , 1989.
1988
Heath, L. S., A. L. Rosenberg, and B. T. Smith, "The Physical Mapping Problem for Parallel Architectures", Journal of the Association for Computing Machinery, vol. 35, pp. pp. 603-634. , 1988.
1987
Heath, L. S., "Embedding Outerplanar Graphs in Small Books", SIAM Journal on Algebraic and Discrete Methods, vol. 8, pp. pp. 198-218. , 1987.
Heath, L. S., and S. Istrail, The Pagenumber of Genus $g$ Graphs is $O(g),$, , pp. pp. 388-397. , 1987.
1984
Heath, L. S., Embedding Planar Graphs in Seven Pages, , pp. pp. 74-83. , 1984.