Sequence Analysis and Gene Silencing

lab - CMGS

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

Contact: Alexey Onufriev

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.
2008
Pati A., Jin Y., Klage K., Helm R., Heath L.S., Ramakrishnan N., "CMGSDB: Integrating Heterogeneous Caenorhabditis elegans Data Sources Using Compositional Data Mining", Nucleic Acids Research, vol. 36, pp. D69-76, 2008. Tagged BibTex xml
2007
Mane S.P., Vasquez-Robinet C., Sioson A.A., Heath L.S., Grene R., "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. Tagged BibTex xml
Heath L.S., Sioson A.A., "Multimodal Networks: Structure and Operations", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007. Tagged BibTex xml
Heath L.S., Sioson A.A., "Semantics of Multimodal Network Models,", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007. Tagged BibTex xml
Heath L.S., Pati A., "Predicting Markov Chain Order in Genomic Sequences", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM): IEEE Computer Society Press, 2007. Tagged BibTex xml
Heath L.S., Pati A., "Genomic Signatures in de Bruijn Chains", Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), vol. 4645, pp. pp. 216-227. , 2007. Tagged BibTex xml
Heath L.S., Pati A., "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. Tagged BibTex xml
Pati A., Heath L.S., "Genomic signatures from DNA word graphs (poster)", Grace Hopper Celebration of Women in Computing, , 10/2007. Tagged BibTex xml
2006
Watkinson J.I., Hendricks L., Sioson A.A., Vasquez-Robinet C., Heath L.S., Schuler M., Bohnert H.J., "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. Tagged BibTex xml
Li P H., Sioson A., Mane S P., Ulanov A., Grothaus G., Heath L S., Murali T M., Bohnert H J., Grene R., "Response Diversity of Arabidopsis thaliana Ecotypes in Elevated [Co2] in the Field", Plant Molecular Biology, vol. 62, pp. pp. 593-609, 2006. Tagged BibTex xml
Sioson A.A., Heath L.S., "Some Fundamental Operations on Multimodal Networks in Biology", Philippine Computing Journal , vol. 1, pp. pp. 13-22. , 2006. Tagged BibTex xml
Sioson A.A., Mane S.P., Li P., Sha W., Heath L.S., Bohnert H.J., Grene R., "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. Tagged BibTex xml
Li P H., Mane S P., Sioson A A., Robinet C V., Heath L S., Bohnert H J., Grene R., "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. Tagged BibTex xml
Pati A., Vasquez-Robinet C., Heath L.S., Grene R., Murali T M., "XcisClique: Analysis of Regulatory Bicliques", BMC Bioinformatics, vol. 7, pp. 14 pages in main article; plus 16 pages in 7 additional files, 2006. Tagged BibTex xml
Li P., Sioson A., Mane S P., Ulanov A., Grothaus G., Heath L S., Murali T M., Bohnert H J., Grene R., "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 Tagged BibTex xml
Pati A., Vasquez-Robinet C., Heath L S., Grene R., Murali T M., "XcisClique: Analysis of regulatory bicliques.", BMC Bioinformatics, vol. 7, no. 1, pp. 218, 2006. Abstract Tagged BibTex xml
2005
John C. Gordon, Myers J.B., Folta T., Shoja V., Heath L.S., Onufriev A., "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. Tagged BibTex xml
Brueni D.J., Heath L.S., "The PMU Placement Problem", SIAM Journal on Discrete Mathematics, vol. 19, pp. pp. 744-761. , 2005. Tagged BibTex xml
Mane S., Vasquez-Robinet C., Sioson A.A., Heath L.S., Grene R., "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. Tagged BibTex xml
Pati A., Vasquez-Robinet C., Heath L.S., Grene R., Murali. T M., "XcisClique: Analyzing Regulatory Bicliques in Arabidopsis thaliana (Poster)", 8th Annual Conference on Computational Genomics , Cambridge, MA,, 11/2005. Tagged BibTex xml
2004
Heath L.S., Loehr N.A., "Efficient Algorithms for Finding Conway Polynomials,", Journal of Symbolic Computation , vol. 38, pp. pp. 1003-1024. , 2004. Tagged BibTex xml
Heath L.S., Ribbens C.J., Pemmaraju S.V., "Processor-Efficient Sparse Matrix-Vector Multiplication", Computers and Mathematics with Applications , vol. 48, pp. pp. 589-608. , 2004. Tagged BibTex xml
2003
Watkinson J.I., Sioson A.A., Vasquez-Robinet C., Shukla M., Kumar D., Ellis M., Heath L.S., Ramakrishnan N., Chevone B.I., Watson L.T., van Zyl L., Egertsdotter U., Sederoff R.R., Grene R., "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. Tagged BibTex xml
Slotta D.J., Heath L.S., Ramakrishnan N., Helm R., Potts M., "Clustering Mass Spectrometry Data using Order Statistics", Proteomics, vol. 3, no. 9, pp. pp. 1687-1691. , 2003. Tagged BibTex xml
Heath L.S., Vergara J.C., "Sorting by Short Swaps", Journal of Computational Biology, vol. 10, no. 5, pp. pp. 775-789. , 2003. Tagged BibTex xml
Sioson A.A., Watkinson J.I., Vasquez-Robinet C., Ellis M., Shukla M., Kumar D., Ramakrishnan N., Heath L.S., Grene R., Chevone B.I., Kafadar K., Watson L.T., "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. Tagged BibTex xml
2002
Watkinson J.I., Sioson A.A., Shukla M., Heath L.S., Ramakrishnan N., Chevone B.I., Watson L.T., Weller J.W., Sederoff R.R., van Zyl L., Alscher R.G., "Identifying Changes in Gene Expression During Drought Stress Using Expresso (Poster)", ASPB (American Society of Plant Biologists) Plant Biology 2002, Denver, CO, 08/2002. Tagged BibTex xml
Heath L.S., Ramakrishnan N., Sederoff R.R., Whetten R.W., Chevone B.I., Struble C.A., Jouenn V.Y., Chen D., van Zyl L., Grene R., "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. Tagged BibTex xml
Grene R., Neval Erturk, Heath L.S., "Role of Superoxide Dismutase (SODs) in Controlling Oxidative Stress in Plants", Journal of Experimental Botany, vol. 53, pp. pp. 1331-1341. , 2002. Tagged BibTex xml
Slotta D.J., Heath L.S., Ramakrishnan N., "Clustering Mass Spectrometry Data using Order Statistics (Abstract)", First Annual Proteomics Data Mining Conference, Duke University, Durham, NC, 09/2002. Tagged BibTex xml
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. Tagged BibTex xml
Slotta D.J., Heath L.S., Ramakrishnan N., Helm R., Potts M., "Computational Approaches to Combining Predictive Biological Models", Advanced Simulation Technologies Conference (HPC 2002), 2002, , pp. pp. 75-80. , 2002. Tagged BibTex xml
Heath L.S., Ramakrishnan N., "The Emerging Landscape of Bioinformatics Software Systems", IEEE Computer , vol. 35, pp. pp. 41-45. , 07/2002. Tagged BibTex xml
2001
Rosenberg A.L., Heath L.S., Graph Separators, with Applications, , Norwell, Massachusetts, Kluwer Academic Publishers, pp. 264 pp, 2001. Tagged BibTex xml
Ganley J.L., Heath L.S., "The Pagenumber of $k$-Trees is $O(k)$", Discrete Applied Mathematics , vol. 109, pp. pp. 215-221. , 2001. Tagged BibTex xml
Green E.L., Heath L.S., Struble C.A., "Constructing Homomorphism Spaces and Endomorphism Rings,", Journal of Symbolic Computation , vol. 32, pp. pp. 101-117. , 2001. Tagged BibTex xml
Alscher R.G., Chevone B.I., Heath L.S., Ramakrishnan N., "Expresso -- A Problem Solving Environment for Bioinformatics: Finding Answers With Microarray Technology", Advanced Simulation Technologies Conference (HPC 2001), 2001, , pp. pp. 64-69., 2001. Tagged BibTex xml
Green E.L., Heath L.S., Struble C.A., "Constructing Endomorphism Rings Via Duals", International Symposium on Symbolic and Algebraic Computation (ISSAC 2000), 2001. Tagged BibTex xml
2000
Lenwood S. Heath, Ramakrishnan N., Sederoff R.R., van Zyl L., Chen D., and Y.-H. Sun, Chevone B.I., Li S -H., Ye K., Whetten R., Alscher R.G., "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. Tagged BibTex xml
Heath L.S., Vergara J.C., "Sorting by Short Block-Moves", Algorithmica , vol. 28, pp. pp. 323-352. , 2000. Tagged BibTex xml
1999
Heath L.S., Pemmaraju S.V., Trenk A., "Stack and Queue Layouts of Directed Acyclic Graphs: Part I,", SIAM Journal on Computing , vol. 28, pp. pp. 1510-1539. , 1999. Tagged BibTex xml
Heath L.S., Pemmaraju S.V., "Stack and Queue Layouts of Directed Acyclic Graphs: Part II", SIAM Journal on Computing , vol. 28, pp. pp. 1588-1626, 1999. Tagged BibTex xml
Brunick G.P., Green E.L., Heath L.S., Struble C.A., "Efficient Construction of Drinfel'd Doubles,", International Symposium on Symbolic and Algebraic Computation (ISSAC'99),, 1999. Tagged BibTex xml
Heath L.S., Loehr N.A., "New Algorithms for Generating Conway Polynomials over Finite Fields", Tenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 1999. Tagged BibTex xml
1998
Heath L.S., Vergara J.C., "Sorting by Bounded Block-Moves", Discrete Applied Mathematics , vol. 88, no. 2, pp. pp. 181-206. , 1998. Tagged BibTex xml
Heath L.S., Vergara J.C., "Edge-Packing in Planar Graphs", Theory of Computing Systems , vol. 31, pp. pp. 629-662. , 1998. Tagged BibTex xml
Ganley J.L., Heath L.S., "An Experimental Evaluation of Local Search Heuristics for Graph Partitioning,", Computing , vol. 60, pp. pp. 121-132. , 1998. Tagged BibTex xml
Heath L.S., Vergara J.C., "Edge-Packing Planar Graphs by Cyclic Graphs", Discrete Applied Mathematics , vol. 81, pp. pp. 169-180. , 1998. Tagged BibTex xml
1997
Heath L.S., Pemmaraju S.V., "Stack and Queue Layouts of Posets,", SIAM Journal on Discrete Mathematics , vol. 10, pp. pp. 599-625. , 1997. Tagged BibTex xml
Heath L.S., "Graph Embeddings and Simplicial Maps", Theory of Computing Systems , vol. 30, pp. pp 51-65., 1997. Tagged BibTex xml
Heath L.S., Hix D., Nowell L.T., Wake W.C., Averboch G.A., Labow E., Guyer S.A., Brueni D.J., France R.K., Dalal K., Fox E.A., "Envision: A User-Centered Database of Computer Science Literature", Communications of the ACM , vol. 38, pp. pp. 52-53, 1997. Tagged BibTex xml
Ganley J.L., Heath L.S., "Optimal and Random Partitions of Random Graphs", The Computer Journal , vol. 37, pp. pp. 641-643. , 1997. Tagged BibTex xml
Green E.A., Heath L.S., Keller B.J., "Opal: A System for Computing Noncommutative Gröbner Bases (System Description)", Eighth International Conference on Rewriting Techniques and Applications (RTA-97), 1997. Tagged BibTex xml
1996
Shaffer C.A., Heath L.S., Yang J., "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. Tagged BibTex xml
Nowell L.T., France R.K., Hix D., Heath L.S., Fox E.A., "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. Tagged BibTex xml
Shaffer C.A., Heath L.S., Nielsen J.M., Yang J., "SWAN: A Student-Controllable Data Structure Visualization System", ED-MEDIA 96, pp. pp. 632-637. , 1996. Tagged BibTex xml
Shaffer C.A., Heath L.S., Yang J., Using the SWAN Data Structure Visualization System for Computer Science Education, , pp. pp. 140-144. , 1996. Tagged BibTex xml
Yang J., Shaffer C.A., Heath L.S., "SWAN: A Data Structure Visualization System", Proceedings of Graph Drawing '95, vol. 1027, , pp. pp. 520-523. , 1996. Tagged BibTex xml
1995
Fox E A., Barnette N D., Shaffer C A., Heath L., Wake W., Nowell L T., Lee J A N., Hix D., Hartson H R., "Progress in Interactive Learning with a Digital Library in Computer Science", Proceedings ED-MEDIA 95, World Conf. on Educational Multimedia and Hypermedia, June, 1995. Tagged BibTex xml
Jun Y., Shaffer C.A., Heath L.S., The Swan User''s Manual, Version 1.1, , Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1995. Tagged BibTex xml
Heath L.S., Pemmaraju S.V., "Recognizing Leveled-Planar Dags in Linear Time", Proceedings of Graph Drawing '95, vol. 1027: Springer, pp. pp. 300-311. , 1995. Tagged BibTex xml
Fox E.A., DAGS D.N., Shaffer C.A., Heath L., Wake W.C., Lucy T. Nowell, Lee J A N., Hix D., Hartson R.H., "Progress in Interactive Learning with a Digital Library in Computer Science", World Conference on Educational Multimedia and Hypermedia, 1995, Graz, Austria, , pp. pp. 7-12. , 1995. Tagged BibTex xml
1994
Heath L.S., Pemmaraju S.V., "New Results for the Minimum Weight Triangulation Problem", Algorithmica , vol. 12, pp. pp. 533-552. , 1994. Tagged BibTex xml
Ganley J.L., Heath L.S., "Heuristics for Laying Out Information Graphs", Computing , vol. 52, pp. pp. 389-405. , 1994. Tagged BibTex xml
1993
Shaffer C A., Juvvadi R., Heath L S., "A Generalized Comparison of Quadtree and Bintree Storage Requirements", Image and Vision Computing, vol. 11, no. 7, pp. 402–412, September, 1993. Tagged BibTex xml
Heath L.S., Pemmaraju S.V., Trenk A., "Stack and Queue Layouts of Directed Acyclic Graphs", Planar Graphs , Providence, Rhode Island, American Mathematical Society, pp. pp. 5-1, 1993. Tagged BibTex xml
Heath L.S., Paripati P.K., Roach J.W., "Representing Polyhedra: Faces are Better than Vertices", Computational Geometry: Theory and Applications, vol. 3, pp. pp. 327-351. , 1993. Tagged BibTex xml
Fox E.A., Hix D., Nowell L.T., Brueni D.J., Wake W.C., Heath L.S., Rao D., "Users, User Interfaces, and Objects: Envision, a Digital Library", Journal of the American Society for Information Science , vol. 44, pp. pp. 480-491. , 1993. Tagged BibTex xml
Shaffer C.A., Juvvadi R.R., Heath L.S., "A Generalized Comparison of Quadtree and Bintree Storage Requirements", Image and Vision Computing , vol. 11, pp. pp. 402-412. , 1993. Tagged BibTex xml
Heath L.S., Lower Bounds for Graph Embeddings Via Algebraic Topology (Extended Abstract), , pp. pp. 311-317. , 1993. Tagged BibTex xml
Fox E.A., Heath L.S., Hix D., "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. Tagged BibTex xml
Brueni D.J., Cross B., Fox E.A., Heath L.S., Hix D., Nowell L.T., Wake W.C., What If There Were Desktop Access to the Computer Science Literature?, , pp. pp. 15-22. , 1993. Tagged BibTex xml
1992
Heath L.S., Rosenberg A.L., "Laying Out Graphs Using Queues", SIAM Journal on Computing , vol. 21, pp. pp. 927-958. , 1992. Tagged BibTex xml
Heath L.S., Istrail S., "The Pagenumber of Genus $g$ Graphs is $O(g),$", Journal of the Association for Computing Machinery , vol. 39, pp. pp. 479-501. , 1992. Tagged BibTex xml
Heath L.S., Leighton F., Rosenberg A.L., "Comparing Queues and Stacks as Mechanisms for Laying Out Graphs", SIAM Journal on Discrete Mathematics, vol. 5, pp. pp. 398-412. , 1992. Tagged BibTex xml
Fox E.A., Heath L.S., Chen Q., Daoud A.M., "Practical Minimal Perfect Hash Functions for Large Databases", Communications of the ACM , vol. 35, pp. pp. 105-121. , 1992. Tagged BibTex xml
Fox E.A., Chen Q., Lenwood 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. Tagged BibTex xml
Wartik S., Fox E.A., Heath L.S., Chen Q., "Hashing", Information Retrieval: Data Structures and Algorithms, Engelwood Cliffs, NJ, Prentice-Hall, pp. pp. 293-362. , 1992. Tagged BibTex xml
1991
Fox E.A., Chen Q., Daoud A.M., Heath L.S., "Order-Preserving Minimal Perfect Hash Functions and Information Retrieval,", ACM Transactions on Information Systems , vol. 9, pp. pp. 281-308. , 1991. Tagged BibTex xml
Heath L.S., Edge Coloring Planar Graphs with Two Outerplanar Subgraphs, , pp. pp. 195-202. , 1991. Tagged BibTex xml
1990
Heath L.S., "Covering a Set with Arithmetic Progressions is NP-Complete", Information Processing Letters , vol. 34, pp. 293-298. , 1990. Tagged BibTex xml
Heath L.S., Leighton F., Rosenberg A.L., Graph Layout Using Queues (Extended Abstract), , pp. pp. 305-314. , 1990. Tagged BibTex xml
Heath L.S., Paripati P K., Roach J W., Polyhedra: Faces are Better than Vertices (Extended Abstract), , pp. pp. 191-199. , 1990. Tagged BibTex xml
1989
Fox E.A., Chen Q., Heath L.S., Datta S., "A More Cost Effective Algorithm for Finding Minimal Perfect Hash Functions", Seventeenth Annual ACM Computer Science Conference, 1989,, pp. pp. 114-122. , 1989. Tagged BibTex xml
1988
Heath L.S., Rosenberg A.L., Smith B.T., "The Physical Mapping Problem for Parallel Architectures", Journal of the Association for Computing Machinery, vol. 35, pp. pp. 603-634. , 1988. Tagged BibTex xml
1987
Heath L.S., "Embedding Outerplanar Graphs in Small Books", SIAM Journal on Algebraic and Discrete Methods, vol. 8, pp. pp. 198-218. , 1987. Tagged BibTex xml
Heath L.S., Istrail S., The Pagenumber of Genus $g$ Graphs is $O(g),$, , pp. pp. 388-397. , 1987. Tagged BibTex xml
1984
Heath L.S., Embedding Planar Graphs in Seven Pages, , pp. pp. 74-83. , 1984. Tagged BibTex xml