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| Naren Ramakrishnan Professor and Associate Head for Graduate Studies | Office Hours: | TR: 10:00 a.m. to 12:00 p.m. | |
Naren Ramakrishnan is a professor and associate head for graduate studies in the department of computer science at Virginia Tech. He also serves as an adjunct professor at the Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, India. His research interests include computational science (esp. computational biology), mining scientific data, problem solving environments, and information personalization.
Ramakrishnan is an area editor for IEEE Computer, an editorial board member of Knowledge and Information Systems and the Journal of Intelligent Information Systems. He was a general chair for the Eighth IEEE International Conference on Data Mining (ICDM'08) held in Pisa, Italy, Dec 2008 and program chair of the Seventh IEEE International Conference on Data Mining (ICDM'07).
Honors include an NSF CAREER grant (1999), the New Century Technology Council Innovation award (2000), a Certificate of Teaching Excellence at Virginia Tech (2005), being named to Computerworld's list of "40 under 40" innovative IT people to watch (2007), and a HP Labs innovation grant (2009). He was an invited co-organizer of the recently concluded National Academy of Engineering Frontiers of Engineering Symposium, held in Irvine, CA, Sep 2009. He has received funding from NSF, ONR, NIH, General Motors Research, and HP Labs. Ramakrishnan is an ACM Distinguished Scientist (2009).
 | 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. |
 | URL: http://people.cs.vt.edu/~naren/group.html Contact: Naren Ramakrishnan
Softlab's emphasis is on the design of software systems that provide high-level abstractions to their users, in support of problem solving, knowledge discovery, or, information finding. Our work is highly interdisciplinary, both in the domains outside computer science that we support and in the areas within computer science that we integrate. |
2009
Kang P., Selvarusu N., Ramakrishnan N., Ribbens C.J., Tafti D., Varadarajan S.,
"Modular, Fine-grained Adaptation of Parallel Programs",
International Conference on Computational Science (ICCS 2009): Springer, Heidelberg, pp. 269-279, 2009.
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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.
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Fox E.A., Andrews* C., Fan W., Jiao* J., Kassahun A., Lu* S., Ma* Y., North C., Ramakrishnan N., Scarpa A., Friedman B.H., Sheetz S.D., Shoemaker D., Srinivasan* V., Yang* S., Boutwelle L.,
"A Digital Library for Recovery, Research, and Learning from April 16, 2007 at Virginia Tech",
Traumatology, vol. 14, no. 1, pp. 20 pages, April, 2008.
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Shu* J., Watson L T., Ramakrishnan N., Kamke F A., North C.,
"Unification of problem solving environment implementation layers with XML-based specifications",
Advances in Engineering Software, vol. 39, no. 3, pp. 189-201, March, 2008.
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2007
Ramakrishnan N., Perez-Quinones M A., Shenoy A.,
"Compositional Specification and Realization of Mixed-Initiative Web Dialogs",
International Journal of Web Engineering and Technology, Special Issue Special Issue on User Interface Description Languages, 2007.
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Mishra D., Shaffer C.A., Ramakrishnan N., Watson L.T., Bae K.K., He J., Verstak A.A., Tranter W.H.,
"S4W: a problem-solving environment for wireless system design",
Softw. Pract. Exper., vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
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Saha N., Watson L T., Kafadar K., Ramakrishnan N., Onufriev A., Mane S P., Vasquez-Robinet C.,
"Validation and estimation of parameters for a general probabilistic model of the PCR process",
J. Comp. Biol., vol. 14, pp. 102–117, 2007.
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2006
Vass M.T., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol. 3, no. 2, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 155–164, 2006.
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Vass M., Shaffer C A., Ramakrishnan N., Watson L T., Tyson J J.,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. Vol. 3, no. 2, pp. 155–164, April-June, 2006.
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2005
2004
He J., Verstak A., Watson L T., Stinson C A., Ramakrishnan N., Shaffer C A., Rappaport T S., Anderson C R., Bae K., Jiang J., Tranter W H.,
"Globally Optimal Transmitter Placement for Indoor Wireless Communication Systems",
IEEE Transactions on Wireless Communications, vol. 3, no. 6, pp. 1906–1911, November, 2004.
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Vass M., Allen N., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder and Run Manager",
Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.
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Skidmore R.R., Verstak A., Ramakrishnan N., Rappaport T.S., Watson L.T., He J., Varadarajan S., Shaffer C.A., Chen J., Bae K., Jiang J., Tranter W.H.,
"Towards integrated PSEs for wireless communications: experiences with the S4W and SitePlanner\textregistered projects",
SIGMOBILE Mob. Comput. Commun. Rev., vol. 8, no. 2, New York, NY, USA, ACM, pp. 20–34, 2004.
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2003
Rubin E J., Shaffer C A., Ramakrishnan N., Watson L T., Dymond R., Kibler D., Dietz R., Chanat J., Lohani V., Bosch D., Speir C.,
"From Landscapes to Waterscapes: A PSE for Landuse Change Analysis",
Engineering with Computers, vol. 19, no. 1, pp. 9–25, July, 2003.
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Allen N A., Shaffer C A., Vass M T., Ramakrishnan N., Watson L T.,
"Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment",
Simulation, vol. 79, no. 12, pp. 674–688, December, 2003.
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Allen N., Calzone L., Chen K C., Ciliberto A., Ramakrishnan N., Shaffer C A., Sible J C., Tyson J J., Vass M., Watson L T., Zwolak J.,
"Modeling Regulatory Networks at Virginia Tech",
Omics Journal of Integrative Biology, vol. Vol. 7, no. 3, pp. pages 285–300, Fall, 2003.
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Verstak A., Ramakrishnan N., Watson L.T., He J., Shaffer C.A., Bae K., Jiang J., Tranter W.H., Rappaport T.S.,
"BSML: A binding schema markup language for data interchange in problem solving environments",
Sci. Program., vol. 11, no. 3, Amsterdam, The Netherlands, The Netherlands, IOS Press, pp. 199–224, 2003.
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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.
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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.
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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.
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Krumke S., Liu R., Lloyd E., Marathe M., Ramanathan R., Ravi S.,
"Topology Control Problems Under Symmetric and Asymmetric Thresholds",
Proc. International Conference on Ad hoc and Wireless Networks (ADHOC-NOW'03) , Montreal, Canada, pp. 187--198, October , 2003.
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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.
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Watson L T., Lohani V K., Kibler D F., Dymond R L., Ramakrishnan N., Shaffer C A.,
"Integrated Computing Environments for Watershed Management",
ASCE Journal of Computing in Civil Engineering, vol. 16, no. 4, pp. 259–268, October, 2002.
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Ramakrishnan N., Watson L T., Kafura D G., Ribbens C.J., Shaffer C A.,
"Programming Environments for Multidisciplinary Grid Communities",
Concurrency and Computation: Practice and Experience, vol. 13–15, pp. 1241–1273, Nov–December, 2002.
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He J., Watson L.T., Ramakrishnan N., Shaffer C.A., Verstak A., Jiang J., Bae K., Tranter W.H.,
"Dynamic Data Structures for a Direct Search Algorithm",
Comput. Optim. Appl., vol. 23, no. 1, Norwell, MA, USA, Kluwer Academic Publishers, pp. 5–25, 2002.
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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.
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2001
2000
Shaffer C A., Watson L T., Kafura D G., Ramakrishnan N., Tentner A.,
"Features of Problem Solving Environments for Computational Science",
Proceedings of the 2000 High Performance Computing Symposium (HPC'00): Society for Computer Simulation International, pp. 242–247, 2000.
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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.
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