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naren's picture

Naren Ramakrishnan

Professor and Associate Head for Graduate Studies

Office: 2050B Torg
Email: naren@vt.edu
Phone: (540) 231-8451
Website: http://people.cs.vt.edu/~ramakris/
Office Hours: TR: 10:00 a.m. to 12:00 p.m.
  • About
  • Labs
  • Publications
  • Courses
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Research Interests
  • Computational Biology and Bioinformatics
  • Data Mining
  • High End Computing
  • Knowledge, Data and Information
  • Problem Solving Environments

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).

lab - CMGS

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.

lab - softlab main photo

Softlab

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. Tagged BibTex xml
Kang P., Cao Y., Ramakrishnan N., Ribbens C.J., Varadarajan S., "Modular Implementation of Adaptive Decisions in Stochastic Simulations", Proceedings of the 24th Annual ACM Symposium on Applied Computing (SAC'09): ACM, New York, pp. 995-1001, 2009. Tagged BibTex xml
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
Jin Y., Murali T M., Ramakrishnan N., "Compositional Mining of Multi-relational Biological Datasets", ACM Transactions on Knowledge Discovery from Data, vol. 2, no. 1, March, 2008. Tagged BibTex xml
Cho Y J., Ramakrishnan N., Cao Y., "Reconstructing Chemical Reaction Networks: Data Mining meets System Identification", 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'08), Feb, 2008. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
Bailey-Kellogg C., Ramakrishnan N., Marathe M.V., "Spatial data mining to support pandemic preparedness. ", SIGKDD Explorations, vol. 8, no. 1, pp. 80-82, 2006. Tagged BibTex xml
2005
Liu R., Lloyd E., Marathe M., Ramanathan R., Ravi S., "Algorithmic Aspects of Topology Control Problems For Ad-hoc Networks", ACM/Baltzer J. Mobile Networks and Applications (MONET), vol. 10, pp. 19-34, 2005. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
Allen N.A., Shaffer C.A., Vass M.T., Ramakrishnan N., Watson L.T., "Next generation modeling II - applications: improving the development process for eukaryotic cell cycle models with a modeling support environment", WSC '03: Proceedings of the 35th conference on Winter simulation: Winter Simulation Conference, pp. 782–790, 2003. Tagged BibTex xml
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
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
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. 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., "The Emerging Landscape of Bioinformatics Software Systems", IEEE Computer , vol. 35, pp. pp. 41-45. , 07/2002. Tagged BibTex xml
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. Tagged BibTex xml
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. Tagged BibTex xml
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. 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
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
of the on Environments P., Towards Preferences in Virtual Environment Interfaces, , pp. 63-72, 2002. Tagged BibTex xml
2001
Robert G. Capra I., Perez-Quinones M.A., Ramakrishnan N., WebContext: remote access to shared context, , Orlando, Florida, ACM Press, pp. 1-9, 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
Wingrave C., Bowman D., Ramakrishnan N., "A First Step Towards Nuance-Oriented Interfaces for Virtual Environments", Proceedings of the Virtual Reality International Conference, pp. 181-188, 2001. Tagged BibTex xml
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. Tagged BibTex xml
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
Ramakrishnan N., Ribbens C.J., "Mining and visualizing recommendation spaces for elliptic PDEs with continuous attributes", ACM Trans. Math. Softw., vol. 26, pp. 254–273, 2000. Tagged BibTex xml

2000 Level Courses

  • CS2204: UNIX

4000 Level Courses

  • CS4804: Introduction to Artificial Intelligence

5000 Level Courses

  • CS5634: Data Management in Bioinformatics
  • CS5804: Introduction to Artificial Intelligence

6000 Level Courses

  • CS6604: Advanced Topics in Data and Information

A Digital Library Testbed for Research Related to 4/16/2007 at Virginia Tech

Granting Institution: NSF IIS Special Projects Program
Amount: 199,993

Computational Models for Gene Silencing: Elucidating A Pervasive Biological Defense

Granting Institution: National Science Foundation
Amount: $1,267,410

Discovering the Neural Code: Data Mining Algorithms For Network Reconstruction

Granting Institution: General Motors Corporation
Amount: $220,262

Dryophile Genes To Engineer Stasis-Recovery Of Human Cells

Granting Institution: Office of Naval Research
Amount: $78,358

Formal Models, Algorithms, and Visualizations for Storytelling Analytics

Granting Institution: National Science Foundation
Amount:

III: Medium: Collaborative Research: Integration, Prediction, and Generation of Mixed Mode Information using Graphical Models, with Applications to Protein-Protein Interactions

Granting Institution: National Science Foundation
Amount:

III:Small:Integrated Digital Library Support for Crisis, Tragedy, and Recovery

Granting Institution: National Science Foundation
Amount:

Storytelling in the National Nuclear Archive

Granting Institution: Idaho National Labs
Amount: $10,866

Temporal Data Mining Solutions for Sustainable Data Centers

Granting Institution: Hewlett-Packard Labs Innovation Research
Amount:

The Adaptive Code Kitchen & Flexible Tools for Dynamic Application Composition

Granting Institution: National Science Foundation
Amount: $470,047

 
 
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