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J. Entry, D. Mills, K. Mathee, K. Jayachandran,
R. E. Sojka, G. Narasimhan
Influence of irrigated agriculture on soil microbial diversity,
Applied Soil Ecology,
40(1):146-154, 2008.
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E. Zeng, C. Ding, G. Narasimhan, S. Holbrook
Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction,
LSS Computational Systems Bioinformatics Conference (CSB2008),
To Appear, 2008.
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J. Gudmundsson, G. Narasimhan, M. Smid
Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, To Appear
2008.
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J. Gudmundsson, G. Narasimhan, M. Smid
Plane Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, To Appear
2008.
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J. Gudmundsson, G. Narasimhan, M. Smid
Applications of Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, To Appear
2008.
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J. Gudmundson, C. Levcopoulos, G. Narasimhan, and M. Smid
Approximate Distance Oracles for Geometric Spanners,
ACM Transactions on Algorithms, 4(1), Article 10, 2008.
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PNAS Website
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K. Mathee, G. Narasimhan, C. Valdes, X. Qiu, J. Matewish,
M. Koehrsen, A. Rokas, C. Yandava, R. Engels, E. Zeng,
R. Olavarietta, M. Doud, R. Smith, P. Montgomery, J. White,
P. Godfrey, C. Kodira, B. Birren, J. Galagan, S. Lory,
Dynamics of Pseudomonas aeruginosa genome evolution,
Proceedings of the National Academy of Sciences (PNAS),
105(8):3100-05, 2008.
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IJBRA Website
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P. Buendia and G. Narasimhan,
The Role of Internal Node Sequences and the Molecular Clock in the
Analysis of Serially-Sampled Data,
International Journal of Bioinformatics
Research and Applications (IJBRA),
4(1):107-121, 2008.
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P. Buendia and G. Narasimhan,
Sliding MinPD: Building evolutionary networks of serial samples via
an automated recombination detection approach,
Bioinformatics, 23(22):2993-3000, 2007; doi: 10.1093/bioinformatics/btm413
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T. Milledge, G. Zheng, T. Mullins, and Narasimhan,
SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing
IEEE Conference on Bioinformatics and Bioengineering (BIBE2007) ,
1343-47, 2007.
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E. Zeng, C. Yang, T. Li, and Narasimhan,
On the Effectiveness of Constraints Sets in Clustering Genes
IEEE Conference on Bioinformatics and Bioengineering (BIBE2007) ,
79-86, 2007.
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Gudmundsson, Klein, Narasimhan, Smid, and Wolff (Eds.)
06481 Abstracts Collection -- Geometric Networks and Metric Space Embeddings,
Dagstuhl Seminar Proceedings 06481, p1-21, 2007.
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E. Zeng, K. Mathee, and Narasimhan,
IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics
Data,
LSS Computational Systems Bioinformatics Conference (CSB2007) ,
227-35, 2007.
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J. Yan, K. Zhang, Z. Zhang, S. Chen, and Narasimhan,
A graph reduction method for 2D Snake problems,
IEEE Conference on Computer Vision and Pattern Recognition (CVPR) ,
2007.
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H. Alvarez, D. Chatfield, D. Cox, E. Crumpler, C. D'Cunha,
R. Gutierrez, J. Ibarra, E. Johnson, K. Kumar, Tom
Milledge, G. Narasimhan, M. Sadjadi,
C. Zhang
CyberBridges: A model collaboration infrastructure for
e-Science,
Proceedings of the IEEE CCGrid Conference,
65-72, 2007.
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P. Buendia and G. Narasimhan,
Searching for recombinant donors in a phylogenetic network
of serial samples,
Proceedings of the International Symposium on Bioinformatics
Research and Applications (ISBRA),
109-20, 2007.
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Erliang Zeng and G. Narasimhan,
Enhancing Motif Discovery using Comparative Genomics Data,
Proceedings of the International Symposium on Bioinformatics
Research and Applications (ISBRA),
329-37, 2007.
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G. Narasimhan, M. Smid
Geometric Spanner Networks,
Cambridge University Press, 560p, 2007.
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Book Info
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C. Yang, E. Zeng, K. Mathee, G. Narasimhan
PlasmoTFBM: An intelligent queriable database for predicted
transcription factor binding motifs in Plasmodium
falciparum ,
In Methods of Microarray Data Analysis V ,
McConnell, Lin, Hurban (Eds.), Springer, p121-136, 2007.
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J. Gudmundsson, G. Narasimhan, M. Smid
Distance-preserving Approximations of Polygonal Paths,
Computational Geometry -- Theory and Applications,
36:183-196, 2007.
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W. Peng, Tao Li, and G. Narasimhan,
Mining the Database of Transcription Binding Sites,
Proceedings of the 6th IEEE Symposium on Bioinformatics
and Bioengineering (BIBE), p61-64, 2006.
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Abstract
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P. Buendia, and G. Narasimhan,
Serial NetEvolve: a flexible utility for generating
serially-sampled sequences along a tree or recombinant
network,
Bioinformatics, 22(18):2313-2314, 2006.
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J. Gudmundsson, M. van Kreveld, G. Narasimhan
Region-Restricted Clustering for Geographic Data Mining,
European Symposium on Algorithms (ESA 2006),
Zurich, Sept'06, Lecture Notes in Computer Science, Vol. 4168,
p399-410, 2006.
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D. N. Kuhn, G. Narasimhan, K. Nakamura, J. S. Brown,
R. J. Schnell, A. W. Meerow,
Identification of Cacao TIR NBS-LRR resistance gene analogs
and their use as genetic markers,
Journal of American Society for Horticultural Science,
131(6):806-813, 2006.
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S. Ghandeharizadeh, G. Narasimhan,
Challenges of a "What"-Oriented Framework for On-the-fly
Integration of Biomedical Data,
White Paper in response to National Library of Medicine
Request for Information (RFI) on "Advanced Informatics for
Biomedicine", February 2006.
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C. Yang, D. Mills, K. Mathee, Y. Wang, K. Jayachandran,
M. Sikaroodi, P. Gillevet, J. Entry, G. Narasimhan,
An ecoinformatics tool for microbial community studies:
Supervised classification of Amplicon Length
Heterogeneity (ALH) profiles of 16S rRNA,
Journal of Microbiological Methods, 65(1):49-62, 2006.
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G. Zheng, T. Milledge, E. O. George,
and G. Narasimhan,
Pooling Evidence to Identify Cell Cycle-Regulated Genes,
Proceedings of the International Workshop on Bioinformatics
Research and Applications (IWBRA),
Lecture Notes in Computer Science,
Vol. 3992, Springer Verlag, p694-701, 2006.
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T. Milledge, G. Zheng,
and G. Narasimhan,
Discovering Sequence-Structure Patterns in Proteins with
Variable Secondary Structure,
Proceedings of the International Workshop on Bioinformatics
Research and Applications (IWBRA),
Lecture Notes in Computer Science,
Vol. 3992, Springer Verlag, p702-709, 2006.
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P. Buendia, T. Collins,
and G. Narasimhan,
Reconstructing ancestor-descendant lineages from
serially-sampled data: a comparison study,
Proceedings of the International Workshop on Bioinformatics
Research and Applications (IWBRA),
Lecture Notes in Computer Science,
Vol. 3992, Springer Verlag, p807-814, 2006.
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Springer Website
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V. Renugopalakrishnan, X. Wei, G. Narasimhan,
C. S. Verma, P. Li, and A. Anumanthan,
Enhancement of Protein Thermal Stability: Toward the design of
robust proteins for bionanotechnological
applications,
chapter 8
Bionanotechnology: Proteins to Nanodevices, p117-139, Springer, 2006.
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G. Narasimhan,
CISE-NSF Area Study: Computational Geometry, 2005.
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R. Klein, C. Knauer, G. Narasimhan, and M. Smid,
Exact and Approximation Algorithms for Computing the Dilation Spectrum of Paths, Trees, and Cycles,
To appear, Proc. of ISAAC, Hainan, China, December 2005.
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Publisher Website
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V. Renugopalakrishnan, R. Garduno-Juarez, G. Narasimhan,
C. S. Verma, X. Wei, and P. Li,
Rational Design
of Thermally Stable Proteins: Relevance to Bionanotechnology,
Journal of Nanoscience and
Nanotechnology, 5(11), p1759-1767, 2005.
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C. Yang, E. Zeng, T. Li, G. Narasimhan
A Knowledge-Driven Method to Evaluate Multi-Source Clustering,
Proceedings of the International Symposium on Parallel and
Distributed Processing and Applications (ISPA'05),
Lecture Notes in Computer Science,
Vol. 3759, Springer Verlag, p196-202, 2005.
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C. Yang, E. Zeng, T. Li, G. Narasimhan
Clustering genes using gene expression and
text literature data,
Proceedings of CSB'05, Stanford, CA, p329-340, August 2005.
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T. Milledge, S. Khuri, X. Wei, C. Yang, G. Zheng, G. Narasimhan
Sequence Structure Patterns: Discovery and
Applications,
Proceedings of the 6th Atlantic Symposium on Computational
Biology and Genome Informatics (CBG),
p1282-1285, July 2005.
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Y. Wang, C. Yang, K. Mathee, G. Narasimhan
Clustering using Adaptive Self-Organizing Maps (ASOM) and
Applications,
Proceedings of the International Workshop on Bioinformatics
Research and Applications (IWBRA), Lecture Notes in Computer Science,
Vol. 3515, Springer Verlag, p944-951, 2005.
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M. He, G. Narasimhan, S. Petoukhov, (Editors)
ADVANCES IN BIOINFORMATICS AND ITS APPLICATIONS,
(Series in Mathematical Biology and Medicine), World Scientific
Press, June 2005. [ISBN: 981256148X]
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M. Handfield, J. Mans, G. Zheng, M.C. Lopez, A. Progulske-Fox,
G. Narasimhan, H.V. Baker, R.J. Lamont,
Distinct Expression Profiles Characterize Oral
Epithelium-Microbiota Interactions,
Cellular Microbiology, 7(6):811-823, 2005.
Electronic version of the article published in
Cellular Microbiology is provided: complete citation information for
the final version of the paper, as published in the print edition of
Cellular Microbiology, is available on the Blackwell Synergy online
delivery service, accessible via the journal's website at
http://www.blackwellpublishing.com/cmi or
http://www.blackwell-synergy.com.
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Joachim Gudmundsson, Giri Narasimhan, and Michiel Smid
Fast Pruning of Geometric Spanners,
Lecture Notes in Computer Science, Vol. 3404,
Proc. of the 22th Annual Symposium on Theoretical Aspects
of Computer Science (STACS), p508-520, 2005.
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G. Zheng, E. O. George, G. Narasimhan
Microarray Data Analysis Using Neural Network Classifiers and Gene
Selection Methods,
In Methods of Microarray Data Analysis IV ,
Shoemaker, J. S., Lin, S. M. (Eds.), Springer, p207-222,
2005 [ISBN: 0-387-23074-2].
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Prosenjit Bose, Anil Maheswari, Giri Narasimhan, Michiel Smid and
Norbert Zeh
Approximating geometric bottleneck shortest paths,
Computational Geometry: Theory and Applications,
Vol. 29(3), p233-249, 2004.
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L. Bobadilla, F. Nino, G. Narasimhan
Predicting and Characterizing Metal-Binding Sites Using Support Vector
Machines,
Proceedings of ICBA'04, p307-318, December 2004.
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C. Yang, E. Zeng, K. Mathee, G. Narasimhan
Querying a Database of Regulatory Elements,
Proceedings of ICBA'04, p81-92, December 2004.
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T. Milledge, G. Zheng, G. Narasimhan
Applications of Data Mining in Epitope Prediction,
Proceedings of ICBA'04, p390-401, December 2004.
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Y. Sun, Z. Deng, K. Mathee, G. Narasimhan
Training Set Design for Pattern Discovery with Applications to Protein
Motif Detection,
Proceedings of ICBA'04, p240-251, December 2004.
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C. Yang, E. Zeng, K. Mathee, G. Narasimhan
Mining Regulatory Elements in the Plasmodium falciparum Genome Using
Gene Expression Data,
Proceedings of CAMDA'04: Critical Assessment of
Microarray Data Analysis, Durham, NC, p16-20, November 2004.
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P. Buendia, G. Narasimhan
MinPD: Distance-based Phylogenetic Analysis and Recombination Detection of
Serially-Sampled HIV Quasispecies,
Proceedings of the IEEE Computer Society Bioinformatics Conference,
Stanford, CA, p110-119, 2004.
|
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Abstract |
A. Plata, G. Narasimhan, D. Ohman, J. Barakat, M. Hentzer,
S. Molin, A. Kharazmi, N. Høiby, K. Mathee,
Detection of
Alginate production affects Pseudomonas aeruginosa biofilm
development and architecture, but is not essential for biofilm
formation,
Journal of Medical Microbiology,
Vol. 53(7):679-690, 2004.
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D. Cazalis, T.Milledge, G. Narasimhan
Probe Selection Algorithms,
Proceedings of the SCI Conference, Orlando, July 2004.
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K. Mathee, G. Narasimhan,
Detection of DNA_binding
helix-turn-helix motifs in proteins using the pattern dictionary
method,
Methods in Enzymology, Vol.
370, Chapter 22, 250-264, 2003.
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[Tech. Report]
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M. Andersson, J. Gudmundsson, C. Levcopoulos, and G. Narasimhan
Balanced Partition of Minimum Spanning Trees,
International Journal of Computational Geometry
and Applications , 13(4): 303-316, 2003.
Also Proc. of the 2nd INTL. WORKSHOP on
COMPUTATIONAL GEOMETRY AND APPL. (
CGA'02), Amsterdam, April 2002.
Also, 18th European Workshop on
Computational Geometry, Warszawa, April 10-12, 2002;
And Utrecht University Technical Report, UU-CS-2--2-037
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J. Gudmundsson, G. Narasimhan, M. Smid
Distance-preserving Approximations of Polygonal Paths,
Proceedings of FST&TCS 2003, 217-228, Mumbai, India, December 2003.
|
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G. Zheng, E. O. Goerge, G. Narasimhan
Neural Network Classifiers and Gene Selection Methods for
Microarray Data on Human Lung Adenocarcinoma,
Proceedings of CAMDA'03: Critical Assessment of
Microarray Data Analysis, Durham, NC, 63-67, November 2003.
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X. Wei, D. Kuhn, G. Narasimhan
Degenerate primer design via clustering,
Proceedings of the IEEE Computer Society Bioinformatics Conference,
Stanford, CA, p75-83, August 2003.
|
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Prosenjit Bose, Anil Maheswari, Giri Narasimhan, Michiel Smid and
Norbert Zeh
Approximating geometric bottleneck shortest paths,
Proceedings of the 20th Annual Symposium on Theoretical Aspects
of Computer Science (STACS), Lecture Notes in Computer Science,
Vol. 27, Springer Verlag, p38-49, 2003.
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Abstract
|
T. R. Sutter, X.-R. He, P. Dimitrov, L. Xu, G. Narasimhan,
E. O. George, C. H. Sutter, C. Grubbs,
R. Savory,M. Stephan-Gueldner, D. Kreder, M. J. Taylor,
R. Lubet, T. A. Patterson, T. W. Kensler,
Multiple comparisons model-based clustering and ternary
pattern tree numerical display of gene response to treatment:
Procedure and application to the preclinical evaluation of
chemopreventive agents,
Molecular Cancer Therapeutics, 1(14):1283-1292,
2002.
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G. Narasimhan, C. Bu, Y. Gao, X. Wang, N. Xu, K. Mathee,
Mining Protein Sequences for Motifs,
Journal of Computational Biology, 9(5):707-720,
2002.
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Giri Narasimhan, and Michiel Smid
Approximation algorithms for the bottleneck stretch factor
problem,
Nordic Journal of Computing, 9(1):13-31, 2002.
Also, Proceedings of the 18th Annual Symposium on Theoretical Aspects
of Computer Science (STACS),
Lecture Notes in Computer Science,
Vol. 2010, Springer-Verlag, pp. 502-513, 2001.
Also, University of Magdeburg Technical Report No. 13, 2000.
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Giri Narasimhan, and Kashinath Chatterjee
Graph-theoretic Techniques in D-Optimal Design Problems,
Journal of Statistical Planning and Inference,
102(2):377-387, 2002.
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Joachim Gudmundson, Christos Levcopoulos, and Giri Narasimhan
Fast Greedy Algorithms for Constructing Sparse
Geometric Spanners,
SIAM Journal of Computing, 31(5):1479-1500, 2002.
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Joachim Gudmundson, Christos Levcopoulos, Giri Narasimhan, and Michiel Smid
Approximate Distance Oracles Revisited,
Proc. of ISAAC, Vancouver, Canada, p357-368, November 2002.
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J. Gudmundsson, C. Levcopoulos, G. Narasimhan, and M.Smid
Approximate Distance Oracles for Geometric Graphs,
Proceedings of SODA'02,
828-837, San Francisco, January 2002.
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Christos Levcopoulos, Giri Narasimhan, and Michiel Smid
Improved algorithms for constructing fault tolerant geometric
spanners,
Algorithmica , 32(1): 144-156, 2002.
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B. Bhattacharya, G. Das, A. Mukhopadhyay, and G. Narasimhan
Optimally Computing a Shortest Illuminating Line Segment in a
Simple Polygon,
Computational Geometry: Theory and Applications,
23(1): 1-29, 2002.
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G. Narasimhan and M. Zachariasen
Geometric Minimum Spanning Trees via Well-Separated Pair
Decompositions,
To Appear, Journal of Experimental Algorithms, 2002.
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G. Narasimhan,
Pattern Discovery Applications in Bioinformatics,
Invited Speaker, International Conference on Information
Technology, India, Decemeber 2001.
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B. Bhattacharya, A. Mukhopadhyay, and G. Narasimhan
Two-Guard Walkability of Simple Polygons,
Lecture Notes in Computer Science, Vol. 2125, WADS'01 ,
438-449, 2001.
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.
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Arun Jagota, Giri Narasimhan, and Lubomir Soltes
A Generalization of Maximal Independent Sets,
Discrete Applied Mathematics, 109:3, 223-235, 2001.
|
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J. Gudmundsson, C. Levcopoulos, and G. Narasimhan
Approximating Minimum Manhattan Networks,
Nordic J. of Computing, 8(2):219-232, Summer 2001.
Also Proceedings of APPROX'99 ,
28-37, Berkeley, August 1999.
|
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Moses Charikar, Samir Khuller, David Mount, and Giri Narasimhan
Algorithms for Facility Location Problems with Outliers,
Proceedings of SODA 2001, Washington DC, pp. 642-651, 2001.
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[Poster.ppt];
[Software: BIP]
|
Zhou Ji, Qichang Li, Arne Heydorn, Soren Molin, Kalai Mathee, and
Giri Narasimhan
Quantitative Analysis of Pseudomonas
aeruginosa Biofilm Images using Fractal Dimensions,
ASM Biofilms 2000
, Big Sky, MT, July 16-20, 2000.
SOFTWARE:
Trial Version Available for download.
[Software: BIP]
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Joachim Gudmundson, Christos Levcopoulos, and Giri Narasimhan
Improved Greedy Algorithms for Constructing Sparse
Geometric Spanners,
Proceedings of SWAT, Lecture Notes in Computer
Science, Vol. 1851, Springer Verlag, 314-327, 2000.
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Yuan Gao, Isidore Rigoutsos, Aris Floratos, Laxmi Parida, and Giri
Narasimhan
Unsupervised Building and Exploitation of Composite Descriptors
for Collection of Proteins and Protein Fragments,
IBM Technical Report , 2000.
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Giri Narasimhan, and Michiel Smid
Approximating the Stretch Factor of Euclidean Graphs,
SIAM Journal of Computing,
30(3):978-989, 2000.
|
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Giri Narasimhan, Martin Zachariasen and Jianlin Zhu
Experiments with Computing Geometric Minimum Spanning Trees,
Proceedings of ALENEX'00 ,
pages 183-196, San Francisco, January 2000.
|
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Yuan Gao, Kalai Mathee, Giri Narasimhan, and Xuning Wang
Motif Detection in Protein Sequences,
Proceedings of SPIRE'99 , pages 63-72, Cancun,
September 1999.
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;
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Giri Narasimhan
On Hamiltonian Triangulations in Simple Polygons
International Journal of Computational
Geometry and Applications , Vol. 9, No.3, pages 261-275, 1999
Also in Proc. of WADS 1997
, Halifax, Nova Scotia;
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G. Hernandez, Giri Narasimhan, and L. F. Nino,
Evolutionary Set Matching
Smart Engineering Systems: Neural Networks, Fuzzy Logic,
Evolutionary Programming, Data Mining, and Rough Sets ,
Volume 8, Eds.: C. H. Dagli, M. Akay, A. L. Buczak, O. Ersoy,
B. R. Fernandez, pages 265-272, 1998.
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A. Jagota, Giri Narasimhan, and K.W. Regan
Information Capacity of Binary Weights Associative Memories,
Neurocomputing , 19(1-3):35-58, (1998).
|
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Estie Arkin, Joseph S. B. Mitchell, and Giri Narasimhan
Resource-Constrained Geometric Network Optimization
Proc. of ACM Symposium on
Computational Geometry , Minneapolis, 307-316, 1998.
|
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Christos Levcopoulos, Giri Narasimhan, and Michiel Smid
Efficient algorithms for constructing fault tolerant geometric
spanners,
Proc. of
ACM Symposium on the Theory of Computing , Dallas, 186-195,
1998.
|
[Poster ps Version]
[Abstract ps Version]
[Software: GYM]
|
Yuan Gao, Mu Yang, Xingqiang Wang, Kalai Mathee, and Giri Narasimhan
Detection of HTH Motifs via Data Mining
Poster at
Int'l Conference on Bioinformatics ,
Atlanta, Nov 6-9, 1997.
SOFTWARE:
Go to
GYM Home Page.
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