Giri Narasimhan: Publications


2017

arXiv Consuegra, Martinez, Rangaswami, Narasimhan, Shao, Vietri,
Analyzing adaptive cache replacement strategies,
arXiv:1503.07624, 2017.
  Martinez, Narasimhan, Vietri,
Improved Analysis of Adaptive Cache Replacement Strategies,
Submitted, 2017.
  Cickovski, Peake, Aguiar-Pulido, Narasimhan,
ATria: A Novel Centrality Algorithm Applied To Biological Networks,
BMC Bioinformatics, To Appear 2017.
Link Mesa, Fernandez, Wu, Narasimhan, Greidinger, Mills,
Can SLE classification rules be effectively applied to diagnose unclear SLE cases?
Lupus, 26(2):150-162, 2017.

2016

Link Narasimhan, M., Vietri, Mehta, Rajabli, Aguiar-Pulido, Mathee, Narasimhan,
Predicting Symptom Severity and Contagiousness of Respiratory Viral Infections
F1000Research 2016, 5(ISCB Comm J):1663 (poster) (DOI: 10.7490/f1000research.1112564.1).
Best Poster Award ISMB-SCS.
Link Huang, Kazmierczak, Zhou, Aguiar-Pulido, Narasimhan, Szczesna-Cordary,
Gene Expression Patterns in Transgenic Mouse Models of Hypertrophic Cardiomyopathy Caused by Mutations in Myosin Regulatory Light Chain,
In Special Issue on "Myofilament Modulation of Cardiac Contraction" in Archives of Biochemistry and Biophysics, 601: 121--132, 2016.
  Li, Jean-Baptiste, Riveros, Narasimhan, Zhang, Zhao,
CacheDedup: In-line cache deduplication for Flash Caching,
Proceedings of FAST, 301-314, 2016.
  Cickovski, Aguiar-Pulido, Huang, Mahmud, Narasimhan,
Lightweight Microbiome Analysis Pipeline,
Proceedings of IWBBIO, pp 225--227, 2016.
  Aguiar-Pulido, Suarez-Ulloa, Eirin-Lopez, Narasimhan,
Network-inspired Approaches for Transcriptomic Analyses,
Proceedings of IWBBIO, pp 437--440, 2016.
Link Aguiar-Pulido, Suarez-Ulloa, Huang, Cickovski, Mathee, Narasimhan,
Metagenomics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis,
Evolutionary Bioinformatics, 12(S1):5--16, 2016.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Applications of Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming-Yang Kao, ISBN: 978-3-642-27848-8, pp86-90, 2016.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming-Yang Kao, ISBN: 978-3-642-27848-8, pp846-852, 2016.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Planar Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming-Yang Kao, ISBN: 978-3-642-27848-8, pp1570-1574, 2016.

2015

Cickovski, Peake, Aguiar-Pulido, Narasimhan,
ATria: A Novel Centrality Algorithm Applied To Biological Networks,
Proceedings of ICCABS, October 2015.
  Narasimhan,
Next Generation Microbiome Analysis,
Invited Speaker, ICCABS, October 2015.
Fernandez, Riveros, Campos, Mathee, Narasimhan,
Microbial "Social" Networks,
BMC Genomics, 16(Suppl 11):S6 (Special Issue), 2015.
link R. Mittal, C. V. Lisi, R. Gerring, J. Mittal, K. Mathee, G. Narasimhan, R. K. Azad, Q.Yao, M. Grati, D. Yan, A. A. Eshraghi, S.I. Angeli, F.F. Telischi, X-Z. Liu.
Current concepts in the pathogenesis and treatment of chronic suppurative otitis media. Journal of Medical Microbiology, 64(10):1103--16, DOI: 10.1099/jmm.0.000155, 2015.
link Cickovski, Flor, Irving-Sachs, Novikov, Parda, Narasimhan,
GPUDePiCt: A Parallel Implementation of a Clustering Algorithms for Computing Degenerate Primers on Graphics Processing Units,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2):445-454, 2015.
  Fernandez, Riveros, Aguiar-Pulido, Segal, Campos, Mathee, Zeng, Narasimhan,
Microbiome Analysis: State-of-the-Art and Future Trends,
Chapter 18 in Computational Methods for Next Generation Sequencing Data Analysis
Eds: Mandoiu and Zelikovsky, John Wiley and Sons, p333-351, 2015.
link V. Aguiar-Pulido, V. Suarez-Ulloa, J. M. Eirin-Lopez, J. Pereira, and Narasimhan,
Computational Methods in Epigenetics, In Personalized Epigenetics,
Editor: T. Tollefsbol, Academic Press, Chapter 6, p153-180, ISBN: 978-0-12-420135-4, 2015.
Link J. Yan, K. Zhang, Z. Zhang, S. Chen, and Narasimhan,
Automatic Construction of 3-D Building Model From Airborne LIDAR Data Through 2-D Snake Algorithm,
IEEE Transactions on Geoscience and Remote Sensing, 53(1):3-14, 2015.

2014

arXiv Shao, Consuegra, Rangaswami, Narasimhan,
Analyzing adaptive cache replacement strategies,
Submitted, 2014.
link Campos, Fernandez, Wanner, Holt, Donna, Mendes, Fishman, Infante, Jaric, Silva-Herzog, Schneper, Segal, Moraga, Mathee, Salathe, Narasimhan,
Microbial Associations in the Lungs Differ by Smoking and COPD Status,
Abstract, American Thoracic Society International Conference, 2014.
link Caille, Zincke, Merighi, Balasubramanian, Kumari, Kong, Silva-Herzog, Narasimhan, Schneper, Lory, and Mathee
Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR,
J Bacteriology, 196(22):3890-3902, 2014.
  Narasimhan,
Metagenomics and NGS,
Keynote Speaker, ICCABS and CANGS, June 2014.
Link Balasubramanian, Kumari, Jaric, Fernandez, Turner, Dove, Narasimhan, Lory, Mathee
Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat-shock and the oxidative stress response,
Nucleic Acids Research, 42(2):979-998, 2014. doi: 10.1093/nar/gkt942

2013

  Balasubramanian, Murugapiran, Silva-herzog, Schneper, Yang, Tatke, Narasimhan, and Mathee
Transcription regulatory network in Pseudomonas aeruginosa,
In Bacterial Gene Regulation and Transcriptional Networks, Chapter 13, p199-221, Editor: Madan Babu, Caiser Academic Press, 2013.
  Fernandez, Jaric, Narasimhan
Mining Biomedical Datasets,
Proceedings of STATISTICS-2013, Invited, 2013
Consuegra, Narasimhan
Geometric Avatar Problems,
Proceedings of FSTTCS, 389--400, Leibniz International Proceedings in Informatics Series, Vol 24, 2013.
Link Consuegra, Kumar, Narasimhan
Comment on "On the Uniqueness of Stable Marriage Matchings" [Economic Letters 69(1):1-8, 2000],
Economics Letters, 121(3):468, 2013.
TR Consuegra, Narasimhan, Rangaswami
Vector repacking algorithms for power-aware computing,
Proceedings of Energy-efficient Networks of Computers (E2NC) Workshop, IGCC, 1--8, IEEE, 2013.
Link Jaric, Segal, Silva-Herzog, Schneper, Mathee, Narasimhan,
Better primer design for metagenomic applications by increasing taxonomic distinguishability,
BMC Proceedings, 7(Suppl 7):S4, 2013; doi:10.1186/1753-6561-7-S7-S4
Link Fernandez, Jaric, Schneper, Segal, Silva-Herzog, Campos, Fishman, Salathe, Infante, Mathee, Narasimhan,
A Metagenomic Approach to the Airways Microbiome of Chronic Obstructive Pulmonary Disease (COPD),
29th Southern Biomedical Engineering Conference, 2013.
Link Jaric, Segal, Silva-Herzog, Schneper, Mathee, Narasimhan,
Designing primers with higher taxonomic distinguishability,
29th Southern Biomedical Engineering Conference, 2013.
Link Cattoir, Narasimhan, Skurnik, Aschard, Roux, Ramphal, Jyot and Lory
Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus,
mBio, 3(6):e00410-12, 2013.

2012

Link Zeng, Ding, Mathee, Schneper, Narasimhan,
Gene function prediction and functional network: the role of gene ontology,
In DATA MINING: Foundations and Intelligent Paradigms, Dawn E. Holmes and Lakhmi C. Jain (Eds.), Springer, Chapter 7, p123-162, 2012, ISBN 978-3-642-23150-6.
TR Consuegra, Narasimhan, Rodriguez, Tanigawa
Avatar Problems,
Submitted, 2012.
Link Balasubramanian, Schneper, Merighi, Smith, Narasimhan, Lory, and Mathee
The regulatory repertiore of Pseudomonas aeruginosa AmpC beta-lactamase regulator AmpR includes virulence genes,
PLoS One, 7(3):e34067, 2012. doi:10.1371/journal.pone.0034067

2011

Yang, Medvin, Yoder-Himes, Lory, Narasimhan
CloG: A pipeline for closing gaps in a draft assembly using short reads,
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), p202-207, 2011.
Narasimhan
Invited: Comparative Microbial Genomics,
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), p8, 2011.
  Weeks, Villamor, Tracey, Stoddard, Makemson, Garcia, Gavassa, Philippi, Pitzer, Dewsbury, Narasimhan, McGoron, and Tashakkori
QBIC, an interdisciplinary and quantitative biological sciences curriculum: concept to implementation
Journal of Science Education 12(1):11-14, 2011.

2010

  Mandoiu, Narasimhan, Pan and Zhang
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(4):1-2, 2010.
PubMed Doud, Light, Gonzalez, Narasimhan, and Mathee
Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients,
Human Genomics, 4(3):147-69, 2010.
Link Kocak, Zheng, Narasimhan,George, and Pyne
Differential meta-analysis for testing the relative importance of two competing null hypotheses over multiple experiments,
Journal of the Indian Society of Agricultural Statistics, Special Issue on Statistical Genomics, 64(1):1-10, 2010.
  E. Zeng, C. Yang, T. Li, and G. Narasimhan,
Clustering Genes using Heterogeneous Data Sources
International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 1(2):12-28, 2010.

2009

  Y. Zhang, E. Zeng, T. Li, and G. Narasimhan,
Weighted Consensus Clustering for Identifying Functional Modules In Protein-Protein Interaction Network
International Conference on Machine Learning and Applications (ICMLA), 2009.
Link P. Buendia and G. Narasimhan,
Serial Evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains,
BMC Systems Biology, 3:62, 2009.
Link Editors: I. Mandoiu, G. Narasimhan, and Yanqing Zhang
Bioinformatics Research and Applications,
Conference Proceedings (ISBRA 2009), Lecture Notes in Bioinformatics, Vol. 5542, Springer Verlag, 2009.
Link R. Klein, C. Knauer, G. Narasimhan, and M. Smid,
On the Dilation Spectrum of Paths, Trees, and Cycles,
Computational Geometry -- Theory and Applications, 42:923-33, 2009.
  A. Elshahat, A. Parhizgari, G. Narasimhan, S. Anwar
Portfolio Optimization Using Greedy Algorithm,
Proceedings of Annual Meeting of the Multinational Finance Society, Crete, 2009.
Pubmed M. Doud, E. Zeng, L. Schneper, G. Narasimhan, K.Mathee
Approaches to Analyze Dynamic Microbial Communities such as those seen in Cystic Fibrosis Lung,
Human Genomics, 3(3):246-256, 2009.
Link J. Gudmundsson, M. van Kreveld, G. Narasimhan
Region-Restricted Clustering for Geographic Data Mining,
Computational Geometry -- Theory and Applications (CGTA), 42(3):231-240, 2009.

2008

  E. Zeng, K.Mathee, L. Schneper, G. Narasimhan
A functional network of yeast genes using gene ontology information,
IEEE Conference on Bioinformatics and Biomedicine (BIBM2008), p343-346, Philadelphia, PA, November, 2008.
  G. Zheng and G. Narasimhan,
A Branch-and-bound approach to knowledge-based protein structure assembly,
IEEE Conference on Bioinformatics and Bioengineering (BIBE2008), p1-5, 2008.
  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.
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), p73-84, Stanford, CA, August, 2008.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p360-64, 2008.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Plane Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p653-656, 2008.
Link J. Gudmundsson, G. Narasimhan, M. Smid
Applications of Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p40-43, 2008.
  J. Gudmundson, C. Levcopoulos, G. Narasimhan, and M. Smid
Approximate Distance Oracles for Geometric Spanners,
ACM Transactions on Algorithms, 4(1), Article 10, 2008.
PNAS Website 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.
IJBRA Website 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.

2007

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
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.
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.
Gudmundsson, Klein, Narasimhan, Smid, and Wolff (Eds.)
06481 Abstracts Collection -- Geometric Networks and Metric Space Embeddings,
Dagstuhl Seminar Proceedings 06481, p1-21, 2007.
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.
  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.
  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.
  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.
  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.
G. Narasimhan, M. Smid
Geometric Spanner Networks,
Cambridge University Press, 560p, 2007.
Book Info 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.

J. Gudmundsson, G. Narasimhan, M. Smid
Distance-preserving Approximations of Polygonal Paths,
Computational Geometry -- Theory and Applications, 36:183-196, 2007.
Video
G. Narasimhan,
Pattern Discovery in Bioinformatics,
Henry Stewart Talks Series, 2007.

2006

  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.
Abstract 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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
Springer Website 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.

2005

  G. Narasimhan,
CISE-NSF Area Study: Computational Geometry, 2005.
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.
Publisher Website 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.
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.
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.
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.
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.
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]
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.
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.
 
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].

2004


 
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.
L. Bobadilla, F. Nino, G. Narasimhan
Predicting and Characterizing Metal-Binding Sites Using Support Vector Machines,
Proceedings of ICBA'04, p307-318, December 2004.
C. Yang, E. Zeng, K. Mathee, G. Narasimhan
Querying a Database of Regulatory Elements,
Proceedings of ICBA'04, p81-92, December 2004.
T. Milledge, G. Zheng, G. Narasimhan
Applications of Data Mining in Epitope Prediction,
Proceedings of ICBA'04, p390-401, December 2004.
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.
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.
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.
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.

D. Cazalis, T.Milledge, G. Narasimhan
Probe Selection Algorithms,
Proceedings of the SCI Conference, Orlando, July 2004.

2003

  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.
[Tech. Report]  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

 
J. Gudmundsson, G. Narasimhan, M. Smid
Distance-preserving Approximations of Polygonal Paths,
Proceedings of FST&TCS 2003, 217-228, Mumbai, India, December 2003.

 
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.

 
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.

 
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.

2002

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.

 
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.
  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.
  Giri Narasimhan, and Kashinath Chatterjee
Graph-theoretic Techniques in D-Optimal Design Problems,
Journal of Statistical Planning and Inference, 102(2):377-387, 2002.
  Joachim Gudmundson, Christos Levcopoulos, and Giri Narasimhan
Fast Greedy Algorithms for Constructing Sparse Geometric Spanners,
SIAM Journal of Computing, 31(5):1479-1500, 2002.

 
Joachim Gudmundson, Christos Levcopoulos, Giri Narasimhan, and Michiel Smid
Approximate Distance Oracles Revisited,
Proc. of ISAAC, Vancouver, Canada, p357-368, November 2002.

 
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.
  Christos Levcopoulos, Giri Narasimhan, and Michiel Smid
Improved algorithms for constructing fault tolerant geometric spanners,
Algorithmica , 32(1): 144-156, 2002.

 
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.
  G. Narasimhan and M. Zachariasen
Geometric Minimum Spanning Trees via Well-Separated Pair Decompositions,
To Appear, Journal of Experimental Algorithms, 2002.

2001

  G. Narasimhan, Pattern Discovery Applications in Bioinformatics,
Invited Speaker, International Conference on Information Technology, India, Decemeber 2001.

 
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.
.   Arun Jagota, Giri Narasimhan, and Lubomir Soltes
A Generalization of Maximal Independent Sets,
Discrete Applied Mathematics, 109:3, 223-235, 2001.

 
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.

 
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.

2000

[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]

 
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.
  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.
  Giri Narasimhan, and Michiel Smid
Approximating the Stretch Factor of Euclidean Graphs,
SIAM Journal of Computing, 30(3):978-989, 2000.

 
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.

1999 and earlier

  Yuan Gao, Kalai Mathee, Giri Narasimhan, and Xuning Wang
Motif Detection in Protein Sequences,
Proceedings of SPIRE'99 , pages 63-72, Cancun, September 1999.
;

 
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;
  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.
  A. Jagota, Giri Narasimhan, and K.W. Regan
Information Capacity of Binary Weights Associative Memories,
Neurocomputing , 19(1-3):35-58, (1998).

 
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.

 
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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