Giri Narasimhan: Publications

2025

CS Education		Arunachalam, Lunn, Weiss, Liu, Narasimhan, Perfecting Partnerships: Strengthening Internship Experiences for Computing Students and Employers Submitted, 2025.
Bioinformatics		Adhikari, Sobhan, Sutradhar, Narasimhan, Mondal, PathPCNet: Pathway Principal Component-Based Interpretable Framework for Drug Sensitivity Prediction, Submitted, 2025.
ML; Flood Prediction		Shi, Yin, Myana, Ishtiaq, John, Obeysekara, Leon, Narasimhan, Deep Learning Models for Water Stage Predictions in South Florida, Journal of Water Resources Planning and Management, In Press, DOI: 10.1061/JWRMD5/WRENG-6194 Also arXiv: arXiv:2306.15907
Spanners; Experiments		Shariful, Weathers, Ghosh, Narasimhan, Engineering an algorithm for constructing low-stretch geometric graphs with near-greedy average-degrees Computational Geometry, In Press, 2025. Also arXiv.
Aging & Metabolomics		Awarded on May 1, 2025: Anatomical Society Aging Cell Joint Runner Up Best Paper Prize 2024 by Council of the Anatomical Society. For: Hamsanathan, et al., Aging Cell, 23(4):e14104, April 2024. Paper
ML; Environment		Shi, Jin, Han, Gopalakrishnan, Narasimhan CoDiCast: Conditional Diffusion Model for Global Weather Prediction with Uncertainty Quantification, IJCAI (AI For Social Good), 2025, Also arXiv: arXiv:2409.05975
ML; Environment		Shi, Zhou, Jin, Hu, Narasimhan, Wang, Han Hypercube Retrieval-Augmented Generation for Scientific Question-Answering, Poster presentation, IGUIDE FORUM 2025.
ML; Everglades Reseearch		Rangaraj, Shi, Shirali, Paudel, Wu, Narasimhan, How Effective are Large Time Series Models in Hydrology? A Study on Water Level Forecasting in Everglades, Poster presentation, IGUIDE FORUM 2025.
CS Education		Lunn, Arunachalam, Becerra, Weiss, Liu, Narasimhan, Dipping a Toe into Computing: Offering a Short-Term Program for Students Majoring in Other Fields ITiCSE 2025, Nijmegen, the Netherlands, 2025.
CS Education		Arunachalam, Lunn, Thapalia, Narasimhan, Liu, Weiss, Crafting Opportunities: Establishing a Micro-Internship Program for Computing Students SIGCSE 2025, Poster, 2025.
Survey; ML; Protein Structure	pdf	Shirali, Stebliankin, Karki, Shi, Chapagain, Narasimhan, A Comprehensive Survey of Scoring Functions for Protein Docking Models BMC Bioinformatics, 2025.
ML; Environmental Application	pdf	Shi,, Yin, Leon, Obeysekara, Narasimhan, FIDLAR: Forecast-Informed Deep Learning Architecture for Flood Mitigation Accepted at AAAI-AISI (AI for Social Impact), 2025. Also, arXiv:2402.13371.
Bioinformatics		Mehta, Stebliankin, Mathee, Narasimhan, MetaEdit: Computational Identification of RNA editing in Microbiomes Accepted at ICCABS'25, 2025.

2024

ML; Environmental Application	pdf	Shi, Shirali, Narasimhan, Boosting Time Series Prediction of Extreme Events by Reweighting and Fine-tuning Accepted at IEEE BigData'24, 2024. Also, arXiv:2409.14232.
Bioinformatics	Link	Ruiz-Perez, Gimon, Sazal, Mathee, Narasimhan, Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA mSystems, 9(10):e01303-23, 2024.
CS Education	Link	Arunachalam, Lunn, Weiss, Liu, Narasimhan, Foot in the Door: Developing Opportunities for Computing Undergraduates to Gain Industry Experience SIGCSE 2024 Proceedings of the 55th ACM Technical Symposium on Computer Science Education V. 1, March 2024, Pages 74–80.
Aging & Metabolomics	Link	Hamsanathan, Anthonymuthu, Prosser, Lokshin, Greenspan, Resnick, Perera, Okawa, Narasimhan, Gurkar A Molecular Index for Biological Age identified from the Metabolome and Senescence-associated Secretome in Humans Aging Cell, 23(4):e14104, April 2024. Also Research Square archive. Awarded the Anatomical Society Aging Cell Joint Runner Up Best Paper Prize 2024 by the Council of the Anatomical Society, 1st May 2025.

2023

Causality & Microbiomes	Link	Ruiz-Perez, Gimon, Sazal, Mathee, Narasimhan Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA bioRxiv, 2023. DOI 10.1101/2023.12.12.571384
XAI		Shi, Stebliankin, Narasimhan, The Power of Explainability in Forecast-Informed Deep Learning Models for Flood Mitigation Tackling Climate Change with ML, Poster Presentation, workshop at NeurIPS 2023.
COVID	Link	Clarke, Garba, Barbieri, Acuna, Baum, Rodriguez, Frias, Saldarriaga, Stefano, Mathee, Narasimhan, Brown Detection of SARS-CoV-2 in High-Efficiency Particulate Air (HEPA) Filters of Low-Cost Air Purifiers in Community-Based Organizations Environmental Monitoring and Assessment 195:1320, 2023.
CS Education Software	Link	Akkaya, Uluagac, Narasimhan, Bulman, Gerlach, Mulholland Cyber Expert Badge: Cryptic Cyphers, Daring Defense, Malware Mayhem Minecraft Education September 2023. Developed in collaboration with Minecraft/Microsoft.
ML; Protein Structure	Link	Stebliankin, Shirali, Baral, Shi, Chapagain, Mathee, Narasimhan, Evaluating Protein Binding Interfaces with Transformer Networks Nature Machine Intelligence, 5, 1042-1053, 2023.
CS Education		Barboza, Mello, Arunachalam, Lunn, Narasimhan,Teixeira, Enabling Data Science Education for Business Majors with Blockly-DS ICDE Conference To Appear, 2023.
Microbiome; Pipelines		Nayman, Schwartz, Polanco, Firek, Gumabong, Hofstee, Narasimhan, Cickovski, Mathee, Microbiome Depiction Through User-Adapted Bioinformatic Pipelines and Parameters. J Med Microbiol., 72(10), 2023.
ML; Bias		Wang, Narasimhan, Qiu, Yao, Zhang, Mitigating Multisource Biases in Graph Neural Networks via Real Counterfactual Samples Proc. ICDM 2023.
ML		Shi, Stebliankin, Z. Wang, S. Wang, Narasimhan, Graph Transformer Network for Flood Forecasting with Heterogeneous Covariates Proc. IGUIDE Forum 2023.
Microbiome		Cickovski, Mathee, Aguirre, Tatke, Hermaida, Narasimhan, Stolstorff, Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective PLoS ONE, Accepted for Publication, 2023.
ML; Time Series	Link	Shi, Myana, Stebliankin, Shirali, Narasimhan, Explainable Parallel RCNN with Novel Feature Representation for Time Series Forecasting Lecture Notes in Computer Science, Vol. 14343, Springer, 2023; Also arXiv;.
Drug Resistance	Link	Ambreetha, Parshatd, Castellanos, Narasimhan, Balachandar, Cickovski, Mathee *Genetic determinants of virulence and extensive drug resistance in Pseudomonas aeruginosa* PPA14 isolated from eggplant rhizosphere** bioRxiv.
Spanners; Experiments	Link	Shariful, Weathers, Ghosh, Narasimhan, Engineering an algorithm for constructing low-stretch geometric graphs with near-greedy average-degrees arXiv.
Visualization; Microbiomes	Link	Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles Frontiers in Bioinformatics; Also BioVis at ISMB 2022 and bioRxiv.
CS Education	Link	Arunachalam, Weiss, Liu, Perez, Narasimhan, Lunn, Software Guild: A Workshop to Introduce Women and Non-Binary Undergraduate Students from other Majors to Computing ASEE Conference To Appear, 2023.
Bioinformatics Software	Link	Balbin, Nunez-Castilla, Stebliankin, Baral, Sobhan, Cickovski, Mondal, Narasimhan, Chapagain, Mathee, and Siltberg-Liberles Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes Immunoinformatics 9, 100023, March 2023.
Diet and Microbiomes	Link	Bose, Stebliankin, Cickovski, Saha, Trivedi, Roy, More, Tuteja, Mathee, Narasimhan, Chatterjee Microbiome dysbiosis show strong association of gut-derived altered metabolomic profile in Gulf War Chronic Multisymptom Illness symptom persistence following Western Diet feeding and development of obesity, Intl. J of Molecular Sciences 24(4):4245, 2023. Special Issue "The Microbiota and Its Association with Cellular Transformation and Metabolic Changes".
HIV; Microbiomes	Link	Martin, Martinez, Stebliankin, Tamargo, Campa, Narasimhan, Hernandez, Rodriguez, Teeman, Johnson, Sherman, Baum Diet quality and liver health in people living with HIV in the MASH cohort: A multi-omic analysis of the fecal microbiome and metabolome, Metabolites, 13(2):271, 2023.
ML; Protein Structure	Link	Stebliankin, Shirali, Baral, Chapagain, Narasimhan, PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks Proceedings of RECOMB 2023, LNCS, Vol. 13976, p274-6, 2023.

2022

ML; Public Policy	Link	Cheng, Ganapati, Narasimhan, Yusuf A Machine Learning Based Analysis of 311 Requests in the Miami-Dade County Growth and Change: A Journal of Urban and Regional Policy, 2022, 53(4):1627-1645. DOI: 10.1111/grow.12578
ML; Public Health	Link	Bhoite, Garba, Sacca, Clarke, Narasimhan Predicting COVID-19 Vaccine Hesitancy Among US Adults Using Classification Machine Learning Algorithms and the Household Pulse Survey American Public Health Association (APHA) Conference, Poster, 2022.
Microbiomes	Link	Campos, Cickovski, Fernandez, Jaric, Wanner, Holt, Donna, Mendes, Silva-Herzog, Schneper, Segal, Amador, Riveros, Aguiar-Pulido, Banerjee, Salathe, Mathee Narasimhan, Lower respiratory tract microbiome composition and community interactions in smokers, Access Microbiology, Accepted for publication.
Microbiomes, Multi-omics		Stebliankin, Sazal, Valdes, Mathee, Narasimhan. A novel approach for combining metagenome, metaresistome, metareplicome, and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis, Microbial Genomics, 8(12):000899. Blog related to paper
Microbiomes, AIDS	Link	Martinez, Stebliankin, Hernandez, Martin, Tamargo, Rodriguez, Teeman, Johnson, Seminario, Campa, Narasimhan, Baum. Multi-omic analysis reveals microbiome-related relationships between cocaine use and metabolites, AIDS, 36(15):2089-99, 2022.
Microbiomes, AIDS	Link	Briceno, Caldera, Narasimhan, Gutierrez M, Martinez S, Stebliankin. Protocol for a Pilot Study on the Gut Microbiome and Cardiometabolic Risk Factors in Latinx Emerging Adults in Miami, Florida. Current Developments in Nutrition. 6:1132, 2022.
Microbiomes	Link	Saha, Bose, Stebliankin, Cickovski, Seth, Porter, Brooks, Mathee, Narasimhan, Colwell, Scott, Chatterjee Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models. Nature Scientific Reportsi, 12(1):1-19, 2022.
Mol Mimicry; COVID	Link	Nunez-Castilla, Stebliankin, Baral, Balbin, Sobhan, Cickovski, Mondal, Narasimhan, Chapagain, Mathee, Siltberg-Liberles Potential autoimmunity resulting from molecular mimicry between SARS-CoV-2 Spike and human proteins Viruses, 14(7):1415, 2022; Also bioRxiv, DOI: 10.1101/2021.08.10.455737, 2021. In the news.
Visualization; Microbiomes	Link	Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles Accepted at BioVis COSI at ISMB 2022; Also bioRxiv, DOI: 10.1101/2021.03.22.436520, 2021.
ML; Environment	Link	Shi, Jain, Narasimhan, Time Series Forecasting (TSF) Using Various Deep Learning Models Intl. J of Comp and Systems Engg. (Proceedings of ICMLA 2022). 16(6):224-232, 2022.
Mol Mimicry; COVID	Link	Stebliankin, Baral, Balbin, Nunez-Castilla, Sobhan, Cickovski, Mondal, Siltberg-Liberles, Chapagain, Mathee, Narasimhan, EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2 bioRxiv, DOI: 10.1101/2022.02.05.479274, 2022.
Editorial	Link	Cai, Narasimhan, Skums, Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications IEEE/ACM Trans Comput Biol and Bioinf, 19(1):207-208. 1 Jan-Feb. 2022. DOI: doi: 10.1109/TCBB.2021.3121736.

2021

ML; Cancer	Link	Al Mamun, Tanvir, Sobhan, Mathee, Narasimhan, Holt, Mondal, Multi-run Concrete Autoencoder to Identify Prognostic lncRNAs for 12 Cancers Intl. J of Mol Sciences (IJMS), 22(21):11919; DOI: 10.1109/TCBB.2021.3121736.
Mol Dynamics	Link	Baral, Bhattarai, Hossen, Stebliankin, Gerstman, Narasimhan, Chapagain, Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion Biochem. Biophys. Res. Commun., In Press, 2021; Also bioRxiv, DOI: 10.1101/2021.07.17.452576, 2021.
Public Health	Link	Madhivanan, Krupp, Coudray, Colbert, Ruiz-Perez, Cui, Bokulich, Narasimhan, Mathee, Cook, Schwebke, Roe, Longitudinal assessment of nonavalent vaccine HPV types in a sample of sexually active African American women from ten U.S. cities. Vaccine, 2021 (Accepted)
Mol Mimicry; COVID	Link	Nunez-Castilla, Stebliankin, Baral, Balbin, Sobhan, Cickovski, Mondal, Narasimhan, Chapagain, Mathee, Siltberg-Liberles Potential autoimmunity resulting from molecular mimicry between SARS-CoV-2 Spike and human proteins bioRxiv, DOI: 10.1101/2021.08.10.455737, 2021. In the news.
Causality; Public Policy	Link	Yusuf, Ganapati, Cheng, Narasimhan Causal Inference Methods and their Challenges: The Case of 311 Data Proceedings of DG.O (Digital Government Research) Conference (DG.O'21), 2021. DOI: 10.1145/3463677.3463717
Visualization; Microbiomes	Link	Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles bioRxiv, DOI: 10.1101/2021.03.22.436520, 2021.
Microbiomes	Link	Ruiz-Perez, Coudray, Colbert, Krupp, Kumari, Stebliankin, Mathee, Cook, Schwebke, Narasimhan, Madhivanan Effect of metronidazole on vaginal microbiota assoiated with asymptotic bacterial vaginosis Access Microbiology, 2021;3:000226. (* Equal Contribution) DOI 10.1099/acmi.0.000226
Causality; Microbiomes	Link	Sazal, Stebliankin, Mathee, Narasimhan, Causal Inference in Microbiomes Using Intervention Calculus Scientific Reports, 11:5724, 2021. DOI: 10.1038/s41598-021-84905-3
ML; Microbiomes	Link	Ruiz-Perez, Lugo-Martinez, Bourguignon, Mathee, Lerner, Bar-Joseph, Narasimhan, Dynamic Bayesian networks for integrating multi-omics time-series microbiome data. mSystems, Accepted for Publication, 2021. (* Equal Contribution)
ML; Systems	Link	Rodriguez, Yusuf, Lyons, Paz, Zhao, Liu, Rangaswami, Narasimhan (Equal contribution by first two authors), Learning Cache Replacement with CACHEUS FAST '21 HotCRP
Editorial	pdf	Mandoiu, Murali, Narasimhan, Rajasekaran, Skums, Zelikovsky, Preface for Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019) J Comput Biol, 28(2):115--116, 2021. DOI: 10.1089/cmb.2021.29034.im

2020

pdf	Yusuf, Valdes, Stebliankin, Vietri, Narasimhan EXP4-DFDC: A Non-Stochastic Multi-Armed Bandit for Cache Replacement arXiv arXiv:2009.11330.
Link	Ruiz-Perez, Lugo-Martinez, Bar-Joseph, Narasimhan, Application of Bayesian Techniques to Multi-omic Longitudinal Data LatinX in AI Workshop at ICML 2020.
Link	Martin, Martinez, Stebliankin, Tamargo, Campa, Narasimhan, Baum. Dietary Components and Metabolites Are Associated with Liver Fibrosis in People Living with HIV (PLWH) in the MASH cohort. Current Developments in Nutrition, Volume 4, Issue Supplement_2, 2020.
Book	Editors: I. Mandoiu, T. M. Murali, G. Narasimhan, S. Rajasekaran, P. Skums, A. Zelikovsky. Computational Advances in Bio and Medical Sciences. Springer Verlag. Lecture Notes in Bioinformatics Series, Vol. 12029, 2020. [978-3-030-46164-5 & 978-3-030-46165-2], 2020.
Patent	Narasimhan, Vietri, Aleman Martinez, Systems and methods for managing cache replacement with machine learning US Patent 10,558,583, 2020.
	Sazal, Stebliankin, Mathee, Narasimhan, Causal Inference in Microbiomes Using Intervention Calculus BioRxiv, 2020.
	Cickovski, Manuel, Mathee, Campos Narasimhan, Effects of Various Alpha-1 Antitrypsin Supplement Dosages on the Lung Microbiome and Metabolome To appear in Computational Advances in Bio and Medical Sciences, Chapter 8, Springer Nature Publishers, 2020.
Full Text	Sazal, Mathee, Ruiz-Perez, Cickovski, Narasimhan, Inferring directional relationships in microbial communities using signed Bayesian networks BMC Genomics, 21(Suppl 6):663, 2020.
Full Text	Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan, So you think you can PLS-DA? BMC Bioinformatics, 21 (Suppl 1):2, 2020.
pdf	Mathee, Cickovski, Deoraj, Stolstorff, Narasimhan, The gut microbiome and neuropsychiatric disorders: Implications for attention deficit hyperactivity disorder (ADHD) J Medical Microb., 69(1):14--24, 2020.
Link	Mason et al., Multiple Myeloma DREAM Consortium, Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease Leukemia. 2020. doi:10.1038/s41375-020-0742-z
Link	Madhivanan, Bokulich, Coudray, Colbert, Ruiz-Perez, Krupp, Mathee, Narasimhan, Caporaso, Composition of the Vaginal Microbiome Associated with High Risk HPV Infection and Increased Risk for Cervical Cancer, Abstract, Cancer Epidemiology, Biomarkers and Prevention, 29(3):696, 2020.

2019

	Ruiz-Perez, Lugo-Martinez, Bourguignon, Mathee, Lerner, Bar-Joseph, Narasimhan, Dynamic Bayesian networks for integrating multi-omics time-series microbiome data. BioRxiv, 835124, 2019.
	Ruiz-Perez, Sazal, Park, Cickovski, Lee, Cho, Hwang, Narasimhan, Role of gut microbiota and their temporal interactions in kidney transplant recipients LatinX in AI Workshop at NeurIPS 2019.
	Sazal, Ruiz-Perez, Valdes, Cickovski, Stebliankin, Mehta, Mathee, Narasimhan, Signed Bayesian Networks for Microbiomes LatinX in AI Workshop at NeurIPS 2019.
	Yusuf, Valdes, Stebliankin, Vietri, Narasimhan EXP4-DFDC: A Non-Stochastic Multi-Armed Bandit for Cache Replacement LatinX in AI Workshop at NeurIPS 2019.
Link	Martinez, Campa, Narasimhan, Portuando, Seminario, Jasmin, Baum. Pilot Study on the Effect of Cocaine Use on the Intestinal Microbiome and Metabolome and Inflammation in HIV-Infected Adults in the Miami Adult Studies in HIV (MASH) Cohort (P13-027-19). Current Developments in Nutrition, Volume 3, Issue Supplement_1, June 2019.
Link	Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee, Madhivanan Effect of metronidazole on microbiomes associated with asymptomatic bacterial vaginosis, in Meeting Report Access Microbiology , 1(1A), 2019
Link	Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee, Co-occurrence of bacterial vaginosis and Trichomonas vaginalis among young african american women, Abstract at Sexually Trasmitted Infections, 2019.
Link	Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Mathee, Narasimhan, Bacterial vaginosis and high-risk human papillomavirus coinfection among african american women in the united states, Abstract at Sexually Trasmitted Infections, 2019.
Link	Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee, Madhivanan Effect of metronidazole treatment on recurrent and persistent bacterial vaginosis: a pilot study, Abstract at Sexually Trasmitted Infections, 2019.
Link	Stebliankin, Valdes, Mathee, Narasimhan, Adapting Flint for Calculating Bacterial Replication Rates in Microbiomes, Poster at ISMB 2019. F1000Research 2019, 8(ISCB Comm J):1476 (poster) [doi: 10.7490/f1000research.1117382.1].
Link	Valdes, Stebliankin, Narasimhan, Large Scale Microbiome Profiling in the Cloud Bioinformatics, 35(14):i13-i22, 2019; Presented at ISMB, July 2019.
Link	Buendia, El-Gazzar, Delzoppo, Narasimhan, Three Public Health Use Cases the Blockchain Can Solve Chapter 19, pages 267-295, in Blockchain in Healthcare: Innovations that Empower Patients, Connect Professionals and Improve Care (HIMSS Book Series), Editors: Metcalf, Bass, Hooper, Cahana, Chillon, CRC Press, 2019. ISBN-13: 978-0367031084.
Springer Nature BioRXiv	Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph, Dynamic interaction network inference from longitudinal microbiome data BMC Microbiome, 7:54, 2019. Impact Factor (2018-19): 10.4 Highlights talk at GLBIO 2019; Poster at RECOMB 2019; Oral presentation at SMBE 2019;
Link	Cickovski, Aguiar-Pulido, Narasimhan, MATria, a unified centrality algorithm, BMC Bioinformatics, 20(Suppl 11):278, 2019.

2018

BioRXiv	Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph, Dynamic interaction network inference from longitudinal microbiome data BioRXiv: 10.1101/43062.
Link	Sazal, Ruiz-Perez, Cickovski, Narasimhan, Inferring Relationships in Microbiomes from Signed Bayesian Networks Proceedings of ICCABS Conference, 2018.
Link	Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan, So you think you can PLS-DA? Proceedings of ICCABS Conference, 2018.
Link	Vietri, Rodriguez, Martinez, Lyons, Liu, Rangaswami, Zhao, Narasimhan, Driving Cache Replacement with ML-based LeCaR Proceedings of HotStorage, 2018.
Link	Cickovski, Narasimhan, Constructing lightweight and flexible pipelines using plugin-based microbiome analysis (PluMA), Bioinformatics, 34(17):2881-2888, 2018.
Link Noteworthy	Damaso, Mendel, Mendoza, von Wettberg, Narasimhan, Mills Bioinformatics approach to assess the biogeographic patterns of soil communities: the utility for soil provenance, J Forensic Science, 63(4):1033-42, doi: 10.1111/1556-4029.13741, 2018. Among Noteworthy Articles from 2018 in JFS.
biorXiv	Ruiz-Perez, Narasimhan, So you think you can PLS-DA? bioRxiv doi: 10.1101/123456, 2018.

2017

	Suarez-Ulloa, Aguiar-Pulido, Narasimhan, Eirin-Lopez. Framing epigenetic signatures of the Pacific oyster under environmental stress using network analysis. Biochemistry and Cell Biology, 95(2):184, 2017.
	Cickovski, Aguiar-Pulido, Narasimhan, MATria, a unified centrality algorithm, ICCABS Conference, Accepted, 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, 18(Suppl 8): 239, 2017. doi: 10.1186/s12859-017-1659-z.
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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