Survey; ML;
Protein
Structure
|
|
Shirali, Stebliankin, Karki, Shi, Chapagain, Narasimhan,
A Comprehensive Survey of Scoring Functions for Protein Docking Models
BMC Bioinformatics, In Press, 2024.
|
|
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, 2024. Also
Research Square archive.
|
|
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.
|
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
|
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.
|
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
|
pdf
|
Yusuf, Valdes, Stebliankin, Vietri, Narasimhan
EXP4-DFDC: A Non-Stochastic Multi-Armed Bandit for Cache Replacement
arXiv arXiv:2009.11330.
|
|
Link
|
Hamsanathan, Anthonymuthu, Prosser, Lokshin, Greenspan, Resnick, Perera, Narasimhan, Gurkar,
A Molecular Index for Biological Age identified from the Metabolome and Senescence-associated Secretome in Humans
Research Square 2020.
|
|
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
|
|
|
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
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Cickovski, Aguiar-Pulido, Narasimhan,
MATria, a unified centrality algorithm,
BMC Bioinformatics, 20(Suppl 11):278, 2019.
|
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.
|
|
|
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.
|
|
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
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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.
|
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|
Li, Jean-Baptiste, Riveros,
Narasimhan, Zhang, Zhao,
CacheDedup: In-line cache deduplication for Flash Caching,
Proceedings of FAST, 301-314, 2016.
|
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|
Cickovski, Aguiar-Pulido, Huang, Mahmud, Narasimhan,
Lightweight Microbiome Analysis Pipeline,
Proceedings of IWBBIO, pp 225--227, 2016.
|
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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.
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|
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.
|
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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.
|
|
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.
|
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|
Fernandez, Riveros, Campos, Mathee,
Narasimhan,
Microbial "Social" Networks,
BMC Genomics, 16(Suppl 11):S6 (Special Issue), 2015.
|
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link
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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.
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link
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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.
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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.
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link
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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.
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Link
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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.
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arXiv
|
Shao, Consuegra, Rangaswami,
Narasimhan,
Analyzing adaptive cache replacement strategies,
Submitted, 2014.
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link
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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.
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link
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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.
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Narasimhan,
Metagenomics and NGS,
Keynote Speaker,
ICCABS and CANGS,
June 2014.
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Link
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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
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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.
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Fernandez, Jaric, Narasimhan
Mining Biomedical Datasets,
Proceedings of STATISTICS-2013, Invited,
2013
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Consuegra, Narasimhan
Geometric Avatar Problems,
Proceedings of FSTTCS, 389--400, Leibniz International Proceedings in Informatics Series, Vol 24, 2013.
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Link
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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.
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TR
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Consuegra, Narasimhan, Rangaswami
Vector repacking algorithms for power-aware computing,
Proceedings of Energy-efficient Networks of Computers (E2NC) Workshop, IGCC,
1--8, IEEE, 2013.
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Link
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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
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Link
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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.
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Link
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Jaric, Segal, Silva-Herzog, Schneper, Mathee, Narasimhan,
Designing primers with higher taxonomic distinguishability,
29th Southern Biomedical Engineering Conference,
2013.
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Link
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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.
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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.
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TR
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Consuegra, Narasimhan, Rodriguez, Tanigawa
Avatar Problems,
Submitted,
2012.
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Link
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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
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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.
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Narasimhan
Invited: Comparative Microbial Genomics,
Proceedings of the IEEE 1st International Conference on Computational Advances
in Bio and Medical Sciences (ICCABS),
p8, 2011.
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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.
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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.
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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.
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Link
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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.
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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.
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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.
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Link
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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.
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Link
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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.
|
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Link
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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.
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A. Elshahat, A. Parhizgari, G. Narasimhan, S. Anwar
Portfolio Optimization Using Greedy Algorithm,
Proceedings of Annual Meeting of the Multinational Finance Society, Crete,
2009.
|
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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.
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Link
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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.
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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.
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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.
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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),
p73-84, Stanford, CA, August, 2008.
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Link
|
J. Gudmundsson, G. Narasimhan, M. Smid
Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p360-64, 2008.
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Link
|
J. Gudmundsson, G. Narasimhan, M. Smid
Plane Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p653-656, 2008.
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Link
|
J. Gudmundsson, G. Narasimhan, M. Smid
Applications of Geometric Spanners,
Encyclopedia of Algorithms, Ed. Ming Kao, p40-43, 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
|
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
|
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.
|
|
G. Narasimhan, M. Smid
Geometric Spanner Networks,
Cambridge University Press, 560p, 2007.
|
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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.
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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
|
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
|
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.
|
|
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.
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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.
|
|
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.
|
|
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].
|
|
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.
|
|
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.
|
|
[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.
|
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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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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]
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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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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.
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[Poster ps Version]
[Abstract ps Version]
[Software: GYM]
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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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