Mehta, Stebliankin, Mathee, Narasimhan, (2025) MetaEdit: Computational Identification of RNA editing in Microbiomes Accepted at ICCABS'25.
Shirali, Stebliankin, Karki, Shi, Chapagain, Narasimhan, (2024) A Comprehensive Survey of Scoring Functions for Protein Docking Models, BMC Bioinformatics, In Press.
Ruiz-Perez, Gimon, Sazal, Mathee, Narasimhan, (2024) Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA. mSystems , 9(10):e01303-23. Link
Tanvir, Islam, Sobhan, Luo, Mondal, (2024) MOGAT: An Improved Multi-Omics Integration Framework Using Graph Attention Networks. Int. J. Mol. Sci. , 25(5):2788.
Nayman, Schwartz, Polmann, Gumabong, Nieuwdorp, Cickovski, Mathee, (2024). Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus. Nature Scientific Reports, Accepted for Publication, 2024.
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.
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
Nayman, Schwartz, Polanco, Firek, Gumabong, Hofstee, Narasimhan, Cickovski, Mathee, (2023). Microbiome Depiction Through User-Adapted Bioinformatic Pipelines and Parameters. J Med Microbiol., Accepted for Publication, 2023. Read blog.
Clarke, Garba, Barbieri, Acuna, Baum, Rodriguez, Frias, Saldarriaga, Stefano, Mathee, Narasimhan, Brown, (2023). 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, Accepted for publication.
Stebliankin, Shirali, Baral, Shi, Chapagain, Mathee, Narasimhan, (2023). Evaluating Protein Binding Interfaces with Transformer Networks Nature Machine Intelligence, 2023.
Cickovski, Mathee, Aguirre, Tatke, Hermaida, Narasimhan, Stolstorff, (2023). Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective PLoS ONE., Accepted for Publication, 2023.
Nayman, Schwartz, Polmann, Gumabong, Nieuwdorp, Cickovski, Cickovski, Mathee, (2023). Disrupted Ecology and H. parainfluenzae Distinguish the Gut Microbiota of an Ethnic Minority Predisposed to Type 2 Diabetes Mellitus. bioRxiv., https://doi.org/10.1101/2023.10.01.560393
Tanvir, Ruiz, Ebert, Sobhan, Al Mamun, Mondal, (2023). Quantifying Intratumor Heterogeneity by Key Genes Selected Using Concrete Autoencoder. International Conference on Pattern Recognition and Machine Intelligence, p844-52.
Tanvir, Islam, Sobhan, Luo, Mondal, (2023) MOGAT: An Improved Multi-Omics Integration Framework Using Graph Attention Networks. bioRxivi, 2023.04.01.535195
Shi, Myana, Stebliankin, Shirali, Narasimhan, (2023). Explainable Parallel RCNN with Novel Feature Representation for Time Series Forecasting. Proc. AALTD 2023; and arXiv.
Ambreetha, Parshatd, Castellanos, Narasimhan, Balachandar, Cickovski, Mathee, (2023) Genetic determinants of virulence and extensive drug resistance in Pseudomonas aeruginosa PPA14 isolated from eggplant rhizosphere. bioRxiv
Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, (2023). Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles. Frontiers in Bioinformatics; Vol. 3, 19 June 2023; Also BioVis at ISMB 2022 and bioRxiv.
Balbin, Nunez-Castilla, Stebliankin, Baral, Sobhan, Cickovski, Mondal, Narasimhan, Chapagain, Mathee, and Siltberg-Liberles. (2023) Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes. Immunoinformatics , 9, 100023, March 2023.
Bose, Cickovski, Saha, Trivedi, Stebliankin, Roy, Mathee, Narasimhan, Tuteja, Chatterjee, (2023) 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, Special Issue "The Microbiota and Its Association with Cellular Transformation and Metabolic Changes", 24(4):4245.
Martin, Martinez, Stebliankin, Tamargo, Campa, Narasimhan, Hernandez, Rodriguez, Teeman, Johnson, Sherman, Baum, (2023) 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.
Stebliankin, Shirali, Baral, Chapagain, Narasimhan, (2023). PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks. Proceedings of RECOMB 2023, LNCS, Vol. 13976, p274-6.
Gumabong, Nayman, Cickovski, Narasimhan, Mathee, (2023) Quality Control In 16S-Based Microbiota Compositional Analysis. NCUR 2023 Abstract Accepted.
Nayman, Polanco, Hofstee, Schreiner, Firek, Cickovski, Narasimhan, Mathee, (2022). Microbial Compositions Derived from 16S rRNA Sequencing Reads – Arriving at More Medically Meaningful Results. ASM Microbe, Poster.
Nayman, Schwartz, Firek, Polanco, Gumabong, Cickovski, Narasimhan, Mathee, (2022). Bias in 16S-Based Microbiota Compositions: Improving Inference. Targeting Microbiota, October 2022, Paris, Abstract and Oral Presentation.
Campos, Cickovski, Fernandez, Jaric, Wanner, Holt, Donna, Mendes, Silva-Herzog, Schneper, Segal, Amador, Riveros, Aguiar-Pulido, Banerjee, Salathe, Mathee Narasimhan, (2022). Lower respiratory tract microbiome composition and community interactions in smokers, Access Microbiology, Accepted for publication.
Bhoite, Garba, Sacca, Clarke, Narasimhan, (2022). Predicting COVID-19 Vaccine Hesitancy Among US Adults Using Classification Machine Learning Algorithms and the Household Pulse Survey, American Public Health Association (APHA) Conference 2022, Poster accepted.
Stebliankin, Sazal, Valdes, Mathee, Narasimhan, (2022). 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.
Martinez, Stebliankin, Hernandez, Martin, Tamargo, Rodriguez, Teeman, Johnson, Seminario, Campa, Narasimhan, Baum (2022). Multi-omic analysis reveals microbiome-related relationships between cocaine use and metabolites., AIDS, 36(15):2089-99.
Saha, Bose, Stebliankin, Cickovski, Seth, Porter, Brooks, Mathee, Narasimhan, Colwell, Scott, Chatterjee, (2022) Prior exposure to microcystin alters host gut resistome and is associated with dysregulated immune homeostasis in translatable mouse models. Nature Scientific Reports, 12(1):1-19.
Nunez-Castilla, Stebliankin, Baral, Balbin, Sobhan, Cickovski, Mondal, Narasimhan, Chapagain, Mathee, Siltberg-Liberles, (2022) 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.
Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, (2022).
BioVis COSI at ISMB 2022;
Stebliankin, Baral, Balbin, Nunez-Castilla, Sobhan, Cickovski, Mondal,
Siltberg-Liberles, Chapagain, Mathee, Narasimhan, (2022).
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.
Cai, Narasimhan, Skums (2021)
Guest Editors’ Introduction to the
Special Section on Bioinformatics Research and Applications
IEEE Trans Comput Biol and Bioinf, 19(1):207-208.
1 Jan-Feb. 2022. DOI: doi: 10.1109/TCBB.2021.3121736.
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.
Baral, Bhattarai, Hossen, Stebliankin, Gerstman, Narasimhan, Chapagain, (2021).
Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2
and Implications for Immune Evasion
Madhivanan, Krupp, Coudray, Colbert, Ruiz-Perez, Cui, Bokulich, Narasimhan, Mathee, Cook, Schwebke, (2021)
Longitudinal assessment of nonavalent vaccine HPV types in a sample of sexually active African American women
from ten U.S. cities,
Vaccine, 2021 (Accepted)
Inglis, Mathee, (2021).
JMM Profile: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
J Med Microbiol, 70(3). DOI 10.1099/jmm.0.001336.
Valdes, Stebliankin, Ruiz-Perez, Park, Lee, Narasimhan, (2021).
Microbiome Maps: Hilbert Curve Visualizations of Metagenomic Profiles,
bioRxiv, DOI: 10.1101/2021.03.22.436520.
Ruiz-Perez*, Coudray*, Colbert, Krupp, Kumari, Stebliankin, Mathee, Cook, Schwebke, Narasimhan, Madhivanan (2021)
Effect of metronidazole on vaginal microbiota associated with asymptotic bacterial vaginosis,
Access Microbiology, 2021;3:000226. (* Equal Contribution)
Sazal, Stebliankin, Mathee, Narasimhan. (2021).
Causal Inference in Microbiomes Using Intervention Calculus.
Scientific Reports, 11:5724.
DOI: 10.1038/s41598-021-84905-3
Mandoiu, Murali, Narasimhan, Rajasekaran, Skums, Zelikovsky (2021)
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
Ruiz-Perez*, Lugo-Martinez*, Bourguignon, Mathee,
Bar-Joseph, Narasimhan (2021),
Dynamic Bayesian networks for integrating multi-omics time-series microbiome data.,
mSystems, Accepted for Publication. (* Equal Contribution)
Camilo Valdes,
Scalable Profiling and Visualization for Characterizing Microbiomes,
PhD Dissertation, FIU, 2020.
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.
Ruiz-Perez, Lugo-Martinez, Bar-Joseph, Narasimhan,
Application of Bayesian techniques to multi-omics longitudinal data.,
LXAI @ ICML, 2020.
Narasimhan, Vietri, Aleman Martinez.
Systems and methods for managing cache replacement with machine learning, US Patent 10,558,583, 2020.
Mukund, Mathee,, Subramaniam. (2020).
Plasmin Cascade Mediates Thrombotic Events in SARS-CoV-2 Infection
via Complement and Platelet-Activating Systems.
IEEE Open Journal of Engineering in Medicine and Biology. 2020 Aug 6;1:220-7.
Tanvir,, Mondal. (2020).
Stage-Specific Co-expression Network Analysis for Cancer Biomarker Discovery, IWBNA @ IEEE BIBM.
Sobhan, Mamun, Tanvir,, Alfonso, Valle, Mondal. (2020).
Deep Learning to Discover Genomic Signatures for Racial Disparity in Lung Cancer, Poster @ IEEE BIBM.
Mamun, Duan, Mondal. (2020).
Pan-cancer Feature Selection and Classification Reveals Important Long Non-coding RNAs. DLB2H @ IEEE BIBM.
Mamun, Sobhan, Tanvir,, Dimitroff, Mondal. (2020).
Deep Learning to Discover Cancer Glycome Genes Signifying the Origins of Cancer, DLB2H @ IEEE BIBM.
Sazal, Stebliankin, Mathee, Narasimhan. (2020).
Causal Inference in Microbiomes Using Intervention Calculus. BioRxiv.
Martin, Martinez, Stebliankin, Tamargo, Campa, Narasimhan, Baum (2020).
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.
Cickovski, Manuel, Mathee, Campos Narasimhan. (2020),
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.
Sazal, Mathee, Ruiz-Perez, Cickovski, Narasimhan.
Inferring directional relationships in microbial communities using signed Bayesian networks
BMC Genomics, 21(Suppl 6):663, 2020.
Maharjan, Tanvir,, Chowdhury, Duan, Mondal.
Computational Identification of Biomarker Genes for Lung Cancer Considering Treatment and Non-Treatment Studies, BMC Bioinformatics, 21 (Suppl 9):218, 2020.
Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan.
So you think you can PLS-DA?, BMC Bioinformatics, 21 (Suppl 1):2, 2020.
Mathee, Cickovski, Deoraj, Stolstorff, Narasimhan, (2020),
The gut microbiome and neuropsychiatric disorders: Implications for attention deficit hyperactivity disorder (ADHD)
J Medical Microb, 69(1):14--24.
Mason, ..., Multiple Myeloma DREAM Consortium, et al. (2020),
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,
Bhansali, Bar-Joseph, Narasimhan (2019),
Dynamic Bayesian networks for integrating multi-omics time-series microbiome data.,
BioRxiv 835124, 2019.
Ruiz-Perez, Park, Cickovski, Kim, 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.
LatinX in AI Workshop at ICML 2020.
Martinez, Campa, Narasimhan, Portuando, Seminario, Jasmin, Baum (2019).
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.
Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee (2019)
Co-occurrence of bacterial vaginosis and Trichomonas vaginalis among young african american women,
Abstract at Sexually Trasmitted Infections, 2019.
Madhivanan, Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Mathee, Narasimhan (2019)
Bacterial vaginosis and high-risk human papillomavirus coinfection among african american
women in the United States,
Abstract at Sexually Trasmitted Infections, 2019.
Coudray, Ruiz-Perez, Colbert, Krupp, Kumari, Narasimhan, Mathee, Madhivanan (2019)
Effect of metronidazole treatment on recurrent and persistent bacterial vaginosis: a pilot study,
Abstract at Sexually Trasmitted Infections, 2019.
Stebliankin, Valdes, Mathee, Narasimhan (2019)
Adapting Flint for Calculating Bacterial Replication Rates in Microbiomes, Poster in ISMB 2019.
F1000Research 2019, 8(ISCB Comm J):1476 (poster)
[doi: 10.7490/f1000research.1117382.1
Valdes, Stebliankin, Narasimhan (2019)
Large Scale Microbiome Profiling in the Cloud, ISMB 2019. Bioinformatics, 35(14):i13-i22.
Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph (2019).
Dynamic interaction network inference from longitudinal microbiome data,
BMC Microbiome, 7:54, doi: 0.1186/s40168-019-0660-3. Impact Factor (2018-19): 10.4
Cickovski, Aguiar-Pulido, Narasimhan (2019), MATria, a unified centrality algorithm,
BMC Bioinformatics, 20(Suppl 11):278. Buendia, El-Gazzar, Delzoppo, Narasimhan (2019),
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.
Lugo-Martinez, Ruiz-Perez, Narasimhan, Bar-Joseph (2018).
Dynamic interaction network inference from longitudinal microbiome data, biorXiv Publication.
Sazal, Ruiz-Perez, Cickovski, Narasimhan (2018).
Inferring Relationships in Microbiomes from Signed Bayesian Networks, ICCABS Conference, Accepted for Publication.
Ruiz-Perez, Guan, Madhivanan, Mathee, Narasimhan (2018).
So you think you can PLS-DA?, ICCABS Conference, Accepted for Publication.
Cickovski, T.C., Narasimhan, G. (2018).
Constructing lightweight and flexible pipelines using plugin-based microbiome analysis (PluMA),
Bioinformatics, 34(17):2881-2888
Perez, D., Narasimhan, G. (2018).
So you think you can PLS-DA?,
bioRxiv doi: 10.1101/207225
Damaso, Mendel, Mendoza, von Wettberg, Narasimhan, Mills (2018).
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
Cickovski, Aguiar-Pulido, V., Narasimhan, G. (2017).
MATria: A Unified Centrality Algorithm,
ICCABS Conference, Accepted.
Cickovski, T., Peake, E., Aguiar-Pulido, V., Narasimhan, G. (2017).
ATria: A Novel Centrality Algorithm Applied To Biological Networks,
BMC Bioinformatics, 18(Suppl 8): 239.
doi: 10.1186/s12859-017-1659-z. Mesa, Fernandez, Wu, Narasimhan, Greidinger, Mills. (2017).
Can SLE classification rules be effectively applied to diagnose unclear SLE cases?
Lupus, 26(2):150-162, 2017.
Narasimhan, M., Vietri, Mehta, Rajabli, Aguiar-Pulido, Mathee, Narasimhan. (2016).
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.
Huang, Kazmierczak, Zhou, Aguiar-Pulido, Narasimhan,
Szczesna-Cordary. (2016).
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. Aguiar-Pulido, V., Suarez-Ulloa, V., Huang, W., Cickovski, T., Mathee, K., Narasimhan, G. (2016).
Metagenomics, Metatranscriptomics and Metabolomics Approaches for Microbiome Analysis,
Evolutionary Bioinformatics, 12(S1):5--16, 2016. Cickovski, T., Aguiar-Pulido, V., Huang, W., Mahmud, S., Narasimhan, G. (2016).
Lightweight Microbiome Analysis Pipelines, Proceedings of IWBBIO, pp 225--227.
Aguiar-Pulido, V., Suarez-Ulloa, V., Eirin-Lopez, J.M., Narasimhan, G. (2016).
Network-inspired Approaches for Transcriptomic Analyses, Proceedings of IWBBIO, pp 437--440.
Cickovski, T., Peake, E., Aguiar-Pulido, V., Narasimhan, G. (2015).
ATria: A Novel Centrality Algorithm Applied To Biological Networks,
Accepted for Publication, Proceedings of ICCABS Narasimhan, G. (2015). Next Generation Microbiome Analysis,
Invited Speaker, ICCABS Fernandez, M., Riveros, J.D., Campos, M., Mathee, K., Narasimhan, G. (2015).
Microbial "Social" Networks, BMC Genomics, 16(Suppl 11):S6 (Special Issue) Mittal, R., Lisi, C.V., Gerring, R., Mittal, J., Mathee, K., Narasimhan, G., Azad R. K., Yao, Q., Grati,
M., Yan D., Eshraghi, A.A., Angeli, S. I., Telischi, F.F., Liu, X-Z. (2015).
Current concepts in the pathogenesis and treatment of chronic suppurative otitis media,
Journal of Medical Microbiology, 64: 1103-1116 Cickovski, T., Flor, T., Irving-Sachs, G., Novikov, P., Parda, J., Narasimhan, G. (2015).
GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing
Degenerate Primers on Graphics Processing Units,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2):445-454 Fernandez, M., Aguiar-Pulido, V., Riveros, J., Huang, W., Segal, J., Zeng, E.,
Campos, M., Mathee, K., Narasimhan, G. (2015).
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, pp. 333-351 Aguiar-Pulido, V., Suarez-Ulloa, V., Eirin-Lopez, J.M., Pereira, J., Narasimhan, G. (2015).
Computational Methods in Epigenetics, In
Personalized Epigenetics, Editor: T. Tollefsbol, Elsevier Academic Press, Chapter 6,
pp. 153-180, ISBN: 978-0-12-420135-4 Campos, M., Fernandez, M., Wanner, A., Holt, G.E., Donna, E., Mendes, E.S.,
Fishman, J., Infante, J., Jaric, M., Silva-Herzog, E., Schneper, L., Segal, J., Moraga, D.,
Mathee, K., Salathe, M.A., Narasimhan, G. (2014).
Microbial Associations in the Lungs Differ by Smoking and COPD Status, Abstract in
American Thoracic Society International Conference Caille, O., Zincke, D., Merighi, M., Balasubramanian, D., Kumari, H., Kong, K.F., Silva-Herzog, E.,
Narasimhan, G., Schneper, L., Lory, S., Mathee, K. (2014).
Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR,
Journal of Bacteriology, 196(22):3890-3902 Narasimhan, G. (2014). Metagenomics and NGS, Keynote Speaker, ICCABS and CANGS Balasubramanian, D., Kumari, H., Jaric, M., Fernandez, M., Turner, T.H., Dove, S.L., Narasimhan, G.,
Lory, S., Mathee, K. (2014).
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 Balasubramanian, D., Murugapiran S.K., Silva-herzog, E., Schneper, L., Yang, X., Tatke, G.,
Narasimhan, G., and Mathee, K. (2013). Transcription regulatory network in
Pseudomonas aeruginosa,In Bacterial Gene Regulation and Transcriptional Networks,
Chapter 13, pp. 199-221, Editor: Madan Babu, Caiser Academic Press Fernandez, M., Jaric, M.,Narasimhan, G. (2013). Mining Biomedical Datasets,
Proceedings of STATISTICS-2013, Invited Jaric, M., Segal, J., Silva-Herzog, E., Schneper, L., Mathee, K., Narasimhan, G. (2013).
Better primer design for metagenomic applications by increasing taxonomic distinguishability,
BMC Proceedings, 7(Suppl 7):S4 Fernandez, M., Jaric, M., Schneper, L., Segal, J., Silva-Herzog, E., Campos, M., Fishman, J.,
Salathe, M., Wanner, A., Infante, J., Mathee, K., Narasimhan, G. (2013).
A Metagenomic Approach to the Airways Microbiome of Chronic Obstructive Pulmonary Disease (COPD),
29th Southern Biomedical Engineering Conference Jaric, M., Segal, J., Silva-Herzog, E., Schneper, L., Mathee, K., Narasimhan, G. (2013).
Designing primers with higher taxonomic distinguishability,
29th Southern Biomedical Engineering Conference Cattoir, V., Narasimhan, G., Skurnik, D., Aschard, H., Roux, D., Ramphal, R., Jyot, J. and Lory, S. (2013).
Transcriptional response of mucoid Pseudomonas aeruginosa to human respiratory mucus,
mBio, 3(6):e00410-12 Zeng, E., Ding, C., Mathee, K., Schneper, L., Narasimhan, G. (2012).
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, pp. 123-162, ISBN 978-3-642-23150-6 Balasubramanian, D., Schneper, L., Merighi, M., Smith, R., Narasimhan, G.,
Lory, S., and Mathee, K. (2012).
The regulatory repertiore of Pseudomonas aeruginosa AmpC beta-lactamase
regulator AmpR includes virulence genes,
PLoS One, 7(3):e34067 Yang, X., Medvin, D., Yoder-Himes, D., Lory, S., Narasimhan, G. (2011).
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),
pp. 202-207 Narasimhan, G. (2011). Invited:
Comparative Microbial Genomics,
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS),
p8 Weeks, O.L., Villamor, E., Tracey, P., Stoddard, S., Makemson, J., Garcia, R., Gavassa, S.,
Philippi, T., Pitzer, T., Dewsbury, B., Narasimhan, G., McGoron, A., Tashakkori, A. (2011).
QBIC, an interdisciplinary and quantitative biological sciences curriculum: concept to implementation,
Journal of Science Education 12(1):11-14 Mandoiu, I., Narasimhan, G., Pan Y., Zhang Y. (2010). Guest Editors,
Introduction to the Special Section on Bioinformatics Research and Applications,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(4):1-2 Doud, M.S., Light, M., Gonzalez, G., Narasimhan, G., and Mathee, K. (2010).
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 Kocak, M., Zheng, G., Narasimhan, G.,George, E.O., and Pyne, S. (2010).
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 Zeng E., Yang C., Li T., and Narasimhan G. (2010).
Clustering Genes using Heterogeneous Data Sources,
International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 1(2):12-28 Zhang, Y., Zeng, E., Li, T., and Narasimhan, G. (2009).
Weighted Consensus Clustering for Identifying Functional Modules In Protein-Protein Interaction Network,
International Conference on Machine Learning and Applications (ICMLA) Buendia, P. and Narasimhan G. (2009).
Serial Evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains,
BMC Systems Biology, 3:62 Mandoiu, T., Narasimhan, G., Zhang, Y. (2009). Editors in
Bioinformatics Research and Applications, Conference Proceedings of ISBRA,
Lecture Notes in Bioinformatics, Vol. 5542, Springer Verlag Doud, M., Zeng, E., Schneper, L., Narasimhan, G., Mathee, K. (2009).
Approaches to Analyze Dynamic Microbial Communities such as those seen in Cystic Fibrosis Lung,
Human Genomics, 3(3):246-256 Zeng, E., Mathee, K., Schneper, L., Narasimhan G. (2008). A functional network of yeast genes using gene ontology information, IEEE Conference on Bioinformatics and Biomedicine (BIBM2008), pp. 343-346, Philadelphia, PA Zheng, G. and Narasimhan, G. (2008). A Branch-and-bound approach to knowledge-based protein structure assembly, IEEE Conference on Bioinformatics and Bioengineering (BIBE2008), pp. 1-5 J. Entry, D. Mills, K. Mathee, K. Jayachandran, R. E. Sojka, G. Narasimhan (2008). Influence of irrigated agriculture on soil microbial diversity, Applied Soil Ecology, 40(1):146-154 Zeng, E., Ding, C., Narasimhan, G., Holbrook, S. (2008). Estimating Support for Protein-Protein Interaction Data with Applications to Function Prediction, LSS Computational Systems Bioinformatics Conference (CSB2008), pp. 73-84, Stanford, CA Mathee, K., Narasimhan, G., Valdes, C., Qiu, X., Matewish, J., Koehrsen, M., Rokas, A., Yandava, C., Engels, R., Zeng, E., Olavarietta, R., Doud, M., Smith, R., Montgomery, P., White, J., Godfrey, P., Kodira, C., Birren, B., Galagan, J., Lory, S. (2008). Dynamics of Pseudomonas aeruginosa genome evolution, Proceedings of the National Academy of Sciences (PNAS), 105(8):3100-05 Buendia, P. and Narasimhan, G. (2008). 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 Buendia, P. and Narasimhan, G. (2007). Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach, Bioinformatics, 23(22):2993-3000 Milledge, T., Zheng, G., Mullins, T., Narasimhan G. (2007). SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing, IEEE Conference on Bioinformatics and Bioengineering (BIBE2007), 1343-47 Zeng, E., Yang, C., Li, T., Narasimhan, G. (2007). On the Effectiveness of Constraints Sets in Clustering Genes, IEEE Conference on Bioinformatics and Bioengineering (BIBE2007), 79-86 Zeng, E., Mathee, K., Narasimhan, G. (2007). IEM: An Algorithm for Iterative Enhancement of Motifs Using Comparative Genomics Data, LSS Computational Systems Bioinformatics Conference (CSB2007), 227-35 Alvarez, H., Chatfield, D., Cox, D., Crumpler, E., D'Cunha, C., Gutierrez, R., Ibarra, J., Johnson, E., Kumar, K., Milledge, T., Narasimhan, G., Sadjadi, M., Zhang, C. (2007). CyberBridges: A model collaboration infrastructure for e-Science, Proceedings of the IEEE CCGrid Conference, 65-72 Buendia, P. and Narasimhan, G. (2007). Searching for recombinant donors in a phylogenetic network of serial samples, Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA), 109-20 Zeng, E. and Narasimhan, G. (2007). Enhancing Motif Discovery using Comparative Genomics Data, Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA), 329-37 Yang, C., Zeng, E., Mathee, K., Narasimhan, G. (2007). 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, pp. 121-136 Peng, W., Li, T., Narasimhan, G. (2006). Mining the Database of Transcription Binding Sites, Proceedings of the 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE), pp. 61-64 Buendia, P. and Narasimhan G. (2006). Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network, Bioinformatics, 22(18):2313-2314 Kuhn, D.N., Narasimhan, G., Nakamura, K., Brown, J.S., Schnell, R.J., Meerow, A. W. (2006). 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 Ghandeharizadeh, S. and Narasimhan, G. (2006). 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" Yang, C., Mills, D., Mathee, K., Wang, Y., Jayachandran, K., Sikaroodi, M., Gillevet, P., Entry, J., Narasimhan, G. (2006). 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 Zheng, G., Milledge, T., George, E.O., Narasimhan, G., (2006). 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, pp. 694-701 Milledge, T., Zheng, G., Narasimhan, G. (2006). 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, pp. 702-709 Buendia, P., Collins, T., Narasimhan, G. (2006). 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, pp. 807-814 Renugopalakrishnan, V., Wei, X., Narasimhan, G., Verma, C. S., Li, P., Anumanthan, A. (2006). Enhancement of Protein Thermal Stability: Toward the design of robust proteins for bionanotechnological applications, Chapter 8 of Bionanotechnology: Proteins to Nanodevices, Springer, pp. 117-139
Biochem. Biophys. Res. Commun., In Press, 2021; Also
bioRxiv,
DOI: 10.1101/2021.07.17.452576, 2021.
