Publications


Damaso, Mendel, Mendoza, von Wettberg, Narasimhan, Mills (2017). Bioinformatics approach to assess the biogeographic patterns of soil communities: the utility for soil provenance,, J Forensic Science, Recommended for publication.

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

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