Giri Narasimhan
Publications
selected publications
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Article
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2019Large scale microbiome profiling in the cloud. BIOINFORMATICS. 35:I13-I22.Full Text via DOI: 10.1093/bioinformatics/btz356 Web of Science: 000477703600003
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2019MATria: a unified centrality algorithm. BMC BIOINFORMATICS. 20.Full Text via DOI: 10.1186/s12859-019-2820-7 Web of Science: 000473704900004
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2019Dynamic interaction network inference from longitudinal microbiome data. MICROBIOME. 7.Full Text via DOI: 10.1186/s40168-019-0660-3 Web of Science: 000463725100001
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2018Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA). BIOINFORMATICS. 34.Full Text via DOI: 10.1093/bioinformatics/bty198 Web of Science: 000444317200050
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2018Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance. JOURNAL OF FORENSIC SCIENCES. 63.Full Text via DOI: 10.1111/1556-4029.13741 Web of Science: 000436939200005
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2016Gene expression patterns in transgenic mouse models of hypertrophic cardiomyopathy caused by mutations in myosin regulatory light chain. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 601.Full Text via DOI: 10.1016/j.abb.2016.02.022 Web of Science: 000378015200015
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2016Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. EVOLUTIONARY BIOINFORMATICS. 12:5-16.
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2015Automatic Construction of 3-D Building Model From Airborne LIDAR Data Through 2-D Snake Algorithm. IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING. 53:3-14.Full Text via DOI: 10.1109/TGRS.2014.2312393 Web of Science: 000341536700001
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2015GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Units. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 12:445-454.
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2014Structural and Functional Characterization of Pseudomonas aeruginosa Global Regulator AmpR. JOURNAL OF BACTERIOLOGY. 196:3890-3902.
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2013Transcriptional Regulatory Network in Pseudomonas aeruginosa. BACTERIAL GENE REGULATION AND TRANSCRIPTIONAL NETWORKS. 199-221.Web of Science: 000382950400014
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2012Transcriptional Response of Mucoid Pseudomonas aeruginosa to Human Respiratory Mucus. MBIO. 3.Full Text via DOI: 10.1128/mBio.00410-12 Web of Science: 000313100700019
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2009On the dilation spectrum of paths, cycles, and trees. COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS. 42:923-933.Full Text via DOI: 10.1016/j.comgeo.2009.03.004 Web of Science: 000268622400010
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2009Region-restricted clustering for geographic data mining. COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS. 42:231-240.Full Text via DOI: 10.1016/j.comgeo.2008.08.003 Web of Science: 000262214900005
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2009Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains. BMC SYSTEMS BIOLOGY. 3.
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2008Approximate Distance Oracles for Geometric Spanners. ACM TRANSACTIONS ON ALGORITHMS. 4.Full Text via DOI: 10.1145/1328911.1328921 Web of Science: 000265816600010
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2008Dynamics of Pseudomonas aeruginosa genome evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105:3100-3105.
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2008Influence of irrigated agriculture on soil microbial diversity. APPLIED SOIL ECOLOGY. 40:146-154.Full Text via DOI: 10.1016/j.apsoil.2008.03.012 Web of Science: 000259414100016
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2007Algorithms and Graphs. GEOMETRIC SPANNER NETWORKS. 18-40.Full Text via DOI: 10.1017/CBO9780511546884.003 Web of Science: 000296785300003
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2007Applications of Well-Separated Pairs. GEOMETRIC SPANNER NETWORKS. 178-195.Full Text via DOI: 10.1017/CBO9780511546884.011 Web of Science: 000296785300011
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2007Approximating Shortest Paths in Spanners. GEOMETRIC SPANNER NETWORKS. 415-426.Full Text via DOI: 10.1017/CBO9780511546884.018 Web of Science: 000296785300018
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2007Approximating the Stretch Factor of Euclidean Graphs. GEOMETRIC SPANNER NETWORKS. 242-254.Full Text via DOI: 10.1017/CBO9780511546884.014 Web of Science: 000296785300014
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2007Cones in Higher Dimensional Space and Theta-Graphs. GEOMETRIC SPANNER NETWORKS. 92-107.Full Text via DOI: 10.1017/CBO9780511546884.006 Web of Science: 000296785300006
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2007Designing Approximation Algorithms with Spanners. GEOMETRIC SPANNER NETWORKS. 443-467.Full Text via DOI: 10.1017/CBO9780511546884.020 Web of Science: 000296785300020
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2007Distance-preserving approximations of polygonal paths. COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS. 36:183-196.Full Text via DOI: 10.1016/j.comgeo.2006.05.002 Web of Science: 000244221700003
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2007Enumerating Distances Using Spanners of Bounded Degree. GEOMETRIC SPANNER NETWORKS. 139-147.Full Text via DOI: 10.1017/CBO9780511546884.009 Web of Science: 000296785300009
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2007Fault-Tolerant Spanners. GEOMETRIC SPANNER NETWORKS. 427-442.Full Text via DOI: 10.1017/CBO9780511546884.019 Web of Science: 000296785300019
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2007Further Results and Open Problems. GEOMETRIC SPANNER NETWORKS. 468-482.Full Text via DOI: 10.1017/CBO9780511546884.021 Web of Science: 000296785300021
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2007Geometric Analysis: The Gap Property. GEOMETRIC SPANNER NETWORKS. 108-119.Full Text via DOI: 10.1017/CBO9780511546884.007 Web of Science: 000296785300007
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2007Geometric Analysis: The Leapfrog Property. GEOMETRIC SPANNER NETWORKS. 257-317.Full Text via DOI: 10.1017/CBO9780511546884.015 Web of Science: 000296785300015
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2007Shortcutting Trees and Spanners with Low Spanner Diameter. GEOMETRIC SPANNER NETWORKS. 219-241.Full Text via DOI: 10.1017/CBO9780511546884.013 Web of Science: 000296785300013
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2007Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach. BIOINFORMATICS. 23:2993-3000.
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2007Spanners Based on the Theta-Graph. GEOMETRIC SPANNER NETWORKS. 63-91.Full Text via DOI: 10.1017/CBO9780511546884.005 Web of Science: 000296785300005
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2007The Algebraic Computation-Tree Model. GEOMETRIC SPANNER NETWORKS. 41-59.Full Text via DOI: 10.1017/CBO9780511546884.004 Web of Science: 000296785300004
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2007The Distance Range Hierarchy. GEOMETRIC SPANNER NETWORKS. 385-414.Full Text via DOI: 10.1017/CBO9780511546884.017 Web of Science: 000296785300017
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2007The Dumbbell Theorem. GEOMETRIC SPANNER NETWORKS. 196-218.Full Text via DOI: 10.1017/CBO9780511546884.012 Web of Science: 000296785300012
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2007The Gap-Greedy Algorithm. GEOMETRIC SPANNER NETWORKS. 120-138.Full Text via DOI: 10.1017/CBO9780511546884.008 Web of Science: 000296785300008
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2007The Path-Greedy Algorithm. GEOMETRIC SPANNER NETWORKS. 318-382.Full Text via DOI: 10.1017/CBO9780511546884.016 Web of Science: 000296785300016
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2007The Well-Separated Pair Decomposition. GEOMETRIC SPANNER NETWORKS. 151-177.Full Text via DOI: 10.1017/CBO9780511546884.010 Web of Science: 000296785300010
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2006An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA. JOURNAL OF MICROBIOLOGICAL METHODS. 65:49-62.
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2006Discovering sequence-structure patterns in proteins with variable secondary structure. COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS. 3992:702-709.Web of Science: 000238389400095
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2006Identification of cacao TIR-NBS-LRR resistance gene homologues and their use as genetic markers. JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE. 131:806-813.Web of Science: 000242870500014
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2006Reconstructing ancestor-descendant lineages from serially-sampled data: A comparison study. COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS. 3992:807-814.Web of Science: 000238389400108
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2006Region-restricted clustering for geographic data mining. ALGORITHMS - ESA 2006, PROCEEDINGS. 4168:399-410.Web of Science: 000241478200035
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2006Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network. BIOINFORMATICS. 22:2313-2314.
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2005A knowledge-driven method to evaluate multi-source clustering. PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS - ISPA 2005 WORKSHOPS. 3759:196-202.Web of Science: 000233739300022
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2005Clustering using adaptive self-organizing maps (ASOM) and applications. COMPUTATIONAL SCIENCE - ICCS 2005, PT 2. 3515:944-951.Web of Science: 000230023800120
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2005Exact and approximation algorithms for computing the dilation spectrum of paths, trees, and cycles. ALGORITHMS AND COMPUTATION. 3827:849-858.Web of Science: 000234885900085
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2005Fast pruning of geometric spanners. STACS 2005, PROCEEDINGS. 3404:508-520.Web of Science: 000229009500042
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2002Optimally computing a shortest weakly visible line segment inside a simple polygon. COMPUTATIONAL GEOMETRY-THEORY AND APPLICATIONS. 23.Full Text via DOI: 10.1016/S0925-7721(01)00058-X Web of Science: 000175983400001
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2002Mining protein sequences for motifs. JOURNAL OF COMPUTATIONAL BIOLOGY. 9.Full Text via DOI: 10.1089/106652702761034145 Web of Science: 000179401200002
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Book Chapter
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2007Geometric Spanner Networks Introduction. GEOMETRIC SPANNER NETWORKS. 3-17.Full Text via DOI: 10.1017/CBO9780511546884.002 Web of Science: 000296785300002
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2007Geometric Spanner Networks Preface. GEOMETRIC SPANNER NETWORKS. XIII-+.Full Text via DOI: 10.1017/CBO9780511546884.001 Web of Science: 000296785300001
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Editorial Material
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2013Comment on "On the Uniqueness of Stable Marriage Matchings" [Economic Letters 69(1):1-8,2000]. ECONOMICS LETTERS. 468-468.Full Text via DOI: 10.1016/j.econlet.2013.09.019 Web of Science: 000329145500027
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2010Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 577-578.
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Meeting Abstract
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2017Framing epigenetic signatures of the Pacific oyster under environmental stress using network analysis. BIOCHEMISTRY AND CELL BIOLOGY. 184-184.Web of Science: 000399165600025
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2014Microbial Associations In The Lungs Differ By Smoking And COPD Status. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE.Web of Science: 000209838200712
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Proceedings Paper
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2017MATria: A Unified Centrality Algorithm. 2014 IEEE 4TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS).Web of Science: 000428508600007
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2016CacheDedup: In-line Deduplication for Flash Caching. 14TH USENIX CONFERENCE ON FILE AND STORAGE TECHNOLOGIES (FAST '16). 301-314.Web of Science: 000385264300023
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2015ATria: A Novel Centrality Algorithm Applied To Biological Networks. 2014 IEEE 4TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS).Web of Science: 000377899500008
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2013A Metagenomic Approach to the Airways Microbiome of Chronic Obstructive Pulmonary Disease (COPD). 29TH SOUTHERN BIOMEDICAL ENGINEERING CONFERENCE (SBEC 2013). 151-+.Full Text via DOI: 10.1109/SBEC.2013.84 Web of Science: 000324751700076
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2013Designing Primers with Higher Taxonomic Distinguishability. 29TH SOUTHERN BIOMEDICAL ENGINEERING CONFERENCE (SBEC 2013). 157-+.Full Text via DOI: 10.1109/SBEC.2013.87 Web of Science: 000324751700079
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2013Vector Repacking Algorithms for Power-Aware Computing. 2013 INTERNATIONAL GREEN COMPUTING CONFERENCE (IGCC).Web of Science: 000333160300027
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2009Meta-analysis of brain tumor microarray data using Oncomine identifies NRF1, Tfam and Myc co-expressed genes: its implications in the development of childhood brain tumors. 18TH WORLD IMACS CONGRESS AND MODSIM09 INTERNATIONAL CONGRESS ON MODELLING AND SIMULATION. 720-726.Web of Science: 000290045000111
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2009Weighted Consensus Clustering for Identifying Functional Modules In Protein-Protein Interaction Networks. EIGHTH INTERNATIONAL CONFERENCE ON MACHINE LEARNING AND APPLICATIONS, PROCEEDINGS. 539-+.Full Text via DOI: 10.1109/ICMLA.2009.94 Web of Science: 000291011600082
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2008A Functional Network of Yeast Genes Using Gene Ontology Information. 2008 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, PROCEEDINGS. 343-+.Full Text via DOI: 10.1109/BIBM.2008.60 Web of Science: 000264284200052
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2007A graph reduction method for 2D snake problems. 2007 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION, VOLS 1-8. 353-+.Web of Science: 000250382800048
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2007CyberBridges - A model collaboration infrastructure for e-Science. CCGRID 2007: SEVENTH IEEE INTERNATIONAL SYMPOSIUM ON CLUSTER COMPUTING AND THE GRID. 65-+.Web of Science: 000247002000008
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2007Enhancing motif refinement by incorporating comparative genomics data. BIOINFORMATICS RESEARCH AND APPLICATIONS, PROCEEDINGS. 329-+.Web of Science: 000246369100030
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2007On the effectiveness of constraints sets in clustering genes. PROCEEDINGS OF THE 7TH IEEE INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, VOLS I AND II. 79-86.Web of Science: 000252958200020
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2007PlasmoTFBM: An intelligent queriable database for predicted transcription factor binding motifs in Plasmodium falciparum. METHODS OF MICROARRAY DATA ANALYSIS V. 121-+.Full Text via DOI: 10.1007/978-0-387-34569-7_9 Web of Science: 000243466200009
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2007Searching for recombinant donors in a phylogenetic network of serial samples. BIOINFORMATICS RESEARCH AND APPLICATIONS, PROCEEDINGS. 109-+.Web of Science: 000246369100010
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2006Enhancement of protein thermal stability: Toward the design of robust proteins for bionanotechnological applications. BIONANOTECHNOLOGY: PROTEINS TO NANODEVICES.Full Text via DOI: 10.1007/978-1-4020-4375-8_8 Web of Science: 000240620800008
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2006Mining the database of transcription binding sites. BIBE 2006: SIXTH IEEE SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, PROCEEDINGS. 61-+.Web of Science: 000242503800008
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2005Clustering genes using gene expression and text literature data. 2005 IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE, PROCEEDINGS. 329-340.PMID: 16447990 Web of Science: 000231800100037
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2005Microarray data analysis using neural network classifiers and gene selection methods. METHODS OF MICROARRAY DATA ANALYSIS IV. 207-222.Full Text via DOI: 10.1007/0-387-23077-7_16 Web of Science: 000225319000016
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2005Sequence-structure patterns: Discovery and applications. Proceedings of the 8th Joint Conference on Information Sciences, Vols 1-3. 1282-1285.Web of Science: 000233670802025
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Review
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2015Current concepts in the pathogenesis and treatment of chronic suppurative otitis media. JOURNAL OF MEDICAL MICROBIOLOGY. 1103-1116.
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chaired theses and dissertations
- Parra, Nestor Andres, Rigid and Non-rigid Point-based Medical Image Registration 2009
- Buendia, Patricia, Phylogenetic analysis of within-host serially-sampled viral data 2006
advised honors theses
Research
principal investigator on
- Multi-Disciplinary High Performance Computing and STEM Education awarded by Army Research Office 2016 - 2017
- The Airway Microbiome in Chronic Obstructive Pulmonary Disease awarded by Florida Department of Health 2010 - 2012
- Design of Vibrio Cholerae Pan-Genome Array. awarded by Harvard Medical School 2009
co-principal investigator on
- An Epigenetic multiplex amplification for the determination of age and body fluid type awarded by U.S. Department of Justice 2018 - 2019
- CSR: Medium: Collaborative Research: NVM-enabled Host-side Caches awarded by National Science Foundation 2016 - 2019
- Alpha Trypsin Deficiency Lung Microbiome Project awarded by Alpha-1 Foundation 2014 - 2017
- CSR: Small: Energy Proportional Storage awarded by National Science Foundation 2010 - 2015
investigator on
- Longitudinal Study of Vaginal Microbiota and Persistent Human Papillomavirus Detection awarded by National Institute of Allergy and Infectious Diseases 2017 - 2020
- MRI: Development of an Instrument for Acquisition, Management, and Analysis of Super-resolution Aerial Imagery awarded by National Science Foundation 2014 - 2019
- Integrative modeling to link vascular phenotype to gene expression awarded by National Institutes of Health 2014 - 2018
- Graduate Research Fellowship Program awarded by National Science Foundation 2012 - 2013
- 2007-2008 MBRS Support of Continuous Research Excellence at FIU. awarded by National Institutes of Health 2007 - 2009
Teaching
teaching activities
- CIS7910-U08: Graduate Research Spring Term 2019
- CIS7910-U17: Graduate Research Fall Term 2019
- CIS7980-U08: Ph.D. Dissertation Fall Term 2019
- CIS7980-U10: Ph.D. Dissertation Spring Term 2019
- IDC6940-U01: Capstone Course in Data Science Fall Term 2019
- IDC6940-U01: Capstone Course in Data Science Spring Term 2019
Contact
full name
- Giri Narasimhan
visualizations
Recent publications and grants in Scholars@FIU
research areas
- Agriculture
- Biochemistry & Molecular Biology
- Biophysics
- Biotechnology & Applied Microbiology
- Business & Economics
- Cell Biology
- Computer Science
- Engineering
- Evolutionary Biology
- General & Internal Medicine
- Genetics & Heredity
- Geochemistry & Geophysics
- Imaging Science & Photographic Technology
- Mathematical & Computational Biology
- Mathematics
- Microbiology
- Remote Sensing
- Respiratory System
- Science & Technology - Other Topics