Narasimhan, Giri

Giri Narasimhan
Close

Positions

Professor, School of Computing and Information Sciences , College of Engineering and Computing

Contact Info

giri@fiu.edu

305-348-3748

selected publications

Article
- 2019
  
  Large scale microbiome profiling in the cloud. BIOINFORMATICS. 35:I13-I22.
  Full Text via DOI: 10.1093/bioinformatics/btz356 Web of Science: 000477703600003
- 2019
  
  MATria: a unified centrality algorithm. BMC BIOINFORMATICS. 20.
  Full Text via DOI: 10.1186/s12859-019-2820-7 Web of Science: 000473704900004
- 2019
  
  Dynamic interaction network inference from longitudinal microbiome data. MICROBIOME. 7.
  Full Text via DOI: 10.1186/s40168-019-0660-3 Web of Science: 000463725100001
- 2018
  
  Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA). BIOINFORMATICS. 34.
  Full Text via DOI: 10.1093/bioinformatics/bty198 Web of Science: 000444317200050
- 2018
  
  Bioinformatics 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
- 2017
  
  ATria: a novel centrality algorithm applied to biological networks. BMC BIOINFORMATICS. 18.
  Full Text via DOI: 10.1186/s12859-017-1659-z PMID: 28617231 Web of Science: 000410134600002
- 2016
  
  Gene 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
- 2016
  
  Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. EVOLUTIONARY BIOINFORMATICS. 12:5-16.
  Full Text via DOI: 10.4137/EBO.S36436 PMID: 27199545 Web of Science: 000382989300002
- 2015
  
  Automatic 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
- 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. 12:445-454.
  Full Text via DOI: 10.1109/TCBB.2014.2355231 PMID: 26357230 Web of Science: 000352788300018
- 2015
  
  Microbial "social networks". BMC GENOMICS. 16.
  Full Text via DOI: 10.1186/1471-2164-16-S11-S6 PMID: 26576770 Web of Science: 000377308500006
- 2014
  
  Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. NUCLEIC ACIDS RESEARCH. 42:979-998.
  Full Text via DOI: 10.1093/nar/gkt942 PMID: 24157832 Web of Science: 000331138100031
- 2014
  
  Structural and Functional Characterization of Pseudomonas aeruginosa Global Regulator AmpR. JOURNAL OF BACTERIOLOGY. 196:3890-3902.
  Full Text via DOI: 10.1128/JB.01997-14 PMID: 25182487 Web of Science: 000343930600009
- 2013
  
  Transcriptional Regulatory Network in Pseudomonas aeruginosa. BACTERIAL GENE REGULATION AND TRANSCRIPTIONAL NETWORKS. 199-221.
  Web of Science: 000382950400014
- 2012
  
  The Regulatory Repertoire of Pseudomonas aeruginosa AmpC beta-Lactamase Regulator AmpR Includes Virulence Genes. PLOS ONE. 7.
  Full Text via DOI: 10.1371/journal.pone.0034067 PMID: 22479525 Web of Science: 000304523400054
- 2012
  
  Transcriptional Response of Mucoid Pseudomonas aeruginosa to Human Respiratory Mucus. MBIO. 3.
  Full Text via DOI: 10.1128/mBio.00410-12 Web of Science: 000313100700019
- 2009
  
  On 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
- 2009
  
  Region-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
- 2009
  
  Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains. BMC SYSTEMS BIOLOGY. 3.
  Full Text via DOI: 10.1186/1752-0509-3-62 PMID: 19531207 Web of Science: 000268145400001
- 2008
  
  Approximate Distance Oracles for Geometric Spanners. ACM TRANSACTIONS ON ALGORITHMS. 4.
  Full Text via DOI: 10.1145/1328911.1328921 Web of Science: 000265816600010
- 2008
  
  Dynamics of Pseudomonas aeruginosa genome evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105:3100-3105.
  Full Text via DOI: 10.1073/pnas.0711982105 PMID: 18287045 Web of Science: 000253567900063
- 2008
  
  Influence 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
- 2007
  
  Algorithms and Graphs. GEOMETRIC SPANNER NETWORKS. 18-40.
  Full Text via DOI: 10.1017/CBO9780511546884.003 Web of Science: 000296785300003
- 2007
  
  Applications of Well-Separated Pairs. GEOMETRIC SPANNER NETWORKS. 178-195.
  Full Text via DOI: 10.1017/CBO9780511546884.011 Web of Science: 000296785300011
- 2007
  
  Approximating Shortest Paths in Spanners. GEOMETRIC SPANNER NETWORKS. 415-426.
  Full Text via DOI: 10.1017/CBO9780511546884.018 Web of Science: 000296785300018
- 2007
  
  Approximating the Stretch Factor of Euclidean Graphs. GEOMETRIC SPANNER NETWORKS. 242-254.
  Full Text via DOI: 10.1017/CBO9780511546884.014 Web of Science: 000296785300014
- 2007
  
  Cones in Higher Dimensional Space and Theta-Graphs. GEOMETRIC SPANNER NETWORKS. 92-107.
  Full Text via DOI: 10.1017/CBO9780511546884.006 Web of Science: 000296785300006
- 2007
  
  Designing Approximation Algorithms with Spanners. GEOMETRIC SPANNER NETWORKS. 443-467.
  Full Text via DOI: 10.1017/CBO9780511546884.020 Web of Science: 000296785300020
- 2007
  
  Distance-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
- 2007
  
  Enumerating Distances Using Spanners of Bounded Degree. GEOMETRIC SPANNER NETWORKS. 139-147.
  Full Text via DOI: 10.1017/CBO9780511546884.009 Web of Science: 000296785300009
- 2007
  
  Fault-Tolerant Spanners. GEOMETRIC SPANNER NETWORKS. 427-442.
  Full Text via DOI: 10.1017/CBO9780511546884.019 Web of Science: 000296785300019
- 2007
  
  Further Results and Open Problems. GEOMETRIC SPANNER NETWORKS. 468-482.
  Full Text via DOI: 10.1017/CBO9780511546884.021 Web of Science: 000296785300021
- 2007
  
  Geometric Analysis: The Gap Property. GEOMETRIC SPANNER NETWORKS. 108-119.
  Full Text via DOI: 10.1017/CBO9780511546884.007 Web of Science: 000296785300007
- 2007
  
  Geometric Analysis: The Leapfrog Property. GEOMETRIC SPANNER NETWORKS. 257-317.
  Full Text via DOI: 10.1017/CBO9780511546884.015 Web of Science: 000296785300015
- 2007
  
  Shortcutting Trees and Spanners with Low Spanner Diameter. GEOMETRIC SPANNER NETWORKS. 219-241.
  Full Text via DOI: 10.1017/CBO9780511546884.013 Web of Science: 000296785300013
- 2007
  
  Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach. BIOINFORMATICS. 23:2993-3000.
  Full Text via DOI: 10.1093/bioinformatics/btm413 PMID: 17717035 Web of Science: 000251197800005
- 2007
  
  Spanners Based on the Theta-Graph. GEOMETRIC SPANNER NETWORKS. 63-91.
  Full Text via DOI: 10.1017/CBO9780511546884.005 Web of Science: 000296785300005
- 2007
  
  The Algebraic Computation-Tree Model. GEOMETRIC SPANNER NETWORKS. 41-59.
  Full Text via DOI: 10.1017/CBO9780511546884.004 Web of Science: 000296785300004
- 2007
  
  The Distance Range Hierarchy. GEOMETRIC SPANNER NETWORKS. 385-414.
  Full Text via DOI: 10.1017/CBO9780511546884.017 Web of Science: 000296785300017
- 2007
  
  The Dumbbell Theorem. GEOMETRIC SPANNER NETWORKS. 196-218.
  Full Text via DOI: 10.1017/CBO9780511546884.012 Web of Science: 000296785300012
- 2007
  
  The Gap-Greedy Algorithm. GEOMETRIC SPANNER NETWORKS. 120-138.
  Full Text via DOI: 10.1017/CBO9780511546884.008 Web of Science: 000296785300008
- 2007
  
  The Path-Greedy Algorithm. GEOMETRIC SPANNER NETWORKS. 318-382.
  Full Text via DOI: 10.1017/CBO9780511546884.016 Web of Science: 000296785300016
- 2007
  
  The Well-Separated Pair Decomposition. GEOMETRIC SPANNER NETWORKS. 151-177.
  Full Text via DOI: 10.1017/CBO9780511546884.010 Web of Science: 000296785300010
- 2006
  
  An ecoinformatics tool for microbial community studies: Supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA. JOURNAL OF MICROBIOLOGICAL METHODS. 65:49-62.
  Full Text via DOI: 10.1016/j.mimet.2005.06.012 PMID: 16054254 Web of Science: 000236814700006
- 2006
  
  Discovering sequence-structure patterns in proteins with variable secondary structure. COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS. 3992:702-709.
  Web of Science: 000238389400095
- 2006
  
  Identification 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
- 2006
  
  Reconstructing ancestor-descendant lineages from serially-sampled data: A comparison study. COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS. 3992:807-814.
  Web of Science: 000238389400108
- 2006
  
  Region-restricted clustering for geographic data mining. ALGORITHMS - ESA 2006, PROCEEDINGS. 4168:399-410.
  Web of Science: 000241478200035
- 2006
  
  Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network. BIOINFORMATICS. 22:2313-2314.
  Full Text via DOI: 10.1093/bioinformatics/btl387 PMID: 16844708 Web of Science: 000240588800023
- 2005
  
  A knowledge-driven method to evaluate multi-source clustering. PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS - ISPA 2005 WORKSHOPS. 3759:196-202.
  Web of Science: 000233739300022
- 2005
  
  Clustering using adaptive self-organizing maps (ASOM) and applications. COMPUTATIONAL SCIENCE - ICCS 2005, PT 2. 3515:944-951.
  Web of Science: 000230023800120
- 2005
  
  Exact and approximation algorithms for computing the dilation spectrum of paths, trees, and cycles. ALGORITHMS AND COMPUTATION. 3827:849-858.
  Web of Science: 000234885900085
- 2005
  
  Fast pruning of geometric spanners. STACS 2005, PROCEEDINGS. 3404:508-520.
  Web of Science: 000229009500042
- 2002
  
  Optimally 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
- 2002
  
  Mining protein sequences for motifs. JOURNAL OF COMPUTATIONAL BIOLOGY. 9.
  Full Text via DOI: 10.1089/106652702761034145 Web of Science: 000179401200002
Book Chapter
- 2007
  
  Geometric Spanner Networks Introduction. GEOMETRIC SPANNER NETWORKS. 3-17.
  Full Text via DOI: 10.1017/CBO9780511546884.002 Web of Science: 000296785300002
- 2007
  
  Geometric Spanner Networks Preface. GEOMETRIC SPANNER NETWORKS. XIII-+.
  Full Text via DOI: 10.1017/CBO9780511546884.001 Web of Science: 000296785300001
Editorial Material
- 2013
  
  Comment 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
- 2010
  
  Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 577-578.
  Full Text via DOI: 10.1109/TCBB.2010.114 PMID: 21058452 Web of Science: 000283559100001
Meeting Abstract
- 2017
  
  Framing epigenetic signatures of the Pacific oyster under environmental stress using network analysis. BIOCHEMISTRY AND CELL BIOLOGY. 184-184.
  Web of Science: 000399165600025
- 2014
  
  Microbial Associations In The Lungs Differ By Smoking And COPD Status. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE.
  Web of Science: 000209838200712
Proceedings Paper
- 2017
  
  MATria: A Unified Centrality Algorithm. 2014 IEEE 4TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS).
  Web of Science: 000428508600007
- 2016
  
  CacheDedup: In-line Deduplication for Flash Caching. 14TH USENIX CONFERENCE ON FILE AND STORAGE TECHNOLOGIES (FAST '16). 301-314.
  Web of Science: 000385264300023
- 2015
  
  ATria: 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
- 2013
  
  A 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
- 2013
  
  Designing 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
- 2013
  
  Vector Repacking Algorithms for Power-Aware Computing. 2013 INTERNATIONAL GREEN COMPUTING CONFERENCE (IGCC).
  Web of Science: 000333160300027
- 2009
  
  Meta-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
- 2009
  
  Weighted 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
- 2008
  
  A 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
- 2007
  
  A graph reduction method for 2D snake problems. 2007 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION, VOLS 1-8. 353-+.
  Web of Science: 000250382800048
- 2007
  
  CyberBridges - A model collaboration infrastructure for e-Science. CCGRID 2007: SEVENTH IEEE INTERNATIONAL SYMPOSIUM ON CLUSTER COMPUTING AND THE GRID. 65-+.
  Web of Science: 000247002000008
- 2007
  
  Enhancing motif refinement by incorporating comparative genomics data. BIOINFORMATICS RESEARCH AND APPLICATIONS, PROCEEDINGS. 329-+.
  Web of Science: 000246369100030
- 2007
  
  On 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
- 2007
  
  PlasmoTFBM: 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
- 2007
  
  Searching for recombinant donors in a phylogenetic network of serial samples. BIOINFORMATICS RESEARCH AND APPLICATIONS, PROCEEDINGS. 109-+.
  Web of Science: 000246369100010
- 2006
  
  Enhancement 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
- 2006
  
  Mining the database of transcription binding sites. BIBE 2006: SIXTH IEEE SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, PROCEEDINGS. 61-+.
  Web of Science: 000242503800008
- 2005
  
  Clustering genes using gene expression and text literature data. 2005 IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE, PROCEEDINGS. 329-340.
  PMID: 16447990 Web of Science: 000231800100037
- 2005
  
  Microarray 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
- 2005
  
  Sequence-structure patterns: Discovery and applications. Proceedings of the 8th Joint Conference on Information Sciences, Vols 1-3. 1282-1285.
  Web of Science: 000233670802025
Review
- 2015
  
  Current concepts in the pathogenesis and treatment of chronic suppurative otitis media. JOURNAL OF MEDICAL MICROBIOLOGY. 1103-1116.
  Full Text via DOI: 10.1099/jmm.0.000155 PMID: 26248613 Web of Science: 000365460900001

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

Fernandez, Misael, An Analytical Workflow for Metagenomic Data and its Application to the Study of Chronic Obstructive Pulmonary Disease (COPD) 2013

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 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

full name

Giri Narasimhan

ORCID iD

https://orcid.org/0000-0003-0535-4871 (confirmed)

visualizations

Recent publications and grants in Scholars@FIU

Co-author Network

Co-investigator Network

publication subject 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
Legal Medicine
Mathematical & Computational Biology
Mathematics
Microbiology
Remote Sensing
Respiratory System
Science & Technology - Other Topics

Citation index-derived subject areas the researcher has published in