Giri Narasimhan

Giri Narasimhan

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Giri Narasimhan

Giri Narasimhan

Publications by authors named "Giri Narasimhan"

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35Publications

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The gut microbiome and neuropsychiatric disorders: implications for attention deficit hyperactivity disorder (ADHD).

J Med Microbiol 2020 Jan;69(1):14-24

Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Florida, USA.

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http://dx.doi.org/10.1099/jmm.0.001112DOI Listing
January 2020

Large scale microbiome profiling in the cloud.

Bioinformatics 2019 Jul;35(14):i13-i22

Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612844PMC
July 2019

MATria: a unified centrality algorithm.

BMC Bioinformatics 2019 Jun 6;20(Suppl 11):278. Epub 2019 Jun 6.

Bioinformatics Research Group (BioRG) & Biomolecular Sciences Institute, School of Computing & Information Sciences, Florida International University, 11200 SW 8th St, Miami, 33199, FL, USA.

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http://dx.doi.org/10.1186/s12859-019-2820-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551236PMC
June 2019

Dynamic interaction network inference from longitudinal microbiome data.

Microbiome 2019 04 2;7(1):54. Epub 2019 Apr 2.

Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, 15213, Pennsylvania, USA.

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http://dx.doi.org/10.1186/s40168-019-0660-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446388PMC
April 2019

Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance.

J Forensic Sci 2018 Jul 22;63(4):1033-1042. Epub 2018 Jan 22.

Department of Biological Sciences, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL 33199.

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http://dx.doi.org/10.1111/1556-4029.13741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028300PMC
July 2018

ATria: a novel centrality algorithm applied to biological networks.

BMC Bioinformatics 2017 Jun 7;18(Suppl 8):239. Epub 2017 Jun 7.

Bioinformatics Research Group (BioRG) & Biomolecular Sciences Institute, School of Computing & Information Sciences, Florida International University, 11200 SW 8th St, Miami, 33196, FL, USA.

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http://dx.doi.org/10.1186/s12859-017-1659-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471957PMC
June 2017

Gene expression patterns in transgenic mouse models of hypertrophic cardiomyopathy caused by mutations in myosin regulatory light chain.

Arch Biochem Biophys 2016 07 22;601:121-32. Epub 2016 Feb 22.

Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA. Electronic address:

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http://dx.doi.org/10.1016/j.abb.2016.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370580PMC
July 2016

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis.

Evol Bioinform Online 2016 12;12(Suppl 1):5-16. Epub 2016 May 12.

Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA.; Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.

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http://dx.doi.org/10.4137/EBO.S36436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869604PMC
May 2016

Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR.

J Bacteriol 2014 Nov 2;196(22):3890-902. Epub 2014 Sep 2.

Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA

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http://dx.doi.org/10.1128/JB.01997-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248820PMC
November 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 Res 2014 Jan 23;42(2):979-98. Epub 2013 Oct 23.

Department of Biological Sciences, College of Arts and Science, Florida International University, Miami, FL 33199, USA, Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA, BioRG, School of Computing and Information Science, College of Engineering and Computing, Florida International University, Miami, FL 33199, USA, Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902932PMC
January 2014

The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes.

PLoS One 2012 29;7(3):e34067. Epub 2012 Mar 29.

Department of Biological Sciences, College of Arts and Science, Florida International University, Miami, Florida, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034067PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315558PMC
November 2012

Guest Editors' introduction to the special section on bioinformatics research and applications.

IEEE/ACM Trans Comput Biol Bioinform 2010 Oct-Dec;7(4):577-8

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http://dx.doi.org/10.1109/tcbb.2010.114DOI Listing
February 2011

Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients.

Hum Genomics 2010 Feb;4(3):147-69

Department of Biological Sciences, College of Arts and Sciences, Florida International University, Miami, FL 33199, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525977PMC
http://dx.doi.org/10.1186/1479-7364-4-3-147DOI Listing
February 2010

Estimating support for protein-protein interaction data with applications to function prediction.

Comput Syst Bioinformatics Conf 2008 ;7:73-84

Bioinformatics Research Group, School of Computing and Information Sciences, Florida International University, Miami, FL 33199, USA.

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August 2009

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains.

BMC Syst Biol 2009 Jun 16;3:62. Epub 2009 Jun 16.

Department of Biology and Center for Computational Science, University of Miami, Coral Gables, FL 33146, USA.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-3-62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709891PMC
June 2009

Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung.

Hum Genomics 2009 Apr;3(3):246-56

Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500232PMC
http://dx.doi.org/10.1186/1479-7364-3-3-246DOI Listing
April 2009

The role of internal node sequences and the molecular clock in the analysis of serially-sampled data.

Int J Bioinform Res Appl 2008 ;4(1):107-21

Department of Biology, Center for Computational Science, University of Miami, USA.

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http://dx.doi.org/10.1504/IJBRA.2008.017167DOI Listing
May 2008

Dynamics of Pseudomonas aeruginosa genome evolution.

Proc Natl Acad Sci U S A 2008 Feb 19;105(8):3100-5. Epub 2008 Feb 19.

Department of Molecular Microbiology and Immunology, College of Medicine, School of Computing and Information Sciences, College of Engineering, Florida International University, Miami, FL 33199, USA.

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http://dx.doi.org/10.1073/pnas.0711982105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268591PMC
February 2008

IEM: an algorithm for iterative enhancement of motifs using comparative genomics data.

Comput Syst Bioinformatics Conf 2007 ;6:227-35

Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, Florida 33199, USA.

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December 2007

Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach.

Bioinformatics 2007 Nov 23;23(22):2993-3000. Epub 2007 Aug 23.

Bioinformatics Research Group (BioRG), School of Computing and Information Science, Florida International University, Miami, FL 33199, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187926PMC
November 2007

Clustering genes using gene expression and text literature data.

Proc IEEE Comput Syst Bioinform Conf 2005 :329-40

Bioinformatics Research Group, School of Computer Science, Florida International University, Miami, FL 33199, USA.

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http://dx.doi.org/10.1109/csb.2005.23DOI Listing
May 2007

Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network.

Bioinformatics 2006 Sep 14;22(18):2313-4. Epub 2006 Jul 14.

Bioinformatics Research Group (BioRG), School of Computing and Information Science, Florida International University Miami, FL 33199, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl387DOI Listing
September 2006

Degenerate primer design via clustering.

Proc IEEE Comput Soc Bioinform Conf 2003 ;2:75-83

School of Computer Science, Florida International University, University Park, Miami, 33199, USA.

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August 2006

MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies.

Proc IEEE Comput Syst Bioinform Conf 2004 :110-9

Bioinformatics Research Group (BioRG), School of Computer Science, Florida International University, Miami, 33199, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195421PMC
July 2006

An eco-informatics tool for microbial community studies: supervised classification of Amplicon Length Heterogeneity (ALH) profiles of 16S rRNA.

J Microbiol Methods 2006 Apr 27;65(1):49-62. Epub 2005 Jul 27.

Bioinformatics Research Group (BioRG), School of Computer Science, Florida International University, Miami, Florida, 33199, USA.

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http://dx.doi.org/10.1016/j.mimet.2005.06.012DOI Listing
April 2006

Distinct transcriptional profiles characterize oral epithelium-microbiota interactions.

Cell Microbiol 2005 Jun;7(6):811-23

Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32610-0424, USA.

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http://dx.doi.org/10.1111/j.1462-5822.2005.00513.xDOI Listing
June 2005

Alginate production affects Pseudomonas aeruginosa biofilm development and architecture, but is not essential for biofilm formation.

J Med Microbiol 2004 Jul;53(Pt 7):679-690

Department of Biological Sciences1 and School of Computer Science2, Florida International University, Miami, FL 33199, USA 3Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA 4Section of Molecular Microbiology, The Technical University of Denmark, DK-2800 Lyngby, Denmark 5Department of Clinical Microbiology, University Hospital of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1099/jmm.0.45539-0DOI Listing
July 2004

Detection of DNA-binding helix-turn-helix motifs in proteins using the pattern dictionary method.

Methods Enzymol 2003 ;370:250-64

Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA.

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http://dx.doi.org/10.1016/S0076-6879(03)70022-6DOI Listing
February 2004

Mining protein sequences for motifs.

J Comput Biol 2002 ;9(5):707-20

Department of Mathematical Sciences, The University of Memphis, Memphis, TN 38152, USA.

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http://dx.doi.org/10.1089/106652702761034145DOI Listing
May 2003