Authors, Title, Journal

Invited Papers in Professional Journals



V. Aguiar-Pulido, W. Huang W, V. Suarez-Ulloa, T. Cickovski, K. Mathee, and G. Narasimhan. Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis. Evol Bioinform Online. May 12;12(Suppl 1):5-16. doi:10.4137/EBO.S36436. eCollection
2016. Review.



K. Mathee, L.L. Silver, and G. Tatke G. 70th Anniversary Collection for the Microbiology Society: Journal of Medical Microbiology. Journal of Medical Microbiology 64(12):1457-61. doi: 10.1099/jmm.0.000186.


R. Mittal, C. V. Lisi, R. Gerring, J. Mittal, K. Mathee, G. Narasimhan, R. K. Azad, Q. Yao, M. Grati, D. Yan, A.A. Eshraghi, S.I. Angeli, F.F. Telischi,
X-Z. Liu. Current concepts in the pathogenesis and treatment of chronic suppurative otitis media. Journal of Medical Microbiology
64(10):1103-16. doi: 10.1099/jmm.0.000155. Epub 2015 Aug 5. [PR]


H. Kumari, D. Balasubramanian, and K. Mathee. Pseudomonas aeruginosa AmpR: An acute-chronic switch regulator. Pathogens and Diseases Mar;73(2):1-14. doi: 10.1111/2049-632X.12208. Epub 2015 Feb 26. [PR]



R. Mittal, J. Kodiyan, R. Gerring, K. Mathee, J-D Li, M. Grati
& X.Z. Liu. Role of innate immunity in the pathogenesis of otitis media. International Journal of Infectious Diseases
259-67. doi: 10.1016/j.ijid.2014.10.015. Epub 2014 Nov 5. [PR]



L. Schneper, N. Maricic, and K. Mathee. Anti-quorum sensing, anti-bacterial, and immunomodulatory properties of Panax ginseng. International Journal of Biomedical and Pharmaceutical Sciences 6:11-24. [PR]



K. F. Kong, L. Schneper, and K. Mathee. Beta-lactam antibiotics: from antibiosis to resistance and bacteriology. Review. Acta Pathologica, Microbiologica, et Immunologica Scandinavica 118(1):1-36. [PR]

  • Listed as a paper “of outstanding interest” by Llarrull et al, 2010 Current Opinion in Microbiology 13:551-557.


M. Doud, E. Zeng, L. Schneper, G. Narasimhan, K. Mathee. Approaches to analyzing dynamic microbial communities such as those seen in cystic fibrosis lung. Human Genomics 3(3):246-256. [PR]



S.Z. Miller, S. King, and K. Mathee. Forensic DNA analysis: An overview of human DNA analysis. International Journal of Forensic Science (Revista de Ciencias Forenses) 1:31-38. [Non PR]



K. Mathee and G. Narasimhan. Detection of DNA-binding helix-turn-helix motifs in proteins using pattern dictionary method. Methods in Enzymology 370:250-264. [Non PR]



K. Hughes, and K. Mathee. The anti-sigma factors. Annual Review of Microbiology 52:231-286. [Non PR]

Peer Reviewed Research Articles



M. Jani, K. Mathee and Azad RK. Identification of novel genomicislands in Liverpool Epidemic Strain of Pseudomonas aeruginosa usingsegmentation and clustering. Frontiers in Microibiology
7:1210. doi: 10.3389/fmicb.2016.01210.


M. Lee*, S. Dhar*, S. De Benedetti, D. Hesek, B. Boggess, B. Blázquez, K. Mathee, and S. Mobashery. Muropeptide pool and the elicitors of ß-lactam-antibiotic resistance in Pseudomonas aeruginosa, Angew Chem Int Ed Engl. 2016 Jun 6;55(24):6882-6. doi: 10.1002/anie.201601693. Epub 2016 Apr 25. [* – contributed equally; ^ – co-corresponding authors]



D. Zincke, D. Balasubramanian, L.L. Silver, and K. Mathee. Characterization of a carbapenem-hydrolyzing enzyme, PoxB, in Pseudomonas aeruginosa PAO1. Antimicrobial Agents Chemotherapy. Nov 30;60(2):936-45. doi: 10.1128/AAC.01807-15.


G. Tatke, H. Kumari, E. Silva-Herzog, L. Ramirez, and K. Mathee. Pseudomonas aeruginosa MifS-MifR two competent system is specific for aketoglutarate utilization. PLOS One Jun 26;10(6):e0129629. doi: 10.1371/journal.pone.0129629.


M. Fernandez, J.D. Riveros, M. Campos, K. Mathee and G. Narasimhan. Microbial “social networks”. BMC Genomics 16(Suppl 11): S6 (Special Issue).



O. Caille, D. Zincke, M. Merighi, D. Balasubramanian, H. Kumari, K-F. Kong, E. Silva-Herzog, G. Narasimhan, L. Schneper, S. Lory, and K. Mathee. Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR. Journal of Bacteriology Nov; 196(22): 3890–3902. doi: 10.1128/JB.01997-14


H. Kumari, D. Balasubramanian, D. Zincke, and K. Mathee. Pseudomonas aeruginosa AmpR plays a role in transient cross-resistance to ß-lactams and non-ß-lactams upon preexposure to subinhibitory
concentrations of antibiotics. Journal of Medical Microbiology Apr; 63(Pt 4): 544-55 J
an 25. doi: 10.1099/jmm.0.070185-0.
Featured in MDLinx web site ( MDLinx is the world’s most up-to-date index of articles that matter in the daily lives of physicians and other healthcare professionals.


H. Kumari*, S.K. Murugapiran*, D. Balasubramanian, L. Schneper, M. Merighi, D. Sarracino, S. Lory, and K. Mathee. LTQ-XL mass spectrometry proteome analysis expands the Pseudomonas aeruginosa AmpR regulon to include cyclic di-GMP phosphodiesterases and phosphoproteins, and identifies novel open reading frames. Journal of Proteome Research Jan 16; 96:328-42. doi: 10.1016/j.jprot.2013.11.018. Epub 2013 Nov 28. [* – contributed equally]


D. Balasubramanian, H. Kumari, M. Jaric, M. Fernandez, K.H. Turner, S.L. Dove, G. Narasimhan, S. Lory and K. Mathee. 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):979-98. doi: 10.1093/nar/gkt942. Epub 2013 Oct 23.


D. Balachandar, M.S. Doud, L. Schneper, D.E. Mills, and K. Mathee. Long-term organic nutrient management fosters the eubacterial community diversity in the Indian semi-arid alfisol as revealed by length heterogeneity-PCR. Communications in Soil Science and Plant Analysis 45:189-203.



M. Jaric, J. Segal, E. Silva-Herzog, L. Schneper, K. Mathee, and G. Narasimhan. Better primer design for metagenomic applications by increasing taxonomic distinguishability. BMC Proceedings 7(Suppl 7):S4 doi:10.1186/1753-6561-7-S7-S4.


D. Balasubramanian, L. Schneper, H. Kumari and K. Mathee. A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence. Nucleic Acids Research 41(1):1-20.



D. Balasubramanian, L. Schneper, M. Merighi, R. Smith, G. Narasimhan, S. Lory, and K. Mathee. The regulatory repertoire of Pseudomonas aeruginosa AmpC ß-lactamase regulator AmpR includes virulence genes. PLoS One 7(3):e34067.


R. Sautter, D. Ramos, O. Ciofu, A. Heydorn, N. Hoiby, A. Kharazmi, C. DeVries, D.E. Ohman, L. Schneper, and K. Mathee. A complex multilevel attack on Pseudomonas aeruginosa algT/U expression and AlgT/U activity results in the loss of alginate production. Gene 498(2):242-53


E. Zeng, C.Ding, K. Mathee, L. Schneper, and G. Narasimhan. Gene function prediction and functional network: The role of gene ontology. Data Mining: Foundations and Intelligent Paradigms, 123-162



V.L.A. Malladi, A.J. Sobczak, N. Maricic, S.K. Murugapiran, L. Schneper, J. Makemson, K. Mathee and S.F. Wnuk. Substituted lactam and cyclic azahemiacetals modulate Pseudomonas aeruginosa quorum sensing. BMC Bioorganic and Medicinal Chemistry. 19:5500-5506 [Co-corresponding author]


C.Z. Li, K. Vandenberg, S. Prabhulkar, X. Zhu, L. Schneper, K. Mathee, C.J. Rosser, and E. Almeide. Paper based point-of-care testing disc for multiplex whole cell bacteria analysis. Biosensors and Bioelectronics 26:4342-8.


K.G. Chan, S. Atkinson, K. Mathee, C.K. Sam, S.R. Chhabra, M. C�mara, C.L. Koh, and P. Williams. Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger) rhizosphere: co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia. BMC Microbiology 11:51.

  • It has been designated as “Highly accessed” paper. The ‘Highly accessed’ designate identifies those articles that have been especially highly accessed, relative to their age, and the journal in which they were published.


D. Balasubramanian, K.F. Kong, S. Jayawardena, S. Leal, R. Sautter, and K. Mathee. Coregulation of ß-lactam resistance, alginate production, and quorum sensing in Pseudomonas aeruginosa. Journal of Medical Microbiology 60(2):147-156.

Featured in

  • MDLinx web site ( MDLinx is the world’s most up-to-date index of articles that matter in the daily lives of physicians and other healthcare professionals.


K.F. Kong, A. Aguila, L. Schneper, and K. Mathee. Pseudomonas aeruginosa β-lactamase induction requires two permeases, AmpG and AmpP. BMC

  • It has been designated as “Highly accessed” paper.


S. Cardenas, M. Scuri, L. Samsell, B. Ducatman, P. Bejarano, A. Auais, M. Doud, K. Mathee, and G. Piedimonte. Neurotropic and neuroimmune responses to early-life Pseudomonas aeruginosa infection in rat lungs. American Journal of Physiology – Lung Cellular and Molecular Physiology 299(3):L334-44.


Z. Song, K.F Kong, H. Wu, N. Maricic, B. Ramalingam, H. Priestap, J.M.E. Quirke, N. Høiby, L. Schneper and K. Mathee. Panax ginseng has anti-infective activity against opportunistic pathogen Pseudomonas aeruginosa by inhibiting quorum sensing, a bacterial communication process critical for establishing infection. Phytomedicine 17(13):1040-1046.


M.S. Doud, M. Light, G. Gonzalez, G. Narsimhan, and K. Mathee. 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):147-169.



M. Herzberg, T. Rezene, C. Ziemba, O. Gillor, and K. Mathee. Impact of higher alginate expression on deposition of Pseudomonas aeruginosa in radial stagnation point flow and reverse osmosis systems. Environmental Science & Technology Journal 43(19):7376-7383.


M.S. Doud, R. Grimes-Zeppegno, E. Molina, N. Miller, D. Balachandar, L. Schneper, R. Poppiti, and K. Mathee. A k2A-positive Klebsiella pneumoniae causes liver and brain abscess in a Saint Kitt’s man. International Journal of Medical Sciences 6(6):301-304.


D. Balasubramanian, and K. Mathee. Comparative transcriptome analyses of Pseudomonas aeruginosa. Human Genomics 3(4):349-61.



E. Zeng, G. Narasimhan, L. Schneper, and K. Mathee. A functional network of yeast genes using gene ontology information. IEEE Conference on Bioinformatics and Biomedicine (BIBM2008) 343-346.


H. Vedala, D.H. Kim, M. Doud, K. Mathee, and W. Choi. Effect of environmental factors on electrical conductivity of single oligo-DNA molecule measured using single-walled carbon nanotube nanoelectrodes. Nanotechnology 19:1-6 (265704)


J. Entry, D. Mills, K. Mathee, K. Jayachandran, R.E. Sojka and G. Narasimhan. Influence of irrigated agriculture on soil microbial diversity. Applied Soil Ecology 40:146-154.


A. Adonizio, S. Leal, F. Ausubel, and K. Mathee. Attenuation of Pseudomonas aeruginosa virulence by medicinal plants in a Caenorhabditis elegans model system. Journal of Medical Microbiology 57:809-813.


A. L. Adonizio, K.F. Kong, and K. Mathee. Inhibition of quorum sensing-controlled virulence factor production in Pseudomonas aeruginosa by South Florida plant extracts. Antimicrobial Agents and Chemotherapy 52:198-203


K. Mathee, G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish , M. Koehrsen, A. Rokas, C. N. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R.
Smith , P. Montgomery, J. White, P. A. Godfrey, C. Kodira, B. Birren, J. Galagan and S. Lory. Dynamics of Pseudomonas aeruginosa genome evolution. Proceedings of National Academy of Sciences USA 105(8):3100-3105.

Highlighted by

  • Genome Technology Online, Feb 20, 2008, “Survival through genome shapeshifting
  • Selected for review by Faculty of 1000 Biology


S. Roy S, H. Vedala, A.D. Roy, D.H. Kim, M. Doud, K. Mathee, H.K. Shin, N. Shimamoto, V. Prasad and W. Choi. Direct electrical measurements on single-molecule genomic DNA using single-walled carbon nanotubes. Nano Letters 8:26-30.

Highlighted by

  • Nanowerk Spotlight, Dec 28, 2007, “DNA electronics in nanotechnology”
  • NewScientist Tech, Dec 4, 2007, “Nanoelectrodes could provide bird flu test”
  • NewScientist, “Nantube electrodes could provide avian flu test”
  • NanoScienceWorks, Jan 2008, “Nanotube electrodes can “match” DNA via signals”
  • Technology Reviews, February 13, 2008, “Wiring up DNA”
  • Nature Spotlight on a related article that appeared in Feb 2008 included our work.


E. Zeng, K. Mathee, and G. Narasimhan. IEM: an algorithm for iterative enhancement of motifs using comparative genomics data. Comput
Syst Bioinformatics Conf. 6:227-35.


D.K. Mills, J.A. Entry, K. Mathee, and P.M. Gillevet. Mini-Review: Assessing Microbial Community Diversity Using Amplicon Length Heterogeneity PCR. Soil Science Society of America Journal 71 March-April



L.I. Moreno, D. K. Mills, J. Entry, R.T. Sautter, and K. Mathee. Microbial metagenome profiling using Amplicon
Length Heterogeneity-Polymerase Chain Reaction (ALH-PCR) proves more effective than elemental analysis in discriminating soil specimens. Journal of Forensic Science 51:1315-1322.


D.K. Mills, J. A. Entry, J.D. Voss, P.M. Gillevet, and K. Mathee. An assessment of the hypervariable domains of the 16S rRNA genes for their value in
determining microbial community diversity: the paradox of traditional ecological indices. FEMS Microbiological Ecology 57:496-503.


A. L. Adonizio, K. Downum, B. C. Bennett, and K. Mathee. Anti-quorum sensing activity of medicinal plants in southern Florida. Journal of Ethnopharamocology 105:427-35.


J. Makemson, A. Eberhard, and K. Mathee. Simple electrospray mass spectrometry detection of acylhomoserine lactones. Luminescence 21:1-6


C. Yang, D. Mills, K. Mathee, Y. Wang, K. Jayachandran, M. Sikaroodi, P. Gillevet, J. Entry, G. Narasimhan. Ecoinformatics tools for microbial diversity studies: Supervised classification of amplicon length heterogeneity (ALH) profiles of 16S rRNA. Journal of Microbiological Methods 65: 49-62.



K.F. Kong, S.R. Jayawardena, S. D. Indulkar, A. del Puerto, C-L. Koh, N. Høiby, and K. Mathee. Pseudomonas aeruginosa AmpR is a global transcriptional factor that regulates expression of AmpC and PoxB b-lactamases, proteases, quorum sensing and other virulence factors. Antimicrobial Agents and Chemotherapy 49:4567-75.

  • Article selected for Journal Highlights in the ASM News December issue. A monthly issue that highlights one article per journal that describes new and exciting developments in microbial research.


K.F. Kong, S.R. Jayawardena, A. Del Puerto, L. Wiehlmann, U. Laabs, B. Tummler, and K. Mathee. Characterization of poxB, a chromosomal-encoded Pseudomonas aeruginosa oxacillinase. Gene 358:82-92


Y. Wang, C. Yang, K. Mathee, and G. Narasimhan. Clustering using Adaptive Self-Organizing Maps (ASOM) and Applications. Lecture Notes in Computer Science 3515: 944-951.


Y. Sun, Z. Deng, G. Narasimhan, and K. Mathee. Training set design for pattern discovery with applications to protein motif detection. Advances in Bioinformatics and its Applications: Series in Mathematical Biology and Medicine 8:240-251.


C. Yang, E. Zeng, K. Mathee, and G. Narasimhan. Querying a database of regulatory elements. Advances in Bioinformatics and its Applications: Series in Mathematical Biology and Medicine 8:81-92.



A.P. Stapper, G. Narasimhan, D.E. Ohman, J. Barakat, M. Hentzer, S. Molin, A. Kharazmi, N. Høiby, K. Mathee. Alginate production affects Pseudomonas aeruginosa biofilm development and architecture, but is not essential for biofilm formation. Journal of Medical Microbiology 53:679-690. 

  • It became one of the 50-most-frequently read articles, at one point ranking number 5.


X.H. Guo, Z.J. Song, H. Wu, P. Yan, X.J. Qin, K. Mathee, N. Høiby, B.J. Tang, X.Q. Qiu, Y.Q. Chen. Effects of pre-immunization with Bacillus Calmette Guerin vaccine on chronic P. aeruginosa lung infection in rats. Current Immunology 24:138-141. (In Chinese)



Z. Song, H. Wu, O. Ciofu, K.F. Kong, N. Høiby, J. Rygaard, A. Kharazmi, K. Mathee. Pseudomonas aeruginosa alginate is refractory to Th1 immune response and impedes host immune clearance in a mouse model of acute lung infection. Journal of Medical Microbiology 52:731-40.



G. Narasimhan, C. Bu, Y. Gao, X. Wang, N. Xu, K. Mathee. Mining protein sequences for motifs. Journal of Computational Biology 9:707-720.


Z.J. Song, H. Wu, K. Mathee, N. Høiby, and A. Kharazmi. Gerimax ginseng regulates both humoral and cellular immunity during chronic Pseudomonas aeruginosa lung infection. Journal of Alternative and Complementary Medicine 8:459-466



A. Morea, K. Mathee, M. J. Franklin, A. Giacomini, M. O’Regan and D. E. Ohman. Characterization of algG encoding C5-epimerase in the alginate biosynthetic gene cluster of Pseudomonas fluorescens. Gene 278:107-114.


H, Wu, Z. Song, M. Givskov, G. Doring, D. Worlitzsch, K. Mathee, J. Rygaard, and N. Hoiby. Pseudomonas aeruginosa mutations in lasI and rhlI quorum sensing systems result in milder chronic lung infection. Microbiology 147:1105-1113.



S. Malhotra, L.A. Silo-Suh, K. Mathee, and D.E. Ohman. Proteome analysis of the effect of mucoid conversion on global protein expression in Pseudomonas aeruginosa strain PAO1 shows induction of disulfide bond isomerase, DsbA. Journal of Bacteriology 182:6999-7006.


H. Wu, Song, Z.J., K. Mathee, M. Hentzer, J.B. Andersen, A. Heydorn, C. Moser, L. Eberl, S. Molin, N. Høiby, and M. Givskov. Detection of N-acylhomoserine lactones in lung tissues of mice infected with Pseudomonas aeruginosa. Microbiology 146:2481-2493.



K. Mathee, O. Ciofu, C. Sternberg, P.W. Lindum, J.I. Campbell, P. Jensen, A.H. Johnsen, M. Givskov, D.E. Ohman, S. Molin, N. Høiby, and A. Kharazmi. Mucoid conversion of Pseudomonas aeruginosa by hydrogen peroxide: a mechanism for virulence activation in the cystic fibrosis lung. Microbiology 145:1349-1357.

  • Article selected for Hot Off The Press in Microbiology Today 26:135; A quarterly issue that highlights new and exciting developments in microbial research.


K. Mathee, C.J. McPherson and D.E. Ohman. Posttranslational control of the algT (algU)-encoded s22 for expression of the
alginate regulon in Pseudomonas aeruginosa and localization of its antagonist proteins MucA and MucB (AlgN). Journal of Bacteriology 179:3711-3720.



K. Mathee, and M.M. Howe. Bacteriophage Mu Mor protein requires s70 to activate the Mu middle promoter. Journal of Bacteriology 175:5314-5323.


K. Mathee, and M.M. Howe. Function of the bacteriophage Mu middle operon. Virology 196:712-721.



K. Mathee, and M.M. Howe. Identification of a positive regulator of the Mu middle operon. Journal of Bacteriology 172:6641-6650.



K. Kalaimathee, C.L. Koh, and Y.F. Ngeow. Plasmid profiles of Neisseria gonorrhoeae in Peninsular Malaysia. Microbiology and Immunology 29:921-926.



C.L. Koh, K. Kalaimathee, and Y.F. Ngeow. Penicillinase-producing Neisseria gonorrhoeae in Peninsular Malaysia. Medical Journal of Malaysia 39:269-271.




M. Fernandez, M. Jaric, L. Schneper, J. Segal, E. Silva-Herzog, M. Campos, J. Fishman, M. Salathe, A.Wanner, J. Infante, K. Mathee, G. Narasimhan. A metagenomic approach to the airways microbiome of chronic obstructive pulmonary disease (COPD). Biomedical Engineering Conference (SBEC),
2013 29th Southern 151 – 152



G. Gonzalez, M. Doud, K. Mathee and G. Narasimhan. Computer-assisted bacterial identification using 16S rRNA sequence data. Book series: FMBE Proceedings 24:239-249. [PR]



C. Yang, E. Zeng, K. Mathee, and G. Narasimhan. Mining Regulatory Elements in the Plasmodium falciparum genome using gene expression data. Proceedings of CAMDA’04: Critical Assessment of Microarray Data Analysis, Durham, NC, p16-20, November 2004. [PR]



C.L. Koh, M.L. Yap, Y.S. Ooi, M.E. Lim, and K. Mathee. Screening of environmental water samples from Malaysia for bacteria producing autoinducers and inhibitors of quorum sensing. Persatuan Genetik Malaysia; University of Malaya; Ministry of Science, Technology & the Environment, Malaysia; and Ministry of Health, Malaysia. 25-27 March 2003; Kuala Lumpur. Proceedings of the 5th National Congress of Genetics. p162-163. [NonPR]


D. Ramos, A. Heydorn, C. Koh, K. Mathee. Loss of alginate production in mucoid Pseudomonas aeruginosa occurs via deregulation of the alternative sigma factor AlgT. Proceedings of the National Conference on Undergraduate Research (NCUR) 2003. p1-9 (9 pages). [PR]


D. Mills, J.A. Entry, K. Mathee, K. Jayachandran, R.E. Sojka, W.J. Busscher. Irrigated agriculture and tillage practices impact microbial community structure. Proceedings of the International Soil Tillage Research Organization, 16th Triennial Conference, July 2003, Brisbane, Australia. p749-754. [NPR]



A Kharazmi, K Mathee, ET Jensen, S Molin, N Høiby. Polymorphonuclear leukocytes and Pseudomonas aeruginosa biofilm. Clinical Microbiology and Infection, 1999


Y. Gao, K. Mathee, G. Narasimhan, X. Wang. Motif Detection in Protein Sequences. Proceedings of SPIRE’99, Cancun, Mexico. p 63-72 (10 pages). [PR]

Book Chapters



S. Pandey, K. Martins, and K. Mathee. Regulation of extracytoplasmic function sigma factor by proteolytic cascade: A comparison between Escherichia coli and Pseudomonas aeruginosa, Invited Book Chapter. John Wileys Publisher.


H. Kumari, D. Balasubramanian, and K. Mathee. Role of small RNAs in Pseudomonas aeruginosa virulence and adaptation, Invited Book Chapter, In Press. John Wileys Publisher.



M. Fernandez, V. Aguiar-Pulido, J. Riveros, W. Huang, J. Segal, E. Zeng, M. Campos, K. Mathee, E. Zeng, and G. Narasimhan, 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, p333-351, 2015.



D. Balasubramanian, S.K. Murugapiran, E. Silva-Herzog, L. Schenper, X. Yang, G. Tatke, G. Narasimhan and K. Mathee. Transcriptional regulatory Network in Pseudomonas aeruginosa. In Bacterial Gene Regulation and Transcriptional Networks. p195-248. M. Babu (Ed.), Horizon Press [PR]



E. Zheng, C. Ding, K. Mathee, L. Schneper and G. Narasimhan. Semantic similarity between genes and its applications in function prediction and functional network generation. Data mining: Medical, Health, Social and Biological Applications. D.E. Holmes (Ed.), Springer. [PR]



C. Yang, E. Zheng, K. Mathee, and G. Narasimhan. PlasmoTFBM: An intelligent queriable database for predicted transcription factor binding motifs in Plasmodium falciparum. Methods in Microarray Data Analysis V: 121-136. McConnell, Lin, Hurban (Eds.), Springer. [PR]



K. Mathee, A. Kharazmi and N. Høiby. Role of exopolysaccharide in biofilm matrix formation: The alginate paradigm. In, Molecular Ecology of Biofilms: Genetic Analysis. P 23-56 Edited by R.J.C. McLean and A.W. Decho. Horizon Scientific Press. [NonPR]



D.E. Ohman, D.E., K. Mathee, C.J. McPherson, C.A. DeVries, S. Ma, D.J. Wozniak and M. Franklin. Regulation of the alginate (algD) operon in Pseudomonas aeruginosa. In, Molecular biology of Pseudomonads. p472-483. Edited by T. Nakazawa, K. Furukawa, D. Haas, S. Silver. American Society for Microbiology, Washington, D.C. [NonPR]

Invited Extended Abstracts [NonPR]



K. Mathee, O. Ciofu, M. Givskov, D.E. Ohman, S. Molin, N. Høiby, and A. Kharazmi. Reactive oxygen species-mediated induction of Pseudomonas aeruginosa alginate production: a possible induction mechanism in cystic fibrosis lungs. Clinical Microbiology and Infection 5:5S8-9.


A. Kharazmi, K. Mathee, E. T. Jensen, S. Molin and N. Høiby. Polymorphonuclear leukocytes and Pseudomonas aeruginosa biofilms. Clinical Microbiology and Infection 5:5S27-28.


D.E. Ohman, S. Malhotra, S. Jain, K. Mathee, and L. A Silo-Suh. Alginate biosynthesis in Pseudomonas aeruginosa: a stress response. Clinical Microbiology and Infection 5:5S11-13.

Other Publications/Books [NonPR]


K. Mathee, Summary of the 1st international conference on Tropical Diseases organized by UniKL. In PetriDish. (2012)


K. Mathee. Magic of Life. Article written for the Sequentia Exhibit at the Patricia and Phillip Frost Art Museum, October 2010-January 2011;


K. Mathee, C.L. Koh, and M. T.J. Ai.  Bacteria cell-to-cell communication: A laboratory manual. Akademi Sains Malaysia”. 38 pages. 2000


K. Mathee, and C.L. Koh. Program and Abstract Book: 7th Asian Conference on Transcription (ACT-VII). 55 pages. 2002

Theses and Dissertation


Bacteriophage Mu middle operon (1992)

PhD Dissertation. University of Tennessee Medical School Memphis, Tennessee
Mentor: Prof. Martha M. Howe


Plasmids in Neisseria gonorrhoeae isolates (1986)M. Sc Thesis, University of Malaya, Malaysia. Mentor: Prof. Chong-Lek Koh


Evaluation of F1 crossbred (Local X German Fawn) for breeding soundness and effect of storage on semen quality (1984)
Honors Thesis, University of Malaya, Malaysia. Mentor: Prof. T.K. Mukharjee

Publications Outside Discipline


K. Mathee. Women in Science: A personal Reflection. FIU Diversity Exchange Magazine, Spring 2001. p12-13.