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Faculty Information

Deepak Saxena, MS, PhD.
Assistant Professor
Basic Science and Craniofacial Biology
Room 921-B Dental Center, 421 First Avenue
Fax: 212-995-4087



1988 BS (Zoology, Physiology) MS University of Baroda, India
1990 MS (Microbiology) MS University of Baroda, India
1996 DBM (Business Management) NM Institute of Management Studies, Mumbai, India
1999 Ph.D. (Microbiology) MS University of Baroda, India
1999-2005 Postdoc New York University


Research Interests / Professional Overview:

We are trying to establish the association between the oral micobiota, chronic inflammation and carcinogenesis. Using squamous cell carcinomas (SCC) and osteonecrosis of the jaw (ONJ) as a model, we want to develop “unique bacterial signature” and identify various bacteria which are predominantly present in SCC and ONJ. The other focus area is to use comparative genomics approach in determining the difference in the genomic composition of bacteria. These patterns of genomic variation across virulent bacteria or the differences between virulent and non virulent strains are used in interpreting both the genomic history of an organism and the functional interpretation of the genomic organization. We use suppression subtractive hybridization and 454 pyrosequencing to identify the genomic variation in the virulent bacteria isolated from subjects with SCC, ONJ or dental caries. Using computer-based approach such as machine learning techniques along with variation in gene patterns we classify bacterial strains involved in human health and disease. Our ultimate goal is to develop microbial/molecular markers for early risk assessment in developing SCC, ONJ and dental caries.


Current Funding:

NIH: Clinical and Translational Science Center, Weill Cornell Medical Center


Pub Med Articles:

Saxena, D


Representative Publications:

Saxena, D., Caufield, PW., Li, Y., Brown, S., Song, J., and Norman, R. 2008. Genetic Classification of Severe Early Childhood Caries Using Subtracted DNA Fragments from Streptococcus mutans. J. Clin. Microbiol. 46:2868-73.

Icoz, I., Saxena, D., Andow, D., Zwahlen, C. and Stotzky, G. 2008. Microbial populations and enzyme activities in soil in situ under transgenic corn expressing Cry proteins from Bacillus thuringiensis. J. Environ. Quality. 37: 647 – 662.

Li, Y., Ge, Y., Saxena, D., Caufield, PW. 2007. Genetic profiling of the oral microbiota associated with severe early childhood caries. J. Clin. Microbiol.45:81-7.

Chen, Z., Saxena, D., Ge, Y., Caufield, P. W., and Li, Y. 2007. Species-specific primers for detection and quantification of Streptococcus mutans in clinical samples. FEMS Microbiol 272:154-62.

Caufield, P.W., Saxena, D., Fitch, D., Li, Y. 2007. Population Structure of Plasmid-Containing Strains of Streptococcus mutans, a Member of the Human Indigenous Biota. J. Bacteriol. 189:1238-43.

Li, Y., Saxena, D., Barnes, VM., Trivedi, HM., Ge, Y., and Xu, T. 2006. PCR-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota. Oral Microbiol. Immunol. 21:333-339.

Saxena, D., Li, Y., Caufield, PW. 2005. Unique Bacterial Gene Segments from Streptococcus mutans with Potential Relevance to Dental Caries Identified by Subtraction DNA Hybridization. J. Clin. Microbiol. 43,3508-3511.

Saxena, D., Stewart, N. C., Altosaar, I., Shu, O., Stotzky, G., 2004. Larvicidal Cry proteins from Bacillus thuringiensis (Bt) are released in root exudates of transgenic Bt corn, potato, and rice but not of Bt canola, cotton, and tobacco plants. Plant Physiol. Biochem. 5, 383-7.

Saxena, D., Flores, S., and Stotzky, G. 2002. Vertical movement in soil of insecticidal Cry1Ab protein from Bacillus thuringiensis. Soil Biol. Biochem. 34: 111-120.

Saxena, D., Flores, S., and Stotzky, G. 2002. Bt toxin is released in root exudates from 12 corn hybrids representing three transformation events. Soil Biol. Biochem. 34: 133-137.

Saxena, D., Ben-Dov, E., Manasherob, R., Barak, Z., Boussiba, S., and Zaritzky, A. 2002. A UV tolerant mutant of Bacillus thuringiensis subsp. kurstaki producing melanin. Curr. Microbiol. 44: 25-30.

Saxena, D. and Stotzky, G. 2001. Bt corn has a higher lignin content than non-Bt corn. Am. J. Bot. 88:1704-1706.

Manasherob, R., Zaritzky, A., Ben-Dov, E., Saxena, D., Barak, Z., and Einav, M. 2001. Effect of accessory proteins P19 and P20 on cytolytic activity of Cyt1Aa from Bacillus thuringiensis subsp israelensis in Escherichia coli. Curr. Microbiol. 43: 355-364.

Saxena, D. and Stotzky, G. 2001. Bt toxin is not taken up from soil by plants. Nature Biotech. 19: 199.

Saxena, D. and Stotzky, G. 2001. Bacillus thuringiensis (Bt) toxin released from root exudates and biomass of Bt corn has no apparent effect on earthworms, nematodes, protozoa, bacteria, and fungi in soil. Soil Biol. Biochem. 33:1225-1230.

Saxena, D., Flores, S., and Stotzky, G. 1999. Insecticidal toxin in root exudates from Bt corn. Nature 402:480.

Book Chapter

Saxena, D. and Stotzky, G. 2003. Fate and Effects in Soil of the Insecticidal Toxins from Bacillus thuringiensis . In Transgenic Plants. ICGEB Biosafety and Italian Ministry of the Environment publication, Trieste, Italy pp. 7-83.