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Faculty Information

Deepak Saxena, MS, PHD

Deepak Saxena, MS, PhD

Associate Professor
Basic Science and Craniofacial Biology
Room 921-B Dental Center, 421 First Avenue
Phone: 212-998-9256
Fax: 212-995-4087


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


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. We use microbiome and metagenomic sequencing methods to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the interactions between species from sequence data. 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. Further, we utilize systems biology and machine learning approaches to classify bacterial strains involved in human health and disease.



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

Lustgarten Foundation


Complete listing available on the NYU Health Sciences Library site.

Search PubMed for articles.

Smruti Pushalkar, Xin Li, Zoya Kurago, Lalitha Ramanathapuram, Satoko Matsumura, Kenneth Fleisher, Robert Glickman, Wenbo Yan, Yihong Li, and Deepak Saxena. 2014. Oral Microbiota and Host Innate Immune Response in Bisphosphonate-Related Osteonecrosis of the Jaw. International Journal of Oral Science, Nature Publish Group. 1-8.

Contantinos P. Zambirinis, Smruti Pushalkar, George Miller and Deepak Saxena. 2014 Pancreatic Cancer, Inflammation and Microbiome The Cancer Journal: The Journal of Principles & Practice of Oncology. 20:195-202.

Liu L, Pushalkar S, Saxena D, LeGeros RZ, Zhang, Y. 2014. Antibacterial property expressed by a novel calcium phosphate glass. JBMR Appl Biomater. 102:423-9

Fleisher KE, Jolly A, Chippada-Venkata UD, Norman RG, Saxena D, Glickman RS. 2013. Osteonecrosis of the Jaw Onset Times are Based on the Route of Bisphosphonate Therapy. J Oral Maxillofac Surg. 71: 513-519.

Kenneth E. Fleisher, Anu Jolly, Robert G. Norman, Deepak Saxena, Robert S. Glickman, 2012. Duration of bisphosphonate therapy and association with osteonecrosis of the jaw. Journal of Oral and Maxillofacial Surgery. 71:513-9

Liu G, Saxena D, Chen Z, Norman RG, Phelan JA, Laverty M, Fisch GS, Corby PM, Abrams W, Malamud D, Li Y. 2012. HIV infection affects Streptococcus mutans levels, but not genotypes. J Dent Res. 91:834-40. Cover image for the September issue of the Journal of Dental Research

Smruti Pushalkar, Xiaojie Ji, Yihong Li, Cherry Estilo and Deepak Saxena 2012. Characterizing oral microflora associated with squamous cell carcinoma tissues. BMC Microbiology. 20:12:144.

Teixeira AH, Pereira ES, Rodrigues LKA, Saxena D, Duarte S, Zanin ICJ. 2012. The photodynamic antimicrobial chemotherapy effect on in vitro and in situ biofilms. Caries Research. 46:549-554

Xi Wei, Smruti Pushalkar, Cherry Estilo, Choyi Wong, Azeez Farooki, Monica Fornier, George Bohle, Joseph Huryn, Yihong Li, Stephen Doty and Deepak Saxena 2012. Molecular Profiling of Oral Microbiota in Jaw Bone Samples of Bisphosphonate Related Osteonecrosis of the Jaw. Oral Disease. 18:602-12

Saxena, D., Li, Y., Pei, Z, Poles, M, Abrams, WR, Malamud, D. 2012. Human microbiome and HIV/AIDS. Curr HIV.AIDS Rep. 9:44-51

Xiaojie Ji, , Smruti Pushalkar, Yihong Li, Robert Glickman, Kenneth Fleisher, and Deepak Saxena. 2012. Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Oral Disease. 18:85-95

Chen Z, Trivedi HM, Chhun N, Varnes MV, Saxena D, Xu T, Li Y*. Using DGGE and 16S rRNA gene sequence analysis to evaluate changes in oral bacterial composition. Chinese Journal of Dental Research. 2011;14:95-103.

S. Duarte, S. P. Kuo, R. M. Murata, C. Y. Chen, D. Saxena, K. J. Huang, and S. Popovic. 2011. Air plasma effect on dental disinfection. Physics of Plasmas Physics of Plasmas 2011;18(7):073503

Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D. 2011. Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol Med Microbiol. 61:269-77 PMCID: PMC3078631

Kenneth E. Fleisher, Garrett Welch, Shailesh Kottal, Ronald G. Craig Deepak Saxena, Robert S. Glickman. 2010. Predicting Risk for Bisphosphonate-Related Osteonecrosis of the Jaws: CTX vs. Radiographic Markers. Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology and Endodontology. 110:509-516. PMID: 20674404

Liu G, Saxena D, Deng H, Norman RG, Chen Z, Abrams WR, Malamud D, Li Y. 2010. Effect of protease inhibitors on the quantitative and qualitative assessment of oral microorganisms. FEMS Microbiol Lett. 312:63-70. PMCID: PMC3018767

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.

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

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

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