Education
- 1996 - Ph.D. University of Poona
- 1990 - MSc. University of Poona
Research Interests
- Cancer Genome and transcriptome analysis
- Understanding sequence and structural patterns in RNA
- Sequence periodicity and Nucleosome positioning
- Understanding chromosomal structural rearrangements by paired end sequencing
- Using splicing arrays to understand the expression of isoforms in different cell types and tissues to identify biomarkers
- Developing and using machine learning methods to understand biological data
Recent Grants
- Analysis of cancer transcriptome: choosing target features that function pleiotropically (IUSB Faculty research grant) $8500
- Acquisition of a computer server for research, research training and education in the STEM departments at Indiana University South Bend. (NSF) $ 47,042
- “Analysis of tumor genomes” (IUSB Faculty research grant) $8500
- “Online course: Applications to Data Mining” (Center for distance learning) $5000
- “Online course development: Introduction to Genomics” (Center for distance learning)$5000
- “Online course development: Introduction to Biostatistics” (Center for distance learning)$5000
- “Understanding the role of intrinsic DNA curvatures in compacting DNA into chromosomes” (IUSB Faculty research grant) $8500
- “Delineating alternative splice events from cancer transcriptome data” (IUSB Faculty research grant) $8500
- “Extracting characteristic features associated with alternatively and constitutively spliced junctions using learning models” (IUSB Faculty research grant) $8500
- “Attracting and retaining Computer Science and Informatics Students” (IUSB Curriculum Development Grant) $3000
- Statistical analysis of microarray data (IUSB Faculty research grant) $6000
- Sequence and structural patterns in RNA splicing (NSF) $620,091
Selected Publications
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- Nair, T. M. Understanding Heterogeneity in Pregnancy-Associated Breast Cancer. In: Proceedings of the IEEE international conference on Bioinformatics and Biomedicine workshops, 1192-1196 (2015)
- Nair, T. M. Analysis of isoform expression from splicing array using multiple comparisons. Methods Mol Biol. (802), 113-21 (2012)
- Nair, T. M., Using learning representation as a means to infer biological functionality. In: Proceeding of the Midwest conference on Artificial intelligence and cognitive science Eds: Vrajitoru D. 51-54 (2010)
- Nair, T.M. Sequence periodicity in nucleosomal DNA and intrinsic curvature BMC Structural Biology 10(supp 1):s8 (2010)
- Nair, T. M. On selecting mRNA isoform features for profiling prostate cancer. Computational Biology and Chemistry 33(6), 421-428 (2009 )
- Nair, T. M. How does the periodicity associated with nucleosomal DNA reflect on its intrinsic curvature? In: Proceeding of the IEEE International conference on Bioinformatics and Biomedicine workshops, 189-193 (2009)
- Li, H.R., Wang-Rodriguez, J., Nair, T.M, Yeakley, J.M.,Kwon, Y-S, Bibikova, M., Zheng, C., Zhou, L., Zhang, K., Downs, T., Fu XD. and Fan, J-B Two-Dimensional Transcriptome Profiling: Identification of Messenger RNA Isoform Signatures in Prostate Cancer from Archived Paraffin-Embedded Cancer Specimens. Cancer Research 66(8), 4079-4088 (2006)
- Zheng, C.L., Kwon, Y.S., Li, H.R., Zhang, K., Coutinho-Mansfield, G., Yang, C., Nair, T.M, Gribskov M, Fu XD. MAASE: An alternative splicing database designed for supporting splicing microarray applications RNA 11(12), 1-10 (2005)
- Eide, D., Clark, S., Nair, T.M., Gehl, M., Gribskov, M., Guerinot, M.L. and Harper, J. Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biology 6, R77.1-R77.13 (2005)
- Gribskov, M., Niedner, H. and Nair, T.M. Perl in bioinformatics In: Encyclopedia of Genetics,Genomics, proteomics and bioinformatics Eds: Dunn, M.J., Jorde, L.B., Little, P.F.R. and Subramaniam, S. Vol 8, 3594-3603 (2005).
Teaching
- INFO-I 421 –Applications of Data Mining
- INFO-I 400/BIOL-L 391 –Introduction to Genomics
- BIOL-L 403 –Biology Senior Seminar(online)
- BIOL-L 391 –Biology of Cancer
- BIOL-L 220 –Introduction to Biostatistics (online)
- CSCI-C 101 –Programming in C++
- CSCI-A 106 –Introduction to computing (online)
- CSCI-A 106 –Introduction to computing
