Name: Murlidharan Nair

Title: Associate Professor of Bioinformatics

Office:  160E Northside Hall

Phone: 574-520-5068

Email: mnair@iusb.edu

Web Page: http://bioinformatics.iusb.edu

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) $620,091.00

Selected Publications ~

• 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 ~

• Spring 2018
• I400/L391 –Introduction to Genomics
• L403 –Biology Senior Seminar(online)
• A106 –Introduction to computing (online)
• Fall 2018
• L391 –Biology of Cancer
• L220 –Introduction to Biostatistics (online)
• A106 –Introduction to computing