Dr. Murli Nair
- Associate Professor of Bioinformatics,
- BSc. University of Poona,
- MSc. University of Poona,
- PhD. Computational Biology University of Poona
- Office: Northside 160E
- Phone: 574-520-5068
- Email: mnair AT iusb.edu
Computational analysis of genetic macromolecules (DNA, RNA and proteins): Understanding the hidden order in genomes by in computo experiments; Developing algorithms for the prediction of biologically and functionally important regions; Support vector machines, Artificial neural networks and hidden markov modeling of biological sequences; Validating theoretical models using experimental observations; Design and development of biological databases; Understanding biological networks
- Nair, T. M. and Gribskov, M. Extracting biological knowledge from SVM models capable of distinguishing alternative and constitutive splicing (submitted)
- Nair, T. M., Li, H.R. and Fu, X.D. Profiling prostate cancer signatures by statistical analysis of mRNA isoform expression. Genome Informatics, P031-2 (2006)
- 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 66,4079-4088(2006)pdf file
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 11,1-10,(2005)pdf file
Eide,D., Clark, S., Nair, T.M.,Gehl, M., Gribskov,M., Guerinot,M.L. and Harper,J.
Charaterization 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)pdf file
Gribskov,M., Niedner, H. and Nair,T.M.
Perl in bioinformatics
In:Dunn, M.J., Jorde, L.B., Little, P.F.R. and Subramaniam, S.(Eds), Encyclopedia of Genetics,Genomics, proteomics and bioinformatics
Zheng, C.L.,Nair,T.M.,, Gribskov,M., Kwon, Y. S., Li, H. R. and Fu,XD.
A database designed to computationally aid an experimental approach to alternate splicing.
Pacific symposium on Biocomputing, pp 78-88, 2004 pdf file
Zheng,C.L., De Sa, V.R., Gribskov,M. and Nair,T.M.
On selecting features from splice junctions: An Analysis using information theoretic and machine learning approaches.
Genome Informatics 14, 73-83 (2003) pdf file
Nair,T. M., Zheng, C. L., Fink, J. L., Stuart, R. O. and Gribskov, M.
Rival Penalized Competitive Learning(RPCL): A topology-determining algorithm for analyzing gene expression data.
Computational Biology and Chemistry 27, 565-574 (2003) pdf file
Tchieu, J., Fana, F., Fink,J.L., Harper,J.,Nair, T.M.,, Niedner, R.H.,Smith, D.W.,Steube, K.,Tam,T.,Veretnik,S.,Wang, D. and Gribskov,M.
The PlantsP and PlantsT Functional Genomics Databases.
Nucleic Acids Research31,342-344(2003)pdf file
Reddy, B.V.B., Nair,T. M., Li, W.W., Shindyalov, I. N. and Bourne, P. E.
Conserved Amino Acid Positions (CKAAPs) in Proteins: Implications in Protein stability and structural integrity
Nair,T. M., Myszka, D.G. and Davis, D.R
Sufrace plasmon resonance kinetic studies of the HIV TAR RNA kissing hairpin complex and its stabilization by 2-thiouridine modification
Nucleic Acids Research 28, 1935-1940 (2000)pdf file
Evidence for intrinsic DNA bends within the human cdc2 promoter
FEBS. Lett.422,94-98 (1998)pdf file
Calliper randomization: A neural network based analysis of E.coli ribosome binding sites
J.Biomol. Struct. and Dyn15(3),611-617(1997)pdf file
Nair, T. M.,
Artificial Neural Networks in Biological Sciences.
In: Elements of Artificial neural networks with selected applications in chemical engineering and chemical and biological sciences (ed: Tambe, S.S., Kulkarni,B.D. and Deshpande, P.B ) pp. 395-437 (1996)pdf file
Nair,T. M., Madhusudan, K, Nagaraja,V, Kulkarni, B. D, Majumdar, H.K, Singh, R
Theoretical permutation gel electrophoretic analysis of a curved DNA fragment located in circular permutation.
Electrophoresis 17, 633-641 (1996)pdf file
Nair,T. M., Tambe, S. S and Kulkarni, B.D
Analysis of transcription control signals using artificial neural networks
Compt-Appl-Biosci 11(3), 293-300 (1995)pdf file
Nair, T. M., Nagaraja, V., and Kulkarni, B. D.
Differential binding of RNA polymerase to the wild type Mu mom promoter and its C independent mutant: A theoretical analysis
Biophysical Chemistry 53(3), 241-245 (1995)pdf file
Nair,T. M. and Kulkarni, B.D
On the role of a mutational database in building artificial intelligence models for understanding gene expression
Cell Biochemistry and Biophysics 27(3), 227-230 (1995)pdf file
Nair, T. M. Madhusudan, K., Nagaraja, V., Kulkarni, B.D., Majumdar, H.K, Singh, R
On the mobility behavior of a curved DNA located in circular permutation
FEBS. Lett.351,321-324(1994)pdf file
Nair, T.M., Tambe, S. S and Kulkarni-B.D
Application of artificial neural network for prokaryotic transcription terminator prediction
FEBS. Lett.346,273-277(1994)pdf file
Nair, T. M. and Kulkarni, B. D.
On the consensus structure within the E.coli promoter
Biophysical Chemistry48(3),383-393(1994)pdf file