Dr. Murli Nair
Associate Professor of Bioinformatics,
BSc. University of Poona,
MSc. University of Poona,
PhD. Computational Biology University of Poona
Office: Northside 160E
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
RNA 11,1-10,(2005)pdf file
,D., Clark, S., Nair, T.M. , Gehl, M., Gribskov ,M., Guerinot ,M.L.and Harper ,J. Charaterizationof 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.
symposiumon Biocomputing, pp 78-88, 2004pdf 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 Research28, 1935-1940 (2000)pdf file
- Nair,T. M.
Evidence for intrinsic DNA bends within the human cdc2 promoter
FEBS. Lett.422,94-98 (1998)pdf file
- Nair,T. M.
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.
Electrophoresis17, 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-Biosci11(3), 293-300 (1995)pdf file
- Nair, T. M., Nagaraja, V., and Kulkarni, B. D.
Differential binding of RNA polymerase to the
wild typeMu mom promoter and its C independent mutant: A theoretical analysis
Biophysical Chemistry53(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 Biophysics27(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