Dr. Murli Nair

Dr. Murli Nair

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@iusb.edu

Research

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

Publications

• Shembarger, R. R., Romito, L. M., and Nair, T. M*., Are there gastric cancer biomarkers in salivary transcriptome? (Submitted/in revision) pdf file(Abstract of the preliminiary work presented at IADR conference)
• Fonseca,T.L., Garcia,T., Fernandes,G. W., Gereben, B., Nair,T.M., and Bianco, A.C. Neonatal thyroxine activation modifies epigenetic programming of the liver. Nature communications 12, 4446 (2021). https://doi.org/10.1038/s41467-021-24748-8) pdf file
• Astarita E.M, Maloney S.M, Hoover C.A, Berkeley B.J, VanKlompenberg M.K, Nair T.M, Prosperi J.R.. Adenomatous Polyposis Coli loss controls cell cycle regulators and response to paclitaxel in MDA-MB-157 metaplastic breast cancer cells. PLoS One. 2021 Aug 9;16(8):e0255738. doi: 10.1371/journal.pone.0255738. PMID: 34370741; PMCID: PMC8351968. pdf file
• Nair, T. M., Building and interpreting artificial neural network models for biological systems Methods in Molecular biology,2021;2190:185-194. doi: 10.1007/978-1-0716-0826-5_8. PMID: 32804366. pdf file
• Nair, T. M., Statistical and artificial neural network-based analysis to understand complexity and heterogeneity in preeclampsia Computational Biology and Chemistry 75,222-230 (2018) pdf file
• Nair, T. M., Understanding heterogeneity in pregnancy-associated breast cancer Bioinformatics and Biomedicine(BIBM)IEEE International Conference, Washington, DC,1192-1196 (2015) pdf file
• Nair, T. M., Analysis of isoform expression from splicing array using multiple comparisons Methods Mol Biol 802, 113-121(2012)pdf file
• Nair, T. M Sequence periodicity in nucleosomal DNA and intrinsic curvature BMC Structural Biology, 10(Suppl1):S8 (2010) pdf file
• Nair, T. M On selecting mRNA isoform features for profiling prostate cancer Computational Biology and Chemistry 33(6), 421-428 (2009 ) pdf file
• Nair, T. M. How does the periodicity associated with nucleosomal DNA reflect on its intrinsic curvature? Proceedings of the IEEE international conference on Bioinformatics and Biomedicine workshops, 189-193 (2009).pdf file
• 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
  Supplementary data1
  Supplementary data2
  Supplementary data3
  Supplementary data4
  
• 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
  Web server http://maase.bioinformatics.iusb.edu
• 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 pdf file
  
• 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
  Protein ScienceVol9(suppl.1),78,(2000)[Abstract]
  
• 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
  
• 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.
  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