Publications - 2004
Anand, B., Namboori, S., Sandhya, S. and Srinivasan, N. (2004).
Influence of protein structural similarities in adding value to genome data.
Indian Journal of Biotechnology (In press).
Banerjee, B., Balasubramanian, S., Ananthakrishna, G., Ramakrishnan, T.V. And Shivashankar, G.V. (2004).
Tracking operator state fluctuations in gene expression in single cells.
Biophysical Journal, 86, 1-8.
Banerjee, S., Lee, J., Venkatesh, K., Wu, C-F. And Hasan, G. (2004).
Loss of flight and associated neuraonal rhythmicity in inositol 1,4,5-trisphosphate
receptor mutants of Drosophila.
Journal of Neuroscience (In press).
Bhaduri, A., Pugalenthi, G and Sowdhamini, R. (2004).
PASS2: an automated database of protein alignments organised as structural superfamilies.
BMC Bioinformatics, 5, 35.
Bhaduri, A., Pugalenthi, G. and Sowdhamini, R. (2004)
PASS2 Nucleic Acids Research,
Bhaduri, A., Pugalenthi, G., Gupta, N. and Sowdhamini, R. (2004).
iMOT: an interactive package for the selection of spatially interacting motifs.
Nucleic Acids Research (In press).
Bhaduri, A., Ravishankar, R. and Sowdhamini, R. (2004).
Conserved spatially interacting motifs of protein superfamilies: Application to
fold recognition and function annotation of genome data.
Proteins: Structure Function Genetics, 54, 657-70.
Bhalla, U.S. (2004).
Signaling in small subcellular volumes. I. Stochastic and diffusion effects on
Biophysical Journal, 87, 733-744.
Bhalla, U.S. (2004).
Signaling in small subcellular volumes. II. Stochastic and diffusion effects on
synaptic network properties.
Biophysical Journal, 87, 745-753.
Bhalla, U.S. (2004).
Models of cell signaling pathways.
Current opinion in Genetics and Development, 14, 375-381.
Bhavesh, N.S., Juneja, J., Udgaonkar, J.B. And Hosur, R.V. (2004).
Native and non-nativeconformational preferences in the urea-unfolded state of barstar.
Protein Science (In press).
Beena, K., Udgaonkar, J. B. and Varadarajan, R. (2004).
Effect of signal peptide on the stability and folding kinetics of maltose binding protein
Biochemistry, 43, 3608-3619.
Blaise, M., Sowdhamini, R., Raghu Prasad Rao, M. and Pradhan, N. (2004).
Evolutionary analysis of ionotropic glutamate receptor sequences and modelling
interactions of agonists with different NMDA receptor subunits.
Journal of Molecular Modeling (In press).
Chakrabarti, S., John, J. and Sowdhamini, R. (2004).
Improvement of comparative modeling by the application of conserved motifs amongst
distantly related proteins as additional restraints.
Journal of Molecular Modeling,10, 69-75.
Chakrabarti, S. and Sowdhamini, R. (2004)
Regions of minimal structural variation among members of protein domain superfamilies:
Application to remote homology detection and modelling using distant relationships.
FEBS Letters, 569, 31-36.
Chakrabarti, O., Veeraraghavalu, K., Tergaonkar, V., Liu, Y., Androphy, E. J., Stanley, M, A. & Krishna. S. (2004)
HPV 16 E6 83 amino acid variants enhance E6 mediated MAPK signalling and
differentially regulate tumorigenesis by Notch signalling and oncogenic Ras.
Journal of Virology, 78, 5934-5945.
Dani A, Chaudhry A, Mukherjee P, Rajagopal D, Bhatia S, George A, Bal V, Rath S, Mayor S. (2004).
The pathway for MHCII-mediated presentation of endogenous proteins involves
peptide transport to the endo-lysosomal compartment.
J Cell Sci 117, 4219-30.
Dutta, D., Anant, S., Ruiz-Gomez, M., Bate, M and VijayRaghavan, K. (2004).
Founder myoblasts and fibre number during adult myogenesis in Drosophila
Development, 131, 3761-3772.
Dhawan, S. and Syal S. (2004)
Mechanisms of Memory-In Dialogue with Susumu Tonegawa.
Current Science, 86(6), 763-765.
Hayashi, L.M., Choi, S., Rao, B.S.S., Jung, Y., Lee, H. K., Zhang, D., Chattarji, S.,
Kirkwood, A. and Tonegawa, S. (2004).
Altered Cortical Synaptic Morphology and Impaired Memory Consolidation in
Forebrain-Specific Dominant-Negative PAK Transgenic Mice.
Neuron, 42, 773-787.
Jhaveri, D., S. Saharan, A. Sen and V. Rodrigues (2004).
Positioning glomeruli in the olfactory lobe of Drosophila by Robo signaling.
Innis, C.A., Anand, P.A. And Sowdhamini, R. (2004).
Prediction of functional sites in proteins using conserved functional group analysis.
Journal of Molecular Biology, 337, 1053-68.
Joshi, R., Venkatesh, K., Srinivas, R., Nair, S. and Hassan, G. (2004).
Genetic dissection of itpr gene function reveals a vital requirement
in aminergic cells of Drosophila larvae.
Genetics, 166, 225-236.
Mayor, S, and Riezman, H. (2004).
Sorting GPI-anchored proteins.
Molecular Cell Biology, 5, 110-120.
Mayor, S, and Rao, M. (2004).
Rafts: Scale dependent active lipid dependent organization at the cell surface.
Traffic, 5, 231-240.
Parikh N, Sade H, Kurian L and Sarin A. (2004)
The Bax amino-terminus is required for negative regulation by the MEK and
Akt signalingpathways in T cells.
Journal of Immunology (In press).
Pradeep, L. and Udgaonkar, J.B. (2004).
Effect of salt on the urea-unfolded form of barstar probed by m value mesurements.
Biochemistry, 43 (In press).
Pradeep, L. and Udgaonkar, J.B. (2004).
Osmolytes induce structure in an early intermediate on the folding pathway of barstar.
Journal of Biological Chemistry, (In press).
Roopa, T., Bhattacharya, S., Kumar, N. and Shivashankar, G.V. (2004).
Dynamics of membrane tubulation and DNA assembly.
Biophysical Journal (In press).
Sabharanjak, S., and Mayor, S. (2004).
Folate receptor endocytosis and trafficking.
Advanced Drug Delivery Reviews, 56, 1099-1109.
Sade, H., Khandre, N. S., Mathew, M. K. and Sarin, A. (2004).
The mitochondrial phase of the glucocorticoid-induced apoptotic response in
thymocytes comprises sequential activation of adenine nucleotide transporter
(ANT)-independent and ANT-dependent events.
European Journal of Immunology, 34, 119-125.
Sade, H., Krishna, S. and Sarin, A. (2004).
The anti-apoptotic effect of Notch-1 requires p56lck-dependent, Akt/PKB-mediated
signaling in T cells.
Journal of Biological Chemistry, 4, 2937-2944.
Sade, H. and Sarin, A. (2004).
Reactive oxygen species regulate quiescent T cell apoptosis via the BH3-only
pro-apoptotic protein BIM.
Cell Death and Differentiation, 11, 416-423.
Saura, C.A., Choi, S., Beglopoulos, V., Malkani, S., Zhang, D., Rao, B.S.S., Chattarji, S.,
Kelleher III, R.J., Kandel, E.R., Duff, K., Kirkwood, A. and Shen, J. (2004).
Loss of presenilin function causes impairments of memory and synaptic
plasticity followed by age-dependent neurodegeneration.
Neuron, 42, 23-36.
Sen, A., Kuruvilla, D., Pinto, L., Sarin, A. and Rodrigues, V. (2004).
Programmed cell death and context dependent activation of the EGF pathway
regulate gliogenesis in the Drosophila olfactory system.
Mechanisms of Development,121, 65-78.
Sharma, P., Varma, R., Sarasij, R.C., Ira., Gousset, K., Krishnamoorthy, G., Rao, M. and Mayor, S. (2004).
Nanoscale organisation of multiple GPI-anchored proteins in living cell membranes.
Cell, 116, 577-589.
Sinha, D., Banerjee, B., Bhattacharya, D., Meeran, F. and Shivashankar, G.V. (2004).
Development of single molecule tracking confocal fluorescence
microscope for gene expression analysis
Current Science (In press).
Srikanth, S and Hasan, G. (2004).
Structure and function of Inositol 1,4,5 -trisphosphate Receptors.
Current Science, 86, 1513-1523.
Srikanth, S., Wang, Z., Tu, H., Nair, S,, Mathew, M.K., Hasan, G. and Ilya Bezprozvanny, I. (2004).
Functional properties of Drosophila melanogaster inositol
1,4,5-trisphosphate receptor mutants.
Biophysics Journal, 86, 3634-3646.
Srikanth, S., Wang, Z., Hasan, G. and Bezprozvanny, I. (2004).
Functional properties of a pore mutant in the Drosophila melanogaster
inositol 1,4,5-trisphosphate receptor.
FEBS Letters (In press).
Sridevi, K., Lakshmikanth, G., Krishnamoorthy, G. and Udgaonkar, J.B. (2004).
Increasing stability reduces conformational heterogeneity in a protein
Journal of Molecular Biology (In press).
Sudarslal, S., Singaravadivelan G., Sharma, S.P., Sikdar, S.K., Krishnan, K.S. and Balram, P. (2004).
Isolation and characterization of biologically active peptides from Indian Marine Snails.
Proceedings of the national seminar on new frontiers in marine bioscience research, 25-33.
Sudarslal, S., Singaravadivelan, G., Ramasamy, P., Ananda, K., Sarma, S.P., Sikdr,
S.K., Krishnan, K.S. and Balaram, P. (2004).
A novel 13 residue acyclic peptide from the marine snail, conus monile,
targets potassium channels.
Biochemistry, Biophysics Research Communication. 317, 682-688.
Varshney, A., Chanda, B. and Mathew, M.K. (2004)
Arranging the elements of the potassium channel: The T1 domain
occludes the cytoplasmic face of the channel.
European Biophysics Journal, 33, 370-376.
Varshney, A. and Mathew, M.K. (2004).
Architecture of a membrane protein: The voltage-gated K+ channel.
Current Science, 87, 166-174.
Vasudeva, K. and Bhalla, U.S. (2004).
Adaptive stochastic-deterministic chemical kinetic simulations.
Bioinformatics, 20, 78-84.
Veeraraghavalu, K., Pett, M., Kumar, R. V., Nair, P., Rangarajan, A., Stanley, M. A & Krishna. S. (2004)
Papillomavirus mediated neoplastic progression is associated with reciprocal changes
in Jagged1 and Manic Fringe expression linked to Notch activation.
Journal of Virology, 78, 8687-8700.
Vig, M., Srivastava, S., Kandpal, U., Sade, H., Lewis, V., Sarin, A., George, A., Bal, V., Durdik,
J.M. And Rath, S. (2004).
Inducible nitric oxide synthase in T cells regulates T cell death and immune memory.
Journal of Clinical Investigation, 113, 1734-42.
Vinayagam, A., Pugalenthi, G., Rajesh, T. and Sowdhamini, R. (2004).
DSDBASE: A consortium of native and modelled disulphide bonds in proteins.
Nucleic Acid Research, 32, D200-202.