2005

Anderson CNK, Ramakrishnan. U, Chan YL & Hadly EA. (2005). 
Serial SIMCOAL: A population genetic model for data from multiple populations and points in time. 
Bioinformatics. 21:1733-1733-1734.

Anil, V.S., Krishnamurthy, P., Kuruvilla, S., Sucharitha, K., Thomas, G. and Mathew, M.K. (2005). 
Regulation of the uptake and distribution of Na+ in shoots of rice (Oryza sativa) variety Pokkali: Role of Ca2+ in salt tolerance response, 
Physiologia Plantarum, 124, 451-464.

Ayyub, C., Sen, A., Gonsalves, F., Kishan, B., Bhandari, P., Shashidhara, L. S., Krishna, S. and Rodrigues, V. (2005). 
Cullin-5 plays multiple roles in cell fate specification and synapse formation during Drosophila development. 
Developmental Dynamics, 232, 865-875.

Banerjee S. and Hasan, G. (2005), 
The InsP3 receptor: its role in neuronal physiology and neurodegeneration. 
Bioessays 27, 1035-1047.

Bhaduri, A. and Sowdhamini, R. (2005). 
Diversity of phosphatases: Study in bacterial and archael genomes 
in 'Mathematical Biology: Recent trends' Peeyush Chandra and B.V. Rathish Kumar (Eds) Copyright © 2006 Anamaya Publishers, New Delhi, India.

Bhaduri, A. and Sowdhamini, R. (2005). 
Genome-wide survey of prokaryotic O-protein phosphatases. 
Journal of Molecular Biology 352, 736-752.

Blaise, M., Bhattacharyya, D., Sowdhamini, R. and Pradhan, N. (2005). 
Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: A molecular dynamics study. 
J Biomol Struct Dyn, 22, 399-410.

Blaise, M.C., Sowdhamini, R. and Pradhan, N. (2005). 
Comparative analysis of different competitive antagonists interaction with NR2A and NR2B subunits of N-methyl-D-aspartate (NMDA) ionotropic glutamate receptor. 
Journal of Molecular Model.

Chakrabarti, S., Anand, P., Bharadwaj, N., Pugalenthi, G. and Sowdhamini, R. (2005). 
SCANMOT: Searching for similar sequences using simultaneous scan of multiple sequence motifs. 
Nucleic Acid Research, 33, 274-276.

Chaudhry, A., S.R. Das, A. Hussain, S. Mayor, A. George, V. Bal, S. Jameel, and S. Rath. (2005). 
The Nef protein of HIV-1 induces loss of cell surface costimulatory molecules CD80 and CD86 in APCs. 
Journal of Immunol.175, 4566-74.

Dutta, D. and VijayRaghavan, K. (2005). 
Metamorphosis and the formation of the adult musculature. 
In Muscle Development in Drosophila. (ed. Helen Sink), Landes Biosciences.

Dutta, D., Shaw, S., Maqbool, T., Pandya, H. and VijayRaghavan, K. (2005). 
Drosophila heartless acts with heartbroken/Dof in muscle founder differentiation. 
PLOS Biology 3, e337.

Gaurav, K., Gupta, N. and Sowdhamini, R. (2005).
FASSM: Enhanced function association in whole genome analysis using sequence and structural Motifs 
in Silico Biology, 5, 40.

Guruharsha, K.G. And VijayRaghavan, K. (2005). 
Discrimination in partnership: Compartment-specific interactions of Hox proteins. 
Journal of Genetics, 83, 223-226.

Hanume Gowd, K., Sabareesh, V., Sudarslal, S., Iyengar, P., Franklin, B., Fernando, A., Dewan, K., Ramaswami, M., Siddhartha, Sarma,P., Sikdar, S., Balaram, P. and Krishnan, K.S. (2005). 
Novel peptides of therapeutic promise from Indian Conidae.
Annals of New York Academy of Sciences, 1056, 462-473.

HarshaRani, G.V., Vayttaden, S.J. and Bhalla, U.S. (2005). 
Electronic data sources for kinetic models of cell signaling. 
Journal of Biochemistry, 137, 653-657.

Hayer, A. and Bhalla, U.S. (2005). 
Molecular switches at the synapse emerge from receptor and kinase traffic. 
Public Library of Science: Computational Biology 1, 137-154.

Karmakar, S., Raghunathan, V. A. and Mayor, S. (2005). 
Phase behaviour of dipalmitoyl phosphatidylcholine (DPPC)-cholesterol membranes.
Journal of Physics: Condensed Matter, 17, 1177-1182.

Kavitha, S., Varshney, A. and Mathew, M.K. (2005). 
N type rapid inactivation in human Kv1.4 channels: functional role of a putative C-terminal helix. 
Molecular Membrane Biology 22, 389-400.

Kirkham, M., Fujita, A., Chadda, R., Nixon, S. J., Kurzchalia, T. V., Sharma, D.K., Pagano, R. E., Hancock, J. F., Mayor, S. and Parton, R. G. (2005). 
Ultrastructural identification of uncoated caveolin-independent early endocytic vehicles. 
Journal of Cell Biology, 168, 465-476.

Krishnan-Ghosh, Y., Whitney, A.M., Balasubramanian, S. (2005). 
Dynamic covalent chemistry on self-templating PNA oligomers; Formation of a bimolecular PNA quadruplex.
Chem.commun, 3068-3070.

Krishnan-Ghosh, Y., Stephens, E., Balasubramanian, S. (2005). 
PNA forms an I-motif. 
Chem cmmun, 5278-5280.

Krishna, S., Banerjee, B., Ramakrishnan, T.V. and Shivashankar, G.V. (2005). 
Origins and implications of long-tailed distributiosn in gene expression. 
Proceedings of the National Academy of Sciences-USA, 102, 4771-4776.

Le Novere, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E., Halstead, M., Klipp, E., Mendes, P. Nielsen, P., Sasuro, H., Shapiro, B., Snoep, J.L., Spence, H.G., Wanner, B.L.(2005). 
Minimal information Requested in the Annotation of biochemical Models (MIRIAM). 
Nature Biotech. 23(12):1509-1515

Mayor, S. (2005). 
ACEing GPI release. 
Nature Structural Molecular Biology, 12, 107-108.

Mayor, S. (2005). 
Coming home. 
Nature. 436:488-9.

Metpally, R.R. and Sowdhamini, R. (2005). 
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis. 
BMC Evolutionary Biology 6, 100.

Metpally, R.R. and Sowdhamini, R. (2005). 
Cross genome phylogenetic analysis of human and Drosophila G-protein-coupled receptors: Application to functional annotation of orphan receptors. 
BMC Genomics, 6, 106.

Mohanty, S.K., Sharma, M., Panicker, M.M., and Gupta, P.K. (2005). 
Controlled induction, enhancement, and guidance of neuronal growth cones by use of line optical tweezers. 
Optics Letters, 30, 2596-2598.

McEwen B.S. and Chattarji, S. (2005). 
Neuroendocrinology of stress effects on the brain and body. 
Handbook of Neurochemistry & Molecular Neurobiology (3rd Ed.), Kluwer Academic/Plenum Publishers (In press).

Mitra, R., Jadhav, S., McEwen, B.S., Vyas, A. and Chattarji, S. (2005). 
Stress duration modulates the spatiotemporal patterns of spine formation in the basolateral amygdala. 
Proceedings of the National Academy of Science-USA, 102, 9371-9376

Mitra, R., Vyas, A., Chatterjee, G. and Chattarji, S. (2005). 
Chronic-stress induced modulation of different states of anxiety-like behavior in female rates. 
Neuroscience Letters, 383, 278-283.

Mountain, JL & Ramakrishnan. U. (2005). 
Individual genetic difference and human population history. 
Human Genomics. 2:4-19.

Narayanan, R., Narayan, A. and Chattarji, S. (2005). 
A probabilistic framework for region-specific remodeling of dendrites in three-dimensional neuraonal reconstructions
.Neural Comput, 17, 75-96.

Nair, P. (2005). 
Epidermal growth factor receptor family and its role in cancer progression. 
Current Science, 88, 890-898.

Pawlak, R., Shankaranarayana Rao, B.S., Melchor, J.P., Chattarji, S., McEwan, B. and Strickland, S. (2005). 
Tissue plasminogen activator and plaminogen mediate stress induced decline of neuronal and cognitive functions in the hippocampus. 
Proceedings of the National Academy of Sciences, 102, 18201-18206.

Pugalenthi, G., Bhaduri, A. and Sowdhamini, R. (2005). 
GenDiS: Genomic distribution of protein structural superfamilies. 
Nucleic Acid Research, 33, 252-255.

Pugalenthi, G., Archunan, G. and Sowdhamini, R. (2005). 
DIAL: a web-based server for the automatic identification of structural domains in proteins. 
Nucleic Acid Research, 30, W130-132.

Pugalethi. G., Bhaduri, A. and R. Sowdhamini. (2005). 
iMOTdb - a comprehensive collection of spatially interacting motifs in protein. 
Nucleic Acid Research, 33, 252-255.

Rajasethupathy, P., Vayttaden, S.J. and Bhalla, U.S. (2005). 
Systems modeling: a pathway to drug discovery. 
Curr Opin Chem Biol. 9, 400-406.

Ramakrishnan. U, Hadly, EA & Mountain, JL. (2005). 
Detecting past population bottlenecks using temporal geentic data. 
Molecular Ecology. 14(10):2915-2922.

Rao, M., and S. Mayor. (2005). 
Use of Forster's resonance energy transfer microscopy to study lipid rafts. 
Biochim Biophys Acta. 1746:221-33.

Karmakar, S., Raghunathan, V. A. and Mayor, S. (2005)
Phase behaviour of dipalmitoyl phosphatidylcholine (DPPC)-cholesterol membranes.
J. Phys.: Condens. Matter 17: S1177-S1182

Rodrigues, V. (2005). 
Prescience and critical thought: The life and science of Jose Campos-Ortega. 
Journal of Genetics (In press).

Sandhya, S., Chakrabarti, S., Abhinandan, K.R., Sowdhamini, R. and Srinivasan, N. (2005).
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. 
Journal of Biomolecular Structure and Dynamics, 23, 283-298.

Sanyal, S., Consoulas, C., Kuromi, H., Basole, A., Mukai, L., Kidokoro, Y., Krishnan, K.S. And Ramaswami, M. (2005).
Analysis of conditional paralytic mutants in Drosophila Sarco-Endoplasmic Reticulum calcium ATPase reveals novel mechanisms regulating membrane excitability.
Genetics, 169, 737-750.

Saxena, A.M., Udgaonkar, J.B. and Krishnamoorthy, G. (2005). 
Protein dynamics and protein folding dynamics revealed by time-resolved fluorescence. 
In 'Fluorescence Spectroscopy in Biology (eds. Hof, M., Hutterer, R. and Fidler, V.) Springer.

Saxena, A.M., Udgaonkar, J.B. and Krishnamoorthy, G. (2005). 
Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with green fluorescent protein
Protein Science 14, 1767-1799.

Sen, A., Shetty, C., Jhaveri, D. and Rodrigues, V. (2005). 
Distinct types of glial cells populate the Drosophila antenna. 
BMC Developmental Biology, 5, 25.

Sharma, P., Asztalos, Z., Ayyub, C., De Bruyne, M., Doran, A.J., Gomex-Hernandez, A., Keane, J., Killeen, J., Kramer, S., Madhavan, M., Roe, H., Sherkhane, P.D., Siddiqi, K., Silva, E., Carlson, J.R., Goodwin, S.F., Heisenberg, Krishnan, K., Kyriacou, C.P., Patridge, L., Riesgo-Escovar, J., Rodrigues, V., Tully T. and O'Kane, C.J. (2005). 
Isogenic autosomes to be applied in optimal screening for novel mutants with viable phenotypes in Drosophila melanogaster. 
Journal of Neurogenetics, 19, 57-85.

Siddhartha, Sarma, P., Senthil Kumar, G., Sudarslal, S., Iengar, P., Ramasamy, P., Sikdar, S.K., Krishnan, K.S. And Balaram, P. (2005). 
Solution structure of Am2766, a highly hydrophobic delta conotoxin from conus amadis that inhibits inactivation of brain voltage gated sodium channels
Chemistry and Biodiversity, 2, 535-556.

Sinha, K.K. and Udgaonkar, J.B. (2005) 
Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: Evidence for a continuous transition. 
Journal of Molecular Biology 353, 704-718.

Thangudu, R.R., Vinayagam, A., Pugalenthi, G., Manonmani, A., Offmann, B. and Sowdhamini, R. (2005). 
Native and modelled disulphide bonds in proteins: Knowledge-based approaches towards structure prediction of disulphide-rich polypeptides. 
Proteins: Structure Function and Bioinformatics, 58, 866-79.

Veeraraghavalu, K., Subbaiah, V. K., Srivastava, S., Chakrabarti, O., Syal, R. and Krishna, S. (2005). 
Complementation of HPV-16 E6/E7 by Jagged1 specific Notch1-PI3K signaling involves pleiotropic oncogenic functions independent of CSL activation. 
Journal of Virology 79, 7889-7898.