Ajay, S.M. and Bhalla, U.S. (2006). 

Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze. 
Physiology, 21, 289-296.

Arvind Govindarajan, A, Rao BSS., Nair, D., Trinh, M., Mawjee, N., Tonegawa, S, and Chattarji, S. (2006). 
Transgenic brain-derived neurotrophic factor expression causes both anxiogenic and antidepressant effects. 
Proceedings of the National Academy of Science, USA 103, 13208-13213.

Balaji, N.S., Mathew, M.K. and Krishnaswamy, S. (2006). 
Functional assay of /S.typhi/ OmpC using reconstituted large unilamellar vesicles: A general method for characterization of outer membrane proteins. 
Biochimie (In press).

Bhadra, R., Sandhya, S., Abhinandan, K.R., Chakrabarti, S., Sowdhamini, R. and Srinivasan, N. (2006). 
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. 
Nucleic Acids Research, 34, W143-W146.

Banerjee, B., Bhattacharya, D. and Shivashankar, G.V. (2006). 
Chromatin assembly exhibits spatio-temporal heterogeneity within the cell nucleus. 
Biophysical Journal, 91, 2297-2303.

Banerjee, S., Joshi, R., Venkiteswaran, G., Agrawal, N., Srikanth, S., Alam, F. and Hasan G (2006). 
Compensation of Inositol 1,4,5-trisphosphate receptor function by altering Sarco-endoplasmic reticulum calcium ATPase activity in the Drosophila flight circuit. 
Journal of Neuroscience, 26, 8278-8288.

Bhattacharya, D., Mazumder, A., Anne, M. and Shivashankar, G.V. (2006). 
Core and linker histones diffuse via distinct mechanisms within living cells. 
Biophysical Journal, 91, 2326-2336.

Belle, E, Ramakrishnan, U., Mountain, J.L. and Barbujani, G. (2006) 
Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans
Proceedings of the National Academy of Sciences of the USA. (in press).

Bennur, S., Shankaranarayana Rao, B.S., Pawlak, R., Strickland, S., McEwan, B.S., and chattarji, S. (2006). 
Stress-induced spine loss in the medical amygdala is mediated by tissue-plasminogen activator. 
Neuroscience (In Press).

Bhaduri, A. and R. Sowdhamini (2006) 
Domain architectural census of eukaryotic gene products containing O-protein phosphatases. 
Gene, 366, 246-255.

Chakrabarti, S., Manohari, G., Pugalenthi, G. and Sowdhamini, R. (2006). 
SSToSS: Sequence Structural Templates of Single-member superfamilies. 
In Silico Biology, 6, 0029.

Chandrashekar, C., Manonmani, A., Babu, M. and Sowdhamini, R. (2006). 
Enhanced structure prediction of gene products containing adenylyl cyclase. 
In Silico Biol. (In press).

Gadkari, R., Sandhya, S., Sowdhamini, R. and Dighe, R.R. (2006). 
The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor.
J. Mol. Cell. Endocrinology (in press).

Gowri, V.S. and Sandhya, S. (2006). 
Recent trends in remote homology detection: an Indian Medley. 
Bioinformation, 3, 94-96.

Ibrahim, M., Kerby, R.L., Puranik, M., Wasbotten, I.H., Youn, H., Roberts, G.P. and Spiro, T.G. (2006). 
Heme displacement mechanism of CooA activation: mutational and Raman spectroscopic evidence. 
Journal of Biological Chemistry, doi:10.1074/jbc.M605568200.

Kalia, M., Kumari, S., Chadda, R., Hill, M.M., Parton, R.g. and Mayor, S. (2006). 
arf6-independent GEECs Fuse with sorting endosomes via a Rab5/PI-3' Kinase-dependent machinery. 
Molecular Biology Cell. epub: June 7.

McEwen, B.S., S. Chattarji. (2006) 
Neuroendocrinology of stress© 
Springer-Verlag Berlin Heidelberg, 1-22.

Malhotra, V. and Mayor, S. (2006). 
Cell biology: the Golgi gorws up. 
Nature, 441, 939-940.

Modi, S., Wani, A.H., Krishnan, Y. (2006).
A PNA-DNA hybrid I-motif-implications for sugar-sugar contacts in i-motif tetramerization. 
Nucleic Acids Research (In press).

Mukhopadhyay, S., Nayak, P.K., Udgaonkar, J.B. And Krishnamoorthy, G. (2006). 
Characterization of the Formation of Amyloid Protofibrils from Barstar by mapping residue-specific fluroscence dynamics. 
Journal of Molecular Biology. 358, 935-942.

Pawlak, R., Rao, BSS., Melchor, J.P., Chattarji, S., McEwan, B. and Strickland, S. (2006). 
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 R. Sowdhamini (2006). 
iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. 
Nucleic Acids Research, 34 (Database issue), D285-286.

Pugalenthi, G., Shameer, K. Srinivasan, N. and Sowdhamini, R. (2006).
HARMONY: a web-server for the assessment of protein structures. 
Nucleic Acids Research, 34, W143-W146.

Puranik, M., Weeks, C.L., Lahaye, D., Kabil, O., taoka, S., Nielsen, S.B., groves, J.T., Banerjee, R. and Spiro, T.G. (2006).
Dynamics of carbon monoxide binding to cystathionine-synthase. 
Journal of Biological Chemistry, 281, 13433-13438.

Rau, K.R., Quinto-Su, P.A., Hellman, A.N. and Venugopalan, V. (2006). 
Pulsed laser microbeam-induced cell lysis: Time-resovled imaging and analysis of hydrodynamic effects. 
Biophysics Journal, 91, 317-329.

Rhana, R., Sandhya, S., Abhinandan, K.R., Chakrabarthi S, Sowdhamini, R. and Srinivasan, N. (2006). 
Cascade PSI-BLAST Web server: A remote homology search tool for relating protein domains. 
Nucleic Acids Research, 34, W143-W146.

Roopa, T. and Shivashankar, G.V. (2006). 
Direct measurement of chromatin fluidity using optical trap modulation force spectroscopy. 
Biophysical Journal (In press).

Sharma, P., Varma, R., and Mayor, S. (2006). 
Biophysical characterization of lipid rafts, 
in Lipid Rafts and Caveolae (eds. Christopher Fielding). wiley-VCH, Verlag Gmbh & Co., KGaA, Weinheim. 278 pages

Rajagopal, D., V. Bal, S. Mayor, A. George, and S. Rath. (2006). 
A role for the Hsp90 molecular chaperone family in antigen presentation to T lymphocytes via major histocompatibilitycomplex class II molecules. 
Eur J Immunol. 36:828-41.

Rajan, R., Clement, J.P. and Bhalla, U.S. (2006) 
Rats smell in stereo. 
Science , 311, 666-670.

Ramdass, B., Maliekal, T,T., Lakshmi, S., Rehman, M., T. T, Rema, P., Nair, P., Mukherjee, G., Reddy, B. K. M., Krishna, S. and Pillai, M. R. (2006). 
Co-expression of Notch1 and NF-KappaB signaling pathway components in human cervical cancer progression.
Gynaecology Oncology (In press).

Rau, K.R., Quinto-Su, P.A., Hellman, A.N. and Venugopalan, V. (2006). 
Pulsed laser microbeam-induced cell Lysis: Time-resolved imaging and analysis of hydrodynamic effects. 
Biophysics, 91, 317-329.

Saxena, A.M., Udgaonkar, J.B. & Krishnamoorthy, G. (2006). 
Characterization of intra-molecular distances and site-specific dynamics in chemically unfolded barstar: evidence for denaturant-dependent non-random structure. 
J. Mol. Biol, 359, 174-189.

Sinha, D., Sastry, S. and Shivashankar, G.V. (2006). 
Probing mRNA conformational heterogeneity using single-moleculefluorescence anisotropy, 
Applied Physics Letters, 88, 3901-3903.

Srikanth, S., Banerjee, S. and Hasan, G. (2006). 
Ectopic expression of a Drosophila InsP3R Channel mutant has dominant-negative effects in vivo. 
Cell Calcium, 39, 187-196.

Sriram, V., Krishnan, K.S. and Mayor, S. (2006). 
Biogenesis of Lysosomes, 
Proc. Ind. Nat. Sci., 72, 19-42.

Subramanyam, D. and Krishna, S. (2006). 
c-Myc substitutes for Notch1-CBF1 functions in cooperative trasformation with papillomavirus oncogenes. 
Virology, 347, 191-198.

Tripathi, L.P. and Sowdhamini, R. (2006). 
Cross-genome comparisons of serine proteases in Arabidopsis and rice. 
BMC Genomics, 7, 200.

Varma, R. and S. Mayor. (2006). 
Homo-FRET microscopy to investigate molecular-scale organization in living cells 
in Cell Imaging.(eds. David Stephens.) Methods Express Series, Scion Publishing Ltd, UK. 301p.

Vyas, A., Jhadav, S. and Chattarji, S. (2006). 
Prolonged behavioral stress enhances synaptic connectivity in the basolateral amygdala. 
Neuroscience (In press).

Wani A., and Udgaonkar, J.B. (2006). 
HX-ESI-MS and optical studies of the unfolding of thioredoxin indicate stabilization of a partially unfolded, aggregation-competent intermediate at low pH. 
Biochemistry 45 (In press).