1.Adurti S., Krishna, S., Mukherjee, G., Bafna, U., Devi, U. and Jayshree, R. S. (2008). Regulatory T cells in a spectrum of HPV induced cervical lesions: cervicitis, cervical intraepithelial neoplasia and squamous cell carcinoma. American Journal of Reproductive Immunology 60, 55-65. 

2.Alva, V., Divya Syamala Devi, P. and Sowdhamini, R. (2008). COILCHECK: an interactive server for the analysis of interface regions in coiled coils. Protein and Peptide Letters, 15, 33-3 

3.Anil A, Premraj R, Kumar P & Mathew MK (2008) A Plant Ca-Pump, Aca2, Relieves Salt Hypersensitivity In Yeast: Modulation Of Cytosolic Calcium Signature And Activation Of Adaptive Na+ Homeostasis /J Biol Chem/ 283, 3497-3506 

4.Anbazhagan, P., Purushotam1, M., Kumar, H. B. K., Kubendran, S., Mukherjee, O., Brahmachari, S. K., Jain,S. and Sowdhamini, R. (2008). Evolutionary analysis of PHJLPPI gene in humans and non-human primates. Bioinformation, 2, 471-474. 

5.Basu, B., Desai, R., Balaji, J., Chaerkady, R., Sriram, V., Maiti, S. and Panicker, M.M. (2008). Serotonin in pre-implantation mouse embryos is localized to the mitochondria and can modulate mitochondrial potential. Reproduction, 135, 1470-1626. 

6. Bhalla, U.S. How to Record a Million Synaptic Weights in a Hippocampal Slice. PLoS Comput. Biol. 2008, 4(6) 

7.Borroni V, Kumari S, Chanda B, Massol R, Chaudhry A, Mayor S, Barrantes FJ. (2008). α-Bungarotoxin Induces Nicotinic Acetylcholine Receptor Internalization via a novel Endocytic Pathway. J. Cell Biol. 181(7): 1179–1193. 

8.Chakraborty, S., Modi, S. and Krishnan, Y. (2008). The RNA2-PNA2 Hybrid I-motif - A novel RNA-based building block. Chemical Communications, 70-72. 

9. Chakraborty, S. and Krishnan, Y. (2008). Kinetic Hybrid I-motifs: Intercepting DNA with RNA to form a DNA2RNA2hybrid i-motif. Biochemistry, 90, 1088-1095. 

10. Chadda, R. and Mayor, S. (2008). PTRF Triggers a Cave In. Cell, 132, 23-24. 

11. Chandra V, Kar-Roy A, Kumari S, Mayor S, Jameel S, (2008) The HEV ORF3 protein modulates EGFR trafficking, STAT3 translocation and the acute phase response, J Virol., 82(14): 7100–7110.. 

12. Chattarji, S. (2008). Stress-induced formation of new synapses in the amygdala. Neuropsychopharmacology, 33, 199–200. 

13. A. Dhawale and US Bhalla (2008). The network and the synapse: 100 years after Cajal. HFSP Journal 2, 12. 

14. Dixit R, Vijayraghavan K, Bate M. (2008) Hox genes and the regulation of movement in Drosophila. Dev Neurobiol. Feb 15; 68(3):309-16. 

15.Gowd, K.H., Dewan KK, Iengar P, Krishnan KS, Balaram P. 2008. Probing peptide libraries from Conus achatinus using mass spectrometry and cDNA sequencing: identification of delta and omega-conotoxins. J Mass Spectrom. 43:791-805. 

16.Gowd KH, Twedea V, Watkinsc M, Krishnan KS, Teichert RW, Bulaje G, Olivera BM 2008. Conantokin-P, an Unusual Conantokin with a Long Disulfide Loop. Toxicon 52: 203-13. 

17. P. Hari, M. Deshpande, N. Sharma, N. Rajadhyaksha, N. Ramkumar, Ken-ichi Kimura, V. Rodrigues, S. Tole. Chip is required for post eclosion behavior in Drosophila. J. Neuroscience. 28(37): 9145-9150. 

18.Kanagarajadurai, K, and Sowdhamini, R. (2008). Sequence and structural analysis of interleukin-8-like chemokine super family. In Silico Biology, 8, 0025. 

19. Khan, A.G., Thattai, M., and *Bhalla, U.S.*(2008). Odor Representations in the Rat Olfactory Bulb Change Smoothly with Morphing Stimuli. Neuron. 57(4):571-85, 

20. Kain P., Chakraborty T. S., Sundaram S., Siddiqi O. Rodrigues V. and Hasan G.(2008). Reduced Odor Responses from Antennal Neurons of Gqα,Phospholipase Cβ, and rdgA Mutants in Drosophila Support a Role for a Phospholipid Intermediate in Insect Olfactory Transduction. J. Neurosci, 28, 4745-4755. 

21.Anoop V Cherian, Kaustubh R Rau ((2008). Pulsed-laser-induced damage in rat corneas: time-resolved imaging ofphysical effects and acute biological response.J Biomed Opt 13, 2:024009 

22.G. Nageswara Rao, Sucheta S. Kulkarni, Sandhya P. Koushika, and Kaustubh R. Rau. (2008) In vivo nanosecond laser axotomy: cavitation dynamics and vesicle transport. Optics Express, 16, 9884-9894 (2008). 

23. Koushika, S. P. (2008). "JIP"ing along the axon: The complex roles of JIPs in axonal transport. Bioessays, 30, 10-14. 

24. Kumari, S. and Mayor, S. (2008). ARF1 is directly involved in dynamin-independent endocytosis. Nature Cell Biology, 10, 30-41. 

25. T T Maliekal, J Bajaj, V Giri, D Subramanyam and S Krishna (2008). The role of Notch signaling in human cervical cancer: implications for solid tumors. Oncogene 27: 5110-5114; doi:10.1038/onc.2008.224 

26. Paul, A.; Sengupta, P.; Krishnan, Y.; Ladame, S. (2008). Combining G-quadruplex targeting motifs on a single PNA scaffold: hybrid (3+1) PNA-DNA bimolecular quadruplex. Chemistry: A Eur.J, 14(28):8682-9 

27. Pugalenthi, G., Suganthan, P.N., Sowdhamini, R. and Chakrabarti, S. (2008). MegaMotifBase: A database of structural motifs in protein families and superfamilies. Nucleic Acids Research, 36, D218-21. 

28. Ramakrishnan, N., and *Bhalla, U.S.* (2008). Memory Switches in Chemical Reaction Space. PLoS Comput. Biol.,4(7) 

29. Rajagopal A, Rao, A.U., Amigo, J., Tian M., Upadhyay, S., Hall, C., Uhm, S., Mathew, M.K., Fleming, M.D., Paw, B.H., Krause, M. and Hamza, I. (2008) Heme homeostasis is regulated by the conserved and concerted functions of HRG-1 proteins. Nature, 453, 1127 – 1131. 

30. Rao, R.P., Suvrathan, A., Miller, M.M., McEwen, B.S., and Chattarji, S. (2008). PTSD: from Neurons to Networks. In: Post-Traumatic Stress Disorder - Basic Science and Clinical Practice. Shiromani, P. LeDoux, J.E. and Keane, T. (Eds). Humana Press.

31. Reddy, C. C. S., Shameer, K., Offmann, B. and Sowdhamini, R. (2008). PUIRE: a webserver for the prediction of domains in Unassigned regions in proteins. BMC Bioinformatics, 9, 281. 

32. Rodrigues, V. and Hummel, T. (2008). Development of the Drosophila olfactory system, In: Brain Development in Drosophila Ed. G. Technau. Landes Bioscience Publishers. 

33. Roopa, T., Basu, A., Mazumder, A., Mahadevan, L. and Shivashankar, G.V. (2008). Dynamics of chromatin decondensation reveals the structural integrity of a mechanically prestressed cell nucleus. Biophysical Journal, 95(6):3028-35 

34. Shah, P.K., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., Bork, P. and Sowdhamini, R. (2008). Enhnaced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families. Gene, 407, 199-217. 

35. Sandhya, S., Pankaj, B., Govind, M. K., Offmann, B., Srinivasan, N. and Sowdamini, R. (2008). CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Structural Biology, 8, 28. 

36. Deepak Kumar Sinha, Bidisha Banerjee, Shovamayee Maharana, & G.V.Shivashankar (2008) Probing the dynamic organization of transcription compartments and gene loci within the nucleus of living cells. Biophysical Journal, 95(11):5432-8 

37. Sundar, A. S., Varghese, S. M., Shameer, K., Karaba, N., Udayakumar, M. and Sowdhamini, R. (2008). STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thallana. Bioinformation, 2, 431-437. 

38. Tripathi, L.P. and Sowdhamini, R. (2008). Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes. BMC Genomics. 9:549. 

39. Vyas, N., Goswami, D., Manomani, A., Sharma, P., Ranganath, H. A., Vijayraghvan, R., Shashidhara, L. S., Sowdhamini, R. and Mayor, S. (2008). Nanoscale organization of Hh is essential for long range signaling. Cell, 133, 1214-27.

40. Daniel, T.L.*, Dieudonne, A., Fox J.L., Myhrvold C.A., Sane S.P., Wark B. (2008). Inertial guidance systems in insects: from the neurobiology to the structural mechanics of biological gyroscopes. Navigation 55(4): 235-240