1. Aghera, N., Earanna, N., Udgaonkar, J.B.(2011). Equilibrium unfolding studies of monellin: the double-chain variant appears to be more stable than the single-chain variant, Biochemistry, 50,13, 2434-2444 | PMID

2. Aghera, N. and Udgaonkar, J.B. (2011) Heterologous expression, purification and characterization of heterodimeric monellin. Protein Expression and Purification, 76, 2, 248-253 | PMID

3. Anand, R., Rai, N. and Thattai, M. (2011). Promoter reliability in modular transcriptional networks. Methods in Enzymology, 497, 31-49 | PMID

4.  Arimoto M., Koushika S.P., Choudhary B.C., Li C., Matsumoto N., Hisamoto N., (2011). The C. elegans JIP3 protein UNC-16 functions as an adaptor to link kinesin-1 to cytoplasmic dynein. Journal of Neuroscience, 31, 6, 2216-2224 | PMID

5. Bajaj, J., Krishna, S.et al (2011) Notch signaling in CD66+ cells drives the progression of human cervical cancers. Cancer research, 71, 14, 4888-4897 | PMID

6. Bhalla, U. S. (2011) Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural network, 24,9, 943-949 | PMID

7. Bhalla, U. S.(2011) Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states. Biophysical Journal, 101, 1, 21-32 | PMID

8. Bhatia, D.Krishnan, Y.et all…(2011) A synthetic icosahedral DNA-based host–cargo complex for functional in vivo imaging. Nature communications, 2, 339- | PMID

9. Bhatia, D., Sharma, S., Krishnan, Y. (2011) Synthetic, biofunctional nucleic acid-based molecular devices. Current Opinion in Biotechnology, 22, 4, 475-484 | PMID

10. Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y. (2011) An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nature Communications, 2, 340. | PMID

11. Chakraborty, T., and Siddiqi, O (2011) Odor reception in antenna and antennal lobe of Drosophila. Fly, 5, 1, 14-17 | PMID

12. Chattarji, S. (2011) Lipocalin comes callin’ on the hippocampus. Procd. Of National Academy of Science USA, 108, 44, 18197-18198 | PMID

13. Chaudhuri, A., Mayor, S., Rao, M. et al (2011) Spatiotemporal regulation of chemical reactions by active cytoskeletal remodeling. Procd. Of National Academy of Science USA, 108, 36, 14825-14830 | PMID

14. Chorna, T and Hasan, G. (2011). The genetics of calcium signaling in Drosophila melanogaster.  Biochem Biophys Acta.  Invited review. | PMID

15. Das, A.Rodrigues, V.et al (2011). Identification and analysis of a glutamatergic local interneuron lineage in the adult Drosophila olfactory system. Neural Systems & Circuits, 1, 1-4 | PMID

16. Das, S., Rodriques, A., Ramaswamy, M. (2011) Plasticity of local gabaergic interneurons drives olfactory habituation.  Procd. Of National Academy of Science USA, 108, 36, E646-E654 | PMID

17. Ramachandran, Gayathri and Udgaonkar, Jayant B. (2011). Understanding the Kinetic Roles of the Inducer Heparin and of Rod-like Protofibrils during Amyloid Fibril Formation byTau Protein. Journal of Biological Chemistry, 286, 45, 38948–38959 |PMID

18. Godbole, A., Mitra, R., Dubey, A.K. Reddy, P.S., Mathew, M.K. Bacterial expression, purification and characterization of a rice voltage-dependent, anion-selective channel isoform, OsVDAC4. Journal of Membrane Biology, 184, 10, 67-80 | PMID

19. Gogia, S., Balaram, H., Puranik, M. (2011). HGPRT distorts the purine ring of nucleotide substrates and perturbs pka of bound xanthosine monophosphate, Biochemistry, 50, 18, 4184-4193 | PMID

20. Gupta, K., Kumar, M., Chandrashekara, K, Krishnan, K.S., Balaram, P. (2011) Combined Electron Transfer Dissociation-Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products, Journal of Proteome Research, 3;11(2):515-22 | PMID

21. Gupta, K., Kumar, M. Balaram, P (2011). Disulfide bond assignments by mass spectrometry of native natural peptides: cysteine pairing in disulfide bonde. Analytical Chemistry , 82, 19, 8313-8319 | PMID

22. Guruharsha, K. G. Vijayraghavan, K. et al (2011) A Protein Complex Network of Drosophila melanogaster. Cell, 147, 3, 690-703 | PMID

23. Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder., M. and Shevchenko, A. (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biology, 12, R8. | PMID

24. Jain, S. and Udgaonkar, J.B. (2011). Defining the pathway of worm-like amyloid fibril formation by the mouse prion protein by delineation of the productive and unproductive oligomerization reactions. Biochemistry, 50, 7, 1153-1161 | PMID

25. Jayanth, N., Puranik, M. (2011). Methylation Stabilizes the Imino Tautomer of damp and Amino Tautomer of dcmp in Solution. The Journal of Physical Chemistry B, 115, 19, 6234-6242 | PMID

26. Jha, A., Ishii, K., Udgaonkar, J.B., Tahara, T. and Krishnamoorthy, G. (2011) Exploration of the correlation between solvation dynamics and internal dynamics of a protein. Biochemistry, 50, 3, 397-408 | PMID

27. Jha, S.K., Dasgupta, A., Malhotra, P. and Udgaonkar, J.B. (2011). Identification of multiple folding pathways of monellin using pulsed -thiol labeling and mass spectrometry. Biochemistry, 50, 15, 3062-3074 | PMID

28. Kalaimathy, S.,  Sowdhamini, R. and  Kanagarajadurai, K. (2011). Critical assessment of structure-based sequence alignment methods at distant relationships. Briefings in Bioinformatics, 12, 2, 163-175 | PMID

29. Krishnamurthy, P., Mathew, M.K. et al (2011) Root apoplastic barriers block Na+ transport to shoots in rice (Oryza sativa L.). Journal of experimental botany, 62, 12, 4215-4228 | PMID

30. Krishnan, K.S., Wu, C.F. (2011) "Entitlement, no! Gratitude, yes!", J. Neurogenet. 25(3):63-77 | PMID

31. Krishnan, Y., Simmel, F. C. (2011). Nucleic Acid Based Molecular Devices. Angewandte Chemie International Edition, 50, 14,  3124-3156 | PMID

32. Kumar, S., Dey, D., Hasan, G. (2011) Patterns of gene expression in Drosophila insp3 receptor mutant larvae reveal a role for insp3 signaling in carbohydrate and energy metabolism. Plos One, 6, 8,  1-9 | PMID

33. Majumder, R., Krishnan, K.S. (2011) Synaptic vesicle recycling: genetic and cell biological studies. Journal of Neurogenetics,  25, 3, 146-157 | PMID

34. Malik, R., Chatterji, S. (2011) Enhanced intrinsic excitability and EPSP-spike coupling accompany enriched environment induced facilitation of LTP in hippocampal CA1 pyramidal neurons. Journal of Neurophysiology, 106, 6, 1-53 | PMID

35. McCann, M., Rodrigues, V., Ramaswamy, M. et al (2011). The Ataxin-2 protein is required for microrna function and synapse-specific long-term olfactory habituation. Procd. Of National Academy of Science USA, 108, 36, E655-E662 | PMID

36. Modi, S. and Krishnan, Y. (2011). A method to map spatiotemporal ph changes inside living cells using a ph-triggered DNA nanoswitch. Methods in Molecular Biology,  749, 61-77 | PMID

37. Mondal S., Ahlawat S., Rau K., Venkatraman V. and Koushika S. P. (2011). Imaging in vivo neuronal transport in genetic model organisms using microfluidic devices.  Traffic, 12, 4, 372-385 | PMID

38. Mukherjee, P. and Vijayraghavan, K. et al (2011). The actin nucleator wasp is required for myoblast fusion during adult Drosophila myogenesis. Development, 138, 11, 2347-2357 | PMID

39. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2011). DNA synthesis across an abasic lesion by yeast Rev1 DNA polymerase. Journal of Molecular Biology, 406, 18-28 | PMID

40. Ratnam, R.,  Bond, W.J.,  Fensham, R.J.,  Hoffmann, W.A.,  Archibald, S.,  Lehmann, C.E.R., Anderson, M.T., S Higgins, S.I. and  Sankaran. M. (2011). When is a forest a savanna and why does it matter?  Global Ecology and Biogeography, 20, 5, 653-660

41. Ravinder, S., Pillai, a.G. Chatterji, S. (2011). Cellular correlates of enhanced anxiety caused by acute treatment with the selective serotonin reuptake inhibitor fluoxetine in rats. Frontiers in Behavioral neuroscience,  5, 88 | PMID

42. Reddy, C.S.R.,  Joshi, A.,  Sudha, S.,  Offmann, B. and  Sowdhamini, R. (2011). Cross-genome comparisons of newly identified domains in Mycoplasma gallisepticum and domain architectures with other Mycoplasmas, Comparative and Functional Genomics, 878973 | PMID

43. Roy, Sudipto and VijayRaghavan,  K. (2011). Developmental Biology: Taking Flight. Current Biology,  22 , 2, R63 | PMID

44. Sane, s.P. and Singh, A. (2011) Water Movement in Vascular Plants: A Primer. Journal of the Indian Institute of Science, 91, 3, 233-242

45. Sane, S. P.(2011). Steady or Unsteady? Uncovering the Aerodynamic Mechanisms of Insect Flight. Journal of Experimental Biology, 214, 349-351 | PMID

46. Sankar, S.S., Udgaonkar, J.B. and Krishnamoorthy, G. (2011). Reduced Fluorescence Lifetime Heterogeneity of 5-Fluorotryptophan in Comparison to Tryptophan in Proteins: Implication for Resonance Energy Transfer Experiments. Journal of Physical Chemistry B. , 115, 22, 7479-7486 | PMID

47. Schwudke, D., Schuhmann, K., Herzog, R., Bornstein, S.R.  and Shevchenko, A. (2011). Shotgun Lipidomics on High Resolution Mass Spectrometers. CSH Persp Biol., 3(9): a004614 | PMID

48. Sekhar, A. and Udgaonkar, J.B. (2011) Fluoroalcohol-induced Modulation of the Pathway of Amyloid Protofibril Formation by Barstar. Biochemistry, 50, 5, 805-819 | PMID

49. Shameer, K.,  Pugalenthi, G.,  Kandaswamy, K.K. and  Sowdhamini, R. (2011). 3dswap-pred: prediction of 3D domain swapping from protein sequence using random forest approach. Protein Peptide Letters, 18, 10, 1010-20 | PMID

50. Shanmugasundaram M. and Puranik, M. (2011). Vibrational markers of structural distortion in adenine nucleobases upon DNA damage. Phys. Chem. Chem. Phys., 13, 9, 3851-3862 | PMID

51. Singh, A.K, Prabhakar, S and Sane, S. P. (2011). The biomechanics of fast prey capture by aquatic bladderworts. Biology Letters, 7, 4, 547-550 | PMID

52. Suvrathan, A. and Chattarji, S. (2011). Fragile X Syndrome and the Amygdala. Current Opinion in Neurobiology, 21, 3, 509 | PMID

53. Swetha, M.G., Mayor, S. et al. (2011) Lysosomal membrane protein composition, acidic ph and sterol content are regulated via a light-dependent pathway in metazoan cells. Traffic, 12, 8, 1037-1055

54. Velho, N., Srinivasan, U. Prashanth, N. S. Laurance, W. F. (2011). Human disease hinders anti-poaching efforts in Indian nature reserves.  Biological Conservation, 144, 9, 2382-2385

55. Sharma A, Nair DT. (2011) Cloning, expression, purification, crystallization and preliminary crystallographic analysis of MsDpo4: a Y-family DNA polymerase from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67(Pt 7):812-6. | PMID

56. Mosier K, Lau C, Wang Y, Venkadesan M, Valero-Cuevas FJ.(2011) Controlling instabilities in manipulation requires specific cortical-striatal-cerebellar networks.J Neurophysiol. 105(3):1295-305. | PMID

57. Spottiswoode CN, Stryjewski KF, Quader S, Colebrook-Robjent JFR, Sorenson MD. (2011) Ancient host specificity within a single species of brood parasitic bird. Proceedings of the National Academy of Science of the USA. 108(43):17738–17742. |PMID 

58. Ray A, Sumangala RC, Ravikanth G, Uma Shaanker R, Quader S. (2011) Isolation and characterization of polymorphic microsatellite loci from the invasive plant Lantana camara L. Conservation Genetics Resources. | DOI

59. 3. Seshasayee ASN, Luscombe NM. (2011) Comparative genomics suggests differential deployment of linear and branched signaling across bacteria. Molecular Biosystems. 7: 3042-3049. | PMID

60. Seshasayee ASN, Sivaraman K, Luscombe NM. (2011) An index of prokaryotic transcription factors. A handbook of transcription factors. Springer. Ed. Timothy Hughes. [Books Review]

61. Seshasayee ASN, Madan Babu M. (2011) Unanticipated intra- and inter-kingdom crosstalk involving small-molecules. Environmental Microbiology Reports (Crystal Ball Feature; 2011) 3: 1-26 [Book Review]

62. Zhao, L.; Deng, X* and Sane, S.P.* (2011). Modulation of leading edge vorticity and aerodynamic forces in flexible flapping wings. Bioinspiration and Biomimetics 6 (2011) 036007. | PMID 

63. G. Senthil Kumar, Sanjeev Upadhyay, M. K. Mathew  & Siddhartha P. Sarma (2011) Solution structure of a novel  hKv1.1 inhibiting scorpion toxin (BTK-2) determined by isotope edited multidimensional NMR spectroscopic methods   Biochim Biophys Acta 1814, 459–469

64. Rahul Shrivastava, Bhakti Basu, Ashwini Godbole, M. K. Mathew, Shree K. Apte & Prashant S. Phale (2011)  Repression of Glucose Inducible Outer Membrane Protein, OprB during Preferential Utilization of Aromatic Compounds in Pseudomonas putida CSV86   Microbiology 157, 1531–1540 | PMID

65. Jain, Shweta and Udgaonkar, Jayant B. (2011). Prion protein aggregation. Current Science, 101, 10, 1311

66. Kumar RS, Riyasdeen A, Dinesh M, Paul CP, Srinag S, Krishnamurthy H, Arunachalam S, Akbarsha MA. (2011) Cytotoxic Property of Surfactant-Cobalt(III) Complexes on a Human Breast Cancer Cell Line. Arch Pharm (Weinheim). 44(7):422-30 |PMID

67. Keshari RS, Jyoti A, Kumar S, Dubey M, Verma A, Srinag BS, Krishnamurthy H,Barthwal MK, Dikshit M (2011) Neutrophil Extracellular Traps Contain Mitochondrial as well as Nuclear DNA and Exhibit Inflammatory Potential. Cytometry A 81(3):238-247. | PMID

68. Schuhmann K, Herzog R, Schwudke D, Metelmann-Strupat W, Bornstein SR, Shevchenko A. (2011) Bottom-up Shotgun Lipidomics by Higher Energy Collisional Dissociation (HCD) on LTQ Orbitrap Mass Spectrometers. Anal Chem. 83(14):5480-7

69. Sundaramurthy Pandurangan, Raashi Sreenivasan, Khader Shameer, Sunita Gakkhar and Sowdhamini Ramanathan. (2011) HORBALFRE program : Higher Order Residue Interactions Based Algorithm for Fold Recognition. Bioinformation, 7(7):352-359. | PMID

70. Djamel Harbi, Marimuthu Parthiban, Deena M.A. Gendoo, Sepehr Ehsani, Manish Kumar, Gerold Schmitt-Ulms, Ramanathan Sowdhamini and Paul M. Harrison (2011) PrionOme: A database of prions and other sequencesrelevant to prion phenomena. Nature Proceedings. npre.2011.6430.1

71. Shameer Khader and Sowdhamini Ramanathan (2011). SEQ2GO: Function annotation of hypothetical proteins using sequence based filtering and domain composition of intermediate homologs. Moscow Conference on Computational Molecular Biology. July 21-24,2011:300-302.

72. Gandhimathi, A., Nair, A. and Sowdhamini, R. (2011) PASS2.4: An update of database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Research. 2011:1–4 | PMID

73. Balasubramanian Nagarathnam, Kannan Sankar, Varadhan Dharnidharka, Veluchamy Balakrishnan, Govindaraju Archunan and Ramanathan Sowdhamini. (2011) TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences. Bioinformation. 7(5):214-221. | PMID

74. Divya P  Syamaladevi, S. Kalaimathy, Naseer Pasha, S. Subramonian and R. Sowdhamini. (2011) A three-step validation following genome-wide data  mining for myosin family members improves search efficiency. In Procceedings of IEEE ICDM 2011 workshop on Biological Data Mining and its Applications in Healthcare (BioDM). | DIO

75. Eshita Mutt, Abhijit Mitra and R. Sowdhamini. (2011) Mining protein sequence databases for remote homologues that can display considerable domain length variations. In Procceedings of IEEE ICDM 2011 workshop on Biological Data Mining and its Applications in Healthcare (BioDM). 2(2):55-77. | DOI

76. Swati Kaushik and R. Sowdhamini. (2011) Structural analysis of prolyl oligopeptidases using molecular docking and molecular dynamics: insights into conformational changes and ligand binding. PLoS One 6(11):e26251. | PMID

77. Lalima L. Madan, S. Veeranna, K. Shameer, Chandra Shekhar, R. Sowdhamini and B. Gopal (2011) Modulation of catalytic activity in multi-domain tyrosine phosphatases. PLoS ONE 6(9): e24766. | PMID

78. Khader Shameer, Prashant N. Shingate, Manjunath, S.C.P., Karthika, M., Ganesan Pugalenthi, Ramanathan Sowdhamini (2011) 3DSwap: Curated Knowledgebase for proteins involved in 3D domain swapping. Database (2011) | PMID

79. Balasubramanian Nagarathnam, Shankar Kannan, Vardhan Dharnidharka, Veluchamy Balakrishnan, Govindaraju Archunan and Ramanathan Sowdhamini. (2011) Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, fly and worm GPCR clusters. Bioinformation. 2011; 7(1): 15–20. | PMID

80. Divya P Syamala Devi and R. Sowdhamini (2011) Evolutionary traces decode molecular mechanism behind fast pace of myosin XI.  BMC Structural Biology 2011, 11:35 | PMID

81. K. Kanagarajadurai, S. Kalaimathy, P. Nagarajan and R. Sowdhamini.(2011) PASS2: A Database of Structure-based sequence alignments of Proteins Structural Domain Superfamilies.  International Journal of Knowledge Discovery in Bioinformatics Journal, 2(4), 53-66