1. Varadarajan R, Szabo A, and Boxer S. G. (1985) Cloning, expression in Escherichia coli, and reconstitution of human myoglobin. Proc Natl  Sci U S A 82, 5681-4.

  2. Varadarajan R, Lambright D. G, and Boxer S. G. (1989) Electrostatic interactions in wild-type and mutant recombinant human myoglobins. Biochemistry 28, 3771-81.

  3. Varadarajan R, Zewert T. E, Gray H. B, and Boxer S. G. (1989) Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin. Science 243, 69-72.

  4. Connelly P. R, Varadarajan R, Sturtevant J. M., and Richards F. M. (1990) Thermodynamics of protein-peptide interactions in the ribonuclease S system studied by titration calorimetry. Biochemistry 29, 6108-14.

  5. Varadarajan R, Richards F. M, and Connelly P. R. (1990) Proteins: The hard sphere, structure and energetics. Current Science 59, 819-24.

  6. Kim E. E, Varadarajan R, Wyckoff H. W, and Richards F. M. (1992) Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures. Biochemistry 31, 12304-14.

  7. Varadarajan R, Connelly P. R, Sturtevant J. M, and Richards F. M. (1992) Heat capacity changes for protein-peptide interactions in the ribonuclease S system. Biochemistry 31, 1421-6.

  8. Varadarajan R, and Richards F. M. (1992) Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities. Biochemistry 31, 12315-27.

  9. Thomson J, Ratnaparkhi G. S, Varadarajan R, Sturtevant J. M, and Richards F. M. (1994) Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S. Biochemistry 33, 8587-93.

  10. Nadig G, Ratnaparkhi G. S, Varadarajan R, and Vishveshwara S. (1996) Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies. Protein Sci 5, 2104-14.

  11. Varadarajan R, Nagarajaram H. A, and Ramakrishnan C. (1996) A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence. Proc Natl Acad Sci U S A 93, 13908-13.

  12. Ganesh C, Shah A. N, Swaminathan C. P, Surolia A, and Varadarajan R. (1997) Thermodynamic characterization of the reversible, two-state unfolding of maltose binding protein, a large two-domain protein. Biochemistry 36, 5020-8.

  13. Ratnaparkhi G. S, and Varadarajan R. (1997) Structural Studies of Protein Unfolding. Current Science 72, 826-30.

  14. Panse V. G, Udgaonkar J. B, and Varadarajan R. (1998) SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state. Biochemistry 37, 14477-83.

  15. Ratnaparkhi G. S, Ramachandran S, Udgaonkar J. B, and Varadarajan R. (1998) Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Biochemistry 37, 6958-66.

  16. Chakrabarti A, Srivastava S, Swaminathan C. P, Surolia A, and Varadarajan R. (1999) Thermodynamics of replacing an alpha-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin. Protein Sci 8, 2455-9.

  17. Chakravarty S, and Varadarajan R. (1999) Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7, 723-32.

  18. Chakshusmathi G, Ratnaparkhi G. S, Madhu P. K, and Varadarajan R. (1999) Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc Natl Acad Sci U S A 96, 7899-904.

  19. Ganesh C, Banerjee A, Shah A, and Varadarajan R. (1999) Disordered N-terminal residues affect the folding thermodynamics and kinetics of maltose binding protein. FEBS Lett 454, 307-11.

  20. Ganesh C, Eswar N, Srivastava S, Ramakrishnan C, and Varadarajan R. (1999) Prediction of the maximal stability temperature of monomeric globular proteins solely from amino acid sequence. FEBS Lett 454, 31-6.

  21. Ganesh C, and Varadarajan R. (1999) The size dependence of protein folding thermodynamics, Indian Academy of Sciences and University Press, Hyderabad.

  22. Ganesh C, and Varadarajan R. (1999) Human Myoglobin, VCH, Weinheim, Germany.

  23. Ghoshal A. K, Swaminathan C. P, Thomas C. J, Surolia A, and Varadarajan R. (1999) Thermodynamic and kinetic analysis of the Escherichia coli thioredoxin-C' fragment complementation system. Biochem J 339 ( Pt 3), 721-7.

  24. Ratnaparkhi G. S, and Varadarajan R. (1999) X-ray crystallographic studies of the denaturation of ribonuclease S. Proteins 36, 282-94.

  25. Sheshadri S, Lingaraju G. M, and Varadarajan R. (1999) Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large deltaCp's. Protein Sci 8, 1689-95.

  26. Chakravarty S, Mitra N, Queitsch I, Surolia A, Varadarajan R, and Dubel S. (2000) Protein stabilization through phage display. FEBS Lett 476, 296-300.

  27. Chakravarty S, and Varadarajan R. (2000) Elucidation of determinants of protein stability through genome sequence analysis. FEBS Lett 470, 65-9.

  28. Panse V. G, Swaminathan C. P, Aloor J. J, Surolia A, and Varadarajan R. (2000) Unfolding thermodynamics of the tetrameric chaperone, SecB. Biochemistry 39, 2362-9.

  29. Panse V. G, Swaminathan C. P, Surolia A, and Varadarajan R. (2000) Thermodynamics of substrate binding to the chaperone SecB. Biochemistry 39, 2420-7.

  30. Panse V. G, Vogel P, Trommer W. E, and Varadarajan R. (2000) A thermodynamic coupling mechanism for the disaggregation of a model peptide substrate by chaperone secB. J Biol Chem 275, 18698-703.

  31. Ratnaparkhi G. S, Awasthi S. K, Rani P, Balaram P, and Varadarajan R. (2000) Structural and thermodynamic consequences of introducing alpha-aminoisobutyric acid in the S peptide of ribonuclease S. Protein Eng 13, 697-702.

  32. Ratnaparkhi G. S, and Varadarajan R. (2000) Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. Biochemistry 39, 12365-74.

  33. Ganesh C, Zaidi F. N, Udgaonkar J. B, and Varadarajan R. (2001) Reversible formation of on-pathway macroscopic aggregates during the folding of maltose binding protein. Protein Sci 10, 1635-44.

  34. Panse V. G, Beena K, Philipp R, Trommer W. E, Vogel P. D, and Varadarajan R. (2001) Electron spin resonance and fluorescence studies of the bound-state conformation of a model protein substrate to the chaperone SecB. J Biol Chem 276, 33681-8.

  35. Ratnaparkhi G. S, and Varadarajan R. (2001) Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. J Biol Chem 276, 28789-98.

  36. Chakravarty S, Bhinge A, and Varadarajan R. (2002) A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding. J Biol Chem 277, 31345-53.

  37. Chakravarty S, and Varadarajan R. (2002) Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41, 8152-61.

  38. Chakshusmathi G, and Varadarajan R. (2002) Protein misfolding and inclusion body resolubilization. PINSA-A 68, 375-84.

  39. Rudresh, Jain R, Dani V, Mitra A, Srivastava S, Sarma S. P, Varadarajan R, and Ramakumar S. (2002) Structural consequences of replacement of an alpha-helical Pro residue in Escherichia coli thioredoxin. Protein Eng 15, 627-33.

  40. Dani V. S, Ramakrishnan C, and Varadarajan R. (2003) MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Protein Eng 16, 187-93.

  41. Padmakumar V. C, and Varadarajan R. (2003) A gradient PCR-based screen for use in site-directed mutagenesis. Anal Biochem 314, 310-5.

  42. Prajapati R. S, Lingaraju G. M, Bacchawat K, Surolia A, and Varadarajan R. (2003) Thermodynamic effects of replacements of Pro residues in helix interiors of maltose-binding protein. Proteins 53, 863-71.

  43. Bajaj K, Chakshusmathi G, Bachhawat-Sikder K, Surolia A, and Varadarajan R. (2004) Thermodynamic characterization of monomeric and dimeric forms of CcdB (controller of cell division or death B protein). Biochem J 380, 409-17.

  44. 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, 3608-19.

  45. Bhinge A, Chakrabarti P, Uthanumallian K, Bajaj K, Chakraborty K, and Varadarajan R. (2004) Accurate detection of protein:ligand binding sites using molecular dynamics simulations. Structure 12, 1989-99.

  46. Chakshusmathi G, Mondal K, Lakshmi G. S, Singh G, Roy A, Ch R. B, Madhusudhanan S, and Varadarajan R. (2004) Design of temperature-sensitive mutants solely from amino acid sequence. Proc Natl Acad Sci U S A 101, 7925-30.

  47. Bajaj K, Chakrabarti P, and Varadarajan R. (2005) Mutagenesis-based definitions and probes of residue burial in proteins. Proc Natl Acad Sci U S A 102, 16221-6.[pdf]

  48. Chakraborty K, Shivakumar P, Raghothama S, and Varadarajan R. (2005) NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water. Biochem J 390, 573-81.

  49. Chakraborty K, Thakurela S, Prajapati R. S, Indu S, Ali P.S, Ramakrishnan C, and Varadarajan R. (2005) Protein stabilization by introduction of cross-strand disulfides. Biochemistry 44, 14638-46.

  50. Das M, Rao B. V, Ghosh S, and Varadarajan R. (2005) Attempts to delineate the relative contributions of changes in hydrophobicity and packing to changes in stability of ribonuclease S mutants. Biochemistry 44, 5923-30.

  51. Sharma D, Balamurali M. M, Chakraborty K, Kumaran S, Jeganathan S, Rashid U, Ingallinella P, and Varadarajan R. (2005) Protein minimization of the gp120 binding region of human CD4. Biochemistry 44, 16192-202.

  52. Varadarajan R, Sharma D, Chakraborty K, Patel M, Citron M, Sinha P, Yadav R, Rashid U, Kennedy S, Eckert D, Geleziunas R, Bramhill D, Schleif W, Liang X, and Shiver J. (2005) Characterization of gp120 and its single-chain derivatives, gp120-CD4D12 and gp120-M9: implications for targeting the CD4i epitope in human immunodeficiency virus vaccine design. J Virol 79, 1713-23.

  53. Chakraborty K, Durani V, Miranda E. R, Citron M, Liang X, Schleif W, Joyce J. G, and Varadarajan R. (2006) Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. Biochem J 399, 483-91.

  54. Prajapati R. S, Sirajuddin M, Durani V, Sreeramulu S, and Varadarajan R. (2006) Contribution of cation-pi interactions to protein stability. Biochemistry 45, 15000-10.

  55. Bajaj  K, Madhusudhan M. S, Adkar B. V, Chakrabarti P, Ramakrishnan C, Sali A, and Varadarajan R. (2007) Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol 3, e241.

  56. Das M, Kobayashi M, Yamada Y, Sreeramulu S, Ramakrishnan C, Wakatsuki S, Kato R, and Varadarajan R. (2007) Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts. J Mol Biol 372, 1278-92.

  57. Mondal K, Dastidar A. G, Singh G, Madhusudhanan S, Gande S. L, Vijayraghavan K, and Varadarajan R. (2007) Design and Isolation of Temperature-sensitive Mutants of Gal4 in Yeast and Drosophila. J Mol Biol 370, 939-50.[pdf]

  58. Mondal K, Raghava S, Barua B, Varadarajan R and Gupta M. N. (2007) Role of stimuli-sensitive polymers in protein refolding: alpha-amylase and CcdB (controller of cell division or death B) as model proteins. Langmuir 23, 70-5.

  59. Mondal K, VijayRaghavan K, and Varadarajan R. (2007) Design and utility of temperature-sensitive Gal4 mutants for conditional gene expression in Drosophila. Fly (Austin) 1, 282-6.

  60. Prajapati R. S, Das M, Sreeramulu S, Sirajuddin M, Srinivasan S, Krishnamurthy V, Ranjani R, Ramakrishnan C, and Varadarajan R. (2007) Thermodynamic effects of proline introduction on protein stability. Proteins 66, 480-91.

  61. Prajapati R. S, Indu S, and Varadarajan R. (2007) Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. Biochemistry 46, 10339-52.

  62. Bajaj K, Dewan P. C, Chakrabarti P, Goswami D, Barua B, Baliga C, and Varadarajan R. (2008) Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB. Biochemistry 47, 12964-73.

  63. Das A, Sood A. K, Maiti P. K, Das M, Varadarajan R, and Rao C. N. R. (2008) Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment. Chem Phys Lett 453, 266-273.

  64. Raghava S, Aquil S, Bhattacharyya S, Varadarajan R, and Gupta M. N. (2008) Strategy for purifying maltose binding protein fusion proteins by affinity precipitation. J Chromatogr A 1194, 90-5.

  65. Raghava S, Barua B, Singh P. K, Das M, Madan L, Bhattacharyya S, Bajaj K, Gopal B, Varadarajan R, and Gupta M. N. (2008) Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies. Protein Sci 17, 1987-97.

  66. Bhattacharya S, and Varadarajan R. (2009) Emerging trends at the interface of Chemistry and Biology: Applications to the design of human therapeutics. Indian Academy of Sciences, Platinum Jubilee P1, 1-11.

  67. Krishnan B, Kulothungan S. R, Patra A. K, Udgaonkar J. B, and Varadarajan R. (2009) SecB-mediated protein export need not occur via kinetic partitioning. J Mol Biol 385, 1243-56.

  68. Kulothungan S. R, Das M, Johnson M, Ganesh C, and Varadarajan R. (2009) Effect of Crowding Agents, Signal Peptide, and Chaperone SecB on the Folding and Aggregation of E. coli Maltose Binding Protein. Langmuir 25, 6637-48.

  69. Bhattacharyya S, Rajan R. E, Swarupa Y, Rathore U, Verma A, Udaykumar R, and Varadarajan R. (2010) Design of a non-glycosylated outer domain-derived HIV-1 gp120 immunogen that binds to CD4 and induces neutralizing antibodies. J Biol Chem 285, 27100-10.[pdf]

  70. Bommakanti G, Citron M. P, Hepler R. W, Callahan C, Heidecker G. J, Najar T. A, Lu X, Joyce J. G, Shiver J. W, Casimiro D. R, ter Meulen J, Liang X, and Varadarajan R. (2010) Design of an HA2-based Escherichia coli expressed influenza immunogen that protects mice from pathogenic challenge. Proc Natl Acad Sci U S A 107, 13701-6. (see also Commentary on paper by Eckert and Kay in same issue at www.pnas.org/cgi/doi/10.1073/pnas.1008672107)[pdf]

  71. Indu S, Kumar S. T, Thakurela S, Gupta M, Bhaskara R. M, Ramakrishnan C and Varadarajan R. (2010) Disulfide conformation and design at helix N-termini. Proteins 78, 1228-42.[pdf]

  72. Aggarwal V, Kulothungan S. R, Balamurali M. M, Saranya S. R, Varadarajan R and Ainavarapu S. R. (2011) Ligand-modulated parallel mechanical unfolding pathways of maltose-binding proteins. J Biol Chem 286, 28056-65.

  73. Haimann M. M, Akdogan Y, Philipp R, Varadarajan R, Hinderberger D, and Trommer W. E. (2011) Conformational changes of the chaperone SecB upon binding to a model substrate--bovine pancreatic trypsin inhibitor (BPTI). Biol Chem 392, 849-58.

  74. Indu S, Kochat V, Thakurela S, Ramakrishnan C, and Varadarajan R. (2011) Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets. Proteins 79, 244-60.[pdf]

  75. Saha P, Barua B, Bhattacharyya S, Balamurali M. M, Schief W. R, Baker D and Varadarajan R. (2011) Design and characterization of stabilized derivatives of human CD4D12 and CD4D1. Biochemistry 50, 7891-900.

  76. Tan K. P, Varadarajan R and Madhusudhan M. S. (2011) DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res 39, W242-8.

  77. Adkar B. V, Tripathi A, Sahoo A, Bajaj K, Goswami D, Chakrabarti P, Swarnkar M. K, Gokhale R. S and Varadarajan R. (2012) Protein model discrimination using mutational sensitivity derived from deep sequencing. Structure 20, 371-81.[pdf]

  78. Gautam S, Dubey P, Singh P, Kesavardana S, Varadarajan R and Gupta M. N. (2012) Smart Polymer Mediated Purification and Recovery of Active Proteins from Inclusion Bodies. Journal of Chromatography A 1235, 10-25.

  79. Saha P, Bhattacharyya S, Kesavardhana S, Miranda E. R, Ali P. S, Sharma D and Varadarajan R. (2012) Designed cyclic permutants of HIV-1 gp120: implications for envelope trimer structure and immunogen design. Biochemistry 51, 1836-47.

  80. Tripathi A, Dewan P. C, Barua B, Varadarajan R. (2012) An additional role for the ccd operon of F-plasmid as a transmissible persistence factor. Proc Natl Acad Sci U S A 109, 12497-502.[pdf]

  81. Gautam S, Dubey P, Singh P, Varadarajan R, Gupta M.N. (2012) Simultaneous refolding and purification of recombinant rpoteins by macro-(affinity ligand) facilitated threel-phase partitioning (MLFTPP) Anal. Biochem 430, 56-64.

  82. Hu X, Saha P, Chen X, Kim D, Devarasetty M, Varadarajan R, Jin M. M. (2012) Cell Surface assembly of HIV gp41 six-helix bundles for facile, quantitative measurement of hetero-oligomeric interactions. J.Am. Chem. Soc. 134, 14642-45.

  83. Bommakanti G, Lu X, Citron M.P, Najar T.A, Heidecker G.J, Ter Meulen J, Varadarajan R, Liang X. (2012) Design of E. coli expressed stalk domain immunogens of H1N1 HA that protect mice from lethal challenge. J. Virol.  86, 13434-44.

  84. Gautam S, Dubey P, Varadarajan R, Gupta M.N. (2012) Role of smart polymers in protein purification and refolding.Bioengineered 3, 286-288.

  85. Bhattacharyya S and Varadarajan R. (2013) Packing in molten globules and native states. Curr Opin Struct Biol. 23, 11-21.

  86. Shembekar N, Mallajosyula V. V, Mishra A, Yeolekar L, Dhere R, Kapre S, Varadarajan R, Gupta S.K. (2013) Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the 'Sa' Antigenic Site. PLoS One. 8, e55516.

  87. Bhattacharyya S, Singh P, Rathore U, Purwar M, Wagner D, Arendt H, Destefano J, Labranche C.C, Montefiori D.C, Phogat S, Varadarajan R. (2013) Design of an E. coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies. J Biol Chem 288, 9815-25.[pdf]

  88. Mallajosyula V.V, Citron M.P, Lu X, Ter Meulen J, Varadarajan R, Liang X. (2013) In vitro and in vivo characterization of designed immunogens derived from CD-helix of the stem of influenza hemagglutinin. Proteins 81,1759-75.

  89. Singh P, Sharma L , Kulothungan S.R, Adkar B.V, Prajapati R.S, Ali P.S.S, Krishnan B, Varadarajan R. (2013) Effect of Signal Peptide on Stability and Folding of Escherichia coli Thioredoxin. PLoS One 8, e63442.

  90. Tan K. P, Nguyen T, Patel S, Varadarajan R, Madhusudhan M.S.(2013) Depth: A Web server to compute depth, cavity sizes, detect potential small-molecule binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res W314-21 (doi: 10.1093/nar/gkt503).

  91. Reichenwallner J, Chakour M, Indu S, Varadarajan R, Trommer  W.E. (2013) Maltose Binding Protein Is Partially Structured in Its Molten Globule State. Appl Magn Reson 44, 983-995

  92. Sridharamurthy R, Doraiswamy H, Patel S, Varadarajan R, and Natarajan V. (2013) Extraction of robust voids and pockets in proteins. EuroVis doi:10.2312/PE.EuroVisShort.EuroVisShort2013.067-071.

  93. Jain P.C and Varadarajan R. (2014) A rapid, efficient and economical inverse PCR-based method for generating a Site-Saturation Mutant library. Anal Biochem 449C, 90-98.doi: 10.1016/j.ab.2013.12.002

  94. Tripathi  A and Varadarajan R (2014)  Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing Curr Opin Struct Biol. 24, 63-71: doi: 10.1016/j.sbi.2013.12.001.

  95. Tripathi A, Dewan P.C, Siddique S.A, Varadarajan R. (2014) MazF induced growth inhibition and persister generation in Escherichia coli. J Biol Chem. 289, 4191-205  doi: 10.1074/jbc.M113.510511

  96. Tan K.P, Khare S, Varadarajan R, Madhusudhan M.S. (2014) TSpred: a web server for the rational design of temperature-sensitive mutants. Nucleic Acids Res. 42(Web Server issue): W277-84: doi: 10.1093/nar/gku319.

  97. Mallajosyula V, Citron M, Ferrara F, Lu X, Callahan C, Heidecker G.J,  Sarma S.P,  Flynn J.A, Temperton N.J, Liang X, Varadarajan R. (2014) Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection. Proc Natl Acad Sci U S A 111, E2514-23 :doi: 10.1073/pnas.1402766111.[pdf]

  98. Rathore U, Kesavardhana S, Mallajosyula V.V, Varadarajan R. (2014) Immunogen Design for HIV-1 and Influenza. BBA - Proteins and Proteomics. 1844,1891-1906 : doi:10.1016/j.bbapap.2014.05.010.

  99. Kesavardhana S, Varadarajan R. (2014) Stabilizing the native trimer of HIV-1 Env by destabilizing the heterodimeric interface of the gp41 post-fusion six helix bundle. J Virol. 88, 9590-604: doi:10.1128/JVI.00494-14.

  100. Shembekar N, Mallajosyula V.V, Chaudhary P, Upadhyay V, Varadarajan R, Gupta S.K. (2014) Humanized antibody neutralizing 2009 pandemic H1N1 virus  Biotechnol J. 9, 1594-603 :  DOI: 10.1002/biot.201400083.

  101. Mallajosyula VA, Citron M, Ferrara F, Temperton NJ, Liang X, Flynn JA and Varadarajan R (2015). Hemagglutinin sequence conservation guided stem immunogen design from influenza A H3 subtype. Front. Immunol. 6, 329. doi: 10.3389/fimmu.2015.00329

  102. Malik A, Mallajosyula VV, Mishra NN, Varadarajan R and Gupta SK (2015) Generation and characterization of monoclonal antibodies specific to avian influenza H5N1 hemagglutinin protein. Monoclon. Antib. Immunodiagn. Immunother. 3, 436-41:  doi: 10.1089/mab.2015.0047.

  103. Sahoo A, Khare S, Devanarayanan S, Jain P, Varadarajan R. (2015) Residue proximity information and protein model discrimination using saturation-suppressor  mutagenesis.  Elife. 4:e09532 doi:10.7554/eLife.09532.[pdf]

  104. Srinivasan S, Ghosh M, Maity S, Varadarajan R, (2016) Broadly neutralizing antibodies for therapy of viral infections. Antibody Technology Journal. 6:329.

  105. Valkenburg SA, Mallajosyula VV, Li OT, Chin AW, Carnell G, Temperton N, Varadarajan R, Poon LL. (2016) Stalking influenza by vaccination with pre-fusion headless HA mini-stem. Sci Rep. doi: 10.1038/srep22666.[pdf]

  106. Baliga C , Majhi S, Mondal K , Bhattacharjee A, VijayRaghavan K, Varadarajan R (2016)  Rational elicitation of cold sensitive phenotypes Proc Natl Acad Sci U S A doi: 10.1073/pnas.1604190113

  107. Shembekar N,  Mallajosyula VA,  Malik A, Saini A, Varadarajan R, Gupta SK (2016) Neutralization and binding profile of monoclonal antibodies generated against influenza A H1N1 viruses. Monoclon. Antib. Immunodiagn. Immunother. 35, 191-8. doi: 10.1089/mab.2016.0015. Epub 2016 Jul 27

  108. Tripathi A, Gupta K, Khare S, Jain P. C, Patel S, Kumar P, Pulianmackal A. J, Aghera N, Varadarajan, R. (2016) Molecular determinants of mutant phenotypes, inferred from saturation mutagenesis data. Mol Biol Evol. 33, 2960-75[pdf]

  109. Baliga C, Varadarajan, R, Aghera N (2016) The homodimeric E. coli toxin CcdB (Controller of Cell Division or Death B protein) folds via parallel pathways. Biochemistry. 55, 6019-31

  110. Vijaykrishnaa. N, Melangatha. G, Kumara. R, Khandeliaa. P, Bawaa. P, Varadarajan. R, Vijayraghavana. U. (2016) The fission yeast pre-mRNA processing factor 18  (prp18+) has intron-specific splicing functions with links to G1-S cell cycle progression. J Biol Chem. 291, 27387-27402. doi: 10.1074/jbc.M116.751289.

  111. Malik A, Mallajosyula V, Mishra NN, Arukha AP, Varadarajan R, Gupta SK. (2016) Generation and characterisation of monoclonal antibodies specific to avian influenza H7N9 haemagglutinin protein. Indian J Med Microbiol. 34:489-494. doi: 10.4103/0255-0857.195366.

  112. Tawfik DS, Varadarajan R. (2016)  Editorial overview: Engineering and design. Curr Opin Struct Biol. 39:v-vi. doi: 10.1016/j.sbi.2016.08.004.

  113. Kesavardhana S, Das R, Citron M, Datta R, Ecto L, Srilatha NS, DiStefano D, Swoyer R, Joyce JG, Dutta S, LaBranche CC, Montefiori DC, Flynn JA, Varadarajan R. (2017) Structure based design of cyclically permuted HIV-1 gp120 trimers that elicit neutralizing antibodies. J Biol Chem.292, 278-291. doi: 10.1074/jbc.M116.725614.[pdf]

  114. Najar TA, Khare S, Pandey R, Gupta SK, Varadarajan R. (2017) Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display. Structure.  25: 395-406. doi: 10.1016/j.str.2016.12.016.[pdf]

  115. Khan L, Kumar R, Thiruvengadam R, Parray HA, Makhdoomi MA, Kumar S, Aggarwal  H, Mohata M, Hussain AW, Das R, Varadarajan R, Bhattacharya J, Vajpayee M,  Murugavel KG, Solomon S, Sinha S, Luthra K. (2017) Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library. Sci Repdoi: 10.1038/srep45163.

  116. Rathore U, Saha P, Kesavardhana S, Kumar AA, Datta R, Devanarayanan S, Das R, Mascola JR, Varadarajan R. (2017) Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral  infectivity. J Biol Chem. doi:10.1074/jbc.M117.788919.

  117. Gupta K, Tripathi A, Sahu A,  Varadarajan R.  (2017) Contribution of the chromosomal ccdAB operon to bacterial drug tolerance. J Bacteriol.  doi: 10.1128/JB.00397-17.

  118. Sutton T C, Chakraborty S, Mallajosyula V V A, Lamirande E W, Ganti1 K, Bock K W, Moore I N,Varadarajan R,Subbarao K (2017) Protective efficacy of influenza group 2 hemagglutinin stem-fragment immunogen 2 vaccines. npj Vaccines doi:10.1038/s41541-017-0036-2.

  119. Jones AT, Chamcha V, Kesavardhana S, Shen X, Beaumont D, Das R, Wyatt LS, LaBranche CC, Stanfield-Oakley S, Ferrari G, Montefiori DC, Moss B, Tomaras GD, Varadarajan R, Amara RR (2017) A trimeric HIV-1 envelope gp120 immunogen induces potent and broad anti-V1V2 loop antibodies against HIV-1 in rabbits and rhesus macaques. J Virol. pii: JVI.01796-17. doi: 10.1128/JVI.01796-17

  120. Gupta K and Varadarajan R (2018)  Insights into protein structure, stability and function from saturation mutagenesis Curr Opin Struct Biol. 50: 117-125  doi.org/10.1016/j.sbi.2018.02.006
  121. Cheedarla N, Hemalatha B, Anangi B, Muthuramalingam K, Selvachithiram M, Sathyamurthi P, Kailasam N, Varadarajan R, Swaminathan S, Tripathy S P, Vaniambadi S K, D. Vadakkupattu R and Hanna L E (2018) Evolution of Neutralization Response in HIV-1 Subtype C-Infected Individuals Exhibiting Broad Cross-Clade Neutralization of HIV-1 Strains. Front. Immunol doi.org/10.3389/fimmu.2018.00618

  122. Najar TA, Khare S, Varadarajan R (2018) Rapid mapping of protein binding sites and conformational epitopes by coupling yeast surface display to chemical labeling and deep sequencing. Methods Mol Biol 1785:77-88. doi: 10.1007/978-1-4939-7841-0_6.

  123. Najar TA, Kar U, Flynn J, Varadarajan R (2018) Isolation of an in vitro affinity-matured, thermostable "Headless" HA stem fragment that binds broadly neutralizing antibodies with high affinity Biochemistry 57: 3817-29. doi: 10.1021/acs.biochem.8b00267

  124. Selmke B, Borbat P, Nickolaus C, Varadarajan R, Freed J, Trommer W. (2018) Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State as Studied by EPR Spectroscopy. Biochemistry doi: 10.1021/acs.biochem.8b00322
  125. Purwar M, Pokorski J, Singh P, Bhattacharyya S, Arendt H, DeStefano J, La Branche CC, Montefiori DC, Finn MGVaradarajan R (2018)  Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles. Vaccine (Accepted)

  126. Rathore U, Purwar M, Vignesh VS, Das  RKumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R (2018)   Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4 binding site neutralizing antibodies. J Biol Chem. doi:10.1074/jbc.RA118.005006  (In Press).