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Patel, Siddharth and Indu, S and Ramakrishnan, C and Varadarajan, Raghavan (2013) PROTEIN DISULFIDE ANALYSIS AND DESIGN. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 296-311.
Tandon, Himani and Sharma, Arun and Wadhwa, Saruchi and Varadarajan, Raghavan and Singh, Ramandeep and Srinivasan, Narayanaswamy and Sandhya, Sankaran (2019) Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 294 (23). pp. 9048-9063.
Khare, Shruti and Bhasin, Munmun and Sahoo, Anusmita and Varadarajan, Raghavan (2019) Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 87 (4). pp. 326-336.
Jones, Andrew T and Shen, Xiaoying and Walter, Korey L and LaBranche, Celia C and Wyatt, Linda S and Tomaras, Georgia D and Montefiori, David C and Moss, Bernard and Barouch, Dan H and Clements, John D and Kozlowski, Pamela A and Varadarajan, Raghavan and Amara, Rama Rao (2019) HIV-1 vaccination by needle-free oral injection induces strong mucosal immunity and protects against SHIV challenge. In: NATURE COMMUNICATIONS, 10 .
Purwar, Mansi and Pokorski, Jonathan K and Singh, Pranveer and Bhattacharyya, Sanchari and Arendt, Heather and DeStefano, Joanne and La Branche, Celia C and Montefiori, David C and Finn, MG and Varadarajan, Raghavan (2018) Design, display and immunogenicity of HIV1 gp120 fragment immunogens on virus-like particles. In: VACCINE, 36 (42). pp. 6345-6353.
Raghunandanan, Sajith and Ramachandran, Ranjit and Gomez, Roshna Lawrence and Devanarayanan, Sivasankar and Bommakanti, Akhila and Kondapi, Anand Kumar and Varadarajan, Raghavan and Kumar, Ramakrishnan Ajay (2018) Rv0474 is a copper-responsive transcriptional regulator that negatively regulates expression of RNA polymerase subunit in Mycobacterium tuberculosis. In: FEBS JOURNAL, 285 (20). pp. 3849-3869.
Rathore, Ujjwal and Purwar, Mansi and Vignesh, Venkada Subramanian and Das, Raksha and Kumar, Aditya Arun and Bhattacharyya, Sanchari and Arendt, Heather and DeStefano, Joanne and Wilson, Aaron and Parks, Christopher and La Branche, Celia C and Montefiori, David C and Varadarajan, Raghavan (2018) Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 293 (39). pp. 15002-15020.
Selmke, Benjamin and Borbat, Peter P and Nickolaus, Chen and Varadarajan, Raghavan and Freed, Jack H and Trommer, Wolfgang E (2018) Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State As Studied by Electron Paramagnetic Resonance Spectroscopy. In: BIOCHEMISTRY, 57 (38). pp. 5507-5512.
Najar, Tariq Ahmad and Kar, Uddipan and Flynn, Jessica A and Varadarajan, Raghavan (2018) Isolation of an in Vitro Affinity-Matured, Thermostable ``Headless'' HA Stem Fragment That Binds Broadly Neutralizing Antibodies with High Affinity. In: BIOCHEMISTRY, 57 (26). pp. 3817-3829.
Gupta, Kritika and Varadarajan, Raghavan (2018) Insights into protein structure, stability and function from saturation mutagenesis. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 50 . pp. 117-125.
Jones, Andrew T. and Chamcha, Venkateswarlu and Kesavardhana, Sannula and Shen, Xiaoying and Beaumont, David and Das, Raksha and Wyatt, Linda S and LaBranche, Celia C and Stanfield-Oakley, Sherry and Ferrari, Guido and Montefiori, David C and Moss, Bernard and Tomaras, Georgia D and Varadarajan, Raghavan and Amaraa, Rama Rao (2018) A Trimeric HIV-1 Envelope gp120 Immunogen Induces Potent and Broad Anti-V1V2 Loop Antibodies against HIV-1 in Rabbits and Rhesus Macaques. In: JOURNAL OF VIROLOGY, 92 (5).
Khan, Lubina and Kumar, Rajesh and Thiruvengadam, Ramachandran and Parray, Hilal Ahmad and Makhdoomi, Muzamil Ashraf and Kumar, Sanjeev and Aggarwal, Heena and Mohata, Madhav and Hussain, Abdul Wahid and Das, Raksha and Varadarajan, Raghavan and Bhattacharya, Jayanta and Vajpayee, Madhu and Murugavel, K G and Solomon, Suniti and Sinha, Subrata and Luthra, Kalpana (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. In: SCIENTIFIC REPORTS, 7 .
Gupta, Kritika and Varadarajan, Raghavan and Tripathi, Arti (2017) Contribution of the chromosomal ccdAB operon to bacterial drug tolerance. In: PROTEIN SCIENCE, 26 (1, SI). p. 165.
Rathore, Ujjwal and Saha, Piyali and Kesavardhana, Sannula and Kumar, Aditya Arun and Datta, Rohini and Devanarayanan, Sivasankar and Das, Raksha and Mascola, John R and Varadarajan, Raghavan (2017) Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 292 (4). pp. 10197-10219.
Najar, Tariq Ahmad and Khare, Shruti and Pandey, Rajesh and Gupta, Satish K and Varadarajan, Raghavan (2017) Mapping Protein Binding Sites and Conformational Epitopes Using Cysteine Labeling and Yeast Surface Display. In: STRUCTURE, 25 (3). pp. 395-406.
Sutton, Troy C and Chakraborty, Saborni and Mallajosyula, Vamsee V A and Lamirande, Elaine W and Ganti, Ketaki and Bock, Kevin W and Moore, Ian N and Varadarajan, Raghavan and Subbarao, Kanta (2017) Protective efficacy of influenza group 2 hemagglutinin stem-fragment immunogen vaccines. In: NPJ VACCINES, 2 .
Kesavardhana, Sannula and Das, Raksha and Citron, Michael and Datta, Rohini and Ecto, Linda and Srilatha, Nonavinakere Seetharam and DiStefano, Daniel and Swoyer, Ryan and Joyce, Joseph G and Dutta, Somnath and LaBranche, Celia C and Montefiori, David C and Flynn, Jessica A and Varadarajan, Raghavan (2017) Structure-based Design of Cyclically Permuted HIV-1 gp120 Trimers That Elicit Neutralizing Antibodies. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 292 (1). 278+.
Vijaykrishna, Nagampalli and Melangath, Geetha and Kumar, Rakesh and Khandelia, Piyush and Bawa, Pushpinder and Varadarajan, Raghavan and Vijayraghavan, Usha (2016) The Fission Yeast Pre-mRNA-processing Factor 18 (prp18(+)) Has Intron-specific Splicing Functions with Links to G(1)-S Cell Cycle Progression. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 291 (53). 27387+.
Baliga, Chetana and Varadarajan, Raghavan and Aghera, Nilesh (2016) Homodimeric Escherichia coli Toxin CcdB (Controller of Cell Division or Death B Protein) Folds via Parallel Pathways. In: BIOCHEMISTRY, 55 (43). pp. 6019-6031.
Tripathi, Arti and Gupta, Kritika and Khare, Shruti and Jain, Pankaj C and Patel, Siddharth and Kumar, Prasanth and Pulianmackal, Ajai J and Aghera, Nilesh and Varadarajan, Raghavan (2016) Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data. In: MOLECULAR BIOLOGY AND EVOLUTION, 33 (11). pp. 2960-2975.
Baliga, Chetana and Majhi, Sandipan and Mondal, Kajari and Bhattacharjee, Antara and VijayRaghavan, K and Varadarajan, Raghavan (2016) Rational elicitation of cold-sensitive phenotypes. In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113 (18). E2506-E2515.
Sahoo, Anusmita and Khare, Shruti and Devanarayanan, Sivasankar and Jain, Pankaj C and Varadarajan, Raghavan (2016) Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis. In: ELIFE, 4 .
Valkenburg, Sophie A and Mallajosyula, Vamsee Aditya V and Li, Olive TW and Chin, Alex WH and Carnell, George and Temperton, Nigel and Varadarajan, Raghavan and Poon, Leo LM (2016) Stalking influenza by vaccination with pre-fusion headless HA mini-stem. In: SCIENTIFIC REPORTS, 6 .
Mallajosyula, Vamsee Aditya V and Citron, Michael and Ferrara, Francesca and Temperton, Nigel J and Liang, Xiaoping and Flynn, Jessica A and Varadarajan, Raghavan (2015) Hemagglutinin sequence conservation guided stem immunogen design from influenza A H3 subtype. In: FRONTIERS IN IMMUNOLOGY, 6 .
Shembekar, Nachiket and Mallajosyula, Vamsee Aditya V and Chaudhary, Piyush and Upadhyay, Vaibhav and Varadarajan, Raghavan and Gupta, Satish Kumar (2014) Humanized antibody neutralizing 2009 pandemic H1N1 virus. In: BIOTECHNOLOGY JOURNAL, 9 (12). pp. 1594-1603.
Rathore, Ujjwal and Kesavardhana, Sannula and Mallajosyula, Vamsee Aditya V and Varadarajan, Raghavan (2014) Immunogen design for HIV-1 and influenza. In: BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844 (11, SI). pp. 1891-1906.
Tripathi, Arti and Dewan, Pooja C and Siddique, Shahbaz A and Varadarajan, Raghavan (2014) MazF-induced Growth Inhibition and Persister Generation in Escherichia coli. In: JOURNAL OF BIOLOGICAL CHEMISTRY, 289 (7). pp. 4191-4205.
Tripathi, Arti and Varadarajan, Raghavan (2014) Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 24 . pp. 63-71.
Kesavardhana, Sannula and Varadarajan, Raghavan (2014) Stabilizing the Native Trimer of HIV-1 Env by Destabilizing the Heterodimeric Interface of the gp41 Postfusion Six-Helix Bundle. In: JOURNAL OF VIROLOGY, 88 (17). pp. 9590-9604.
Tan, Kuan Pern and Khare, Shruti and Varadarajan, Raghavan and Madhusudhan, Mallur Srivatsan (2014) TSpred: a web server for the rational design of temperature-sensitive mutants. In: NUCLEIC ACIDS RESEARCH, 42 (W1). W277-W284.
Jain, Pankaj C and Varadarajan, Raghavan (2014) A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. In: ANALYTICAL BIOCHEMISTRY, 449 . pp. 90-98.
Tan, Kuan Pern and Nguyen, Thanh Binh and Patel, Siddharth and Varadarajan, Raghavan and Madhusudhan, MS (2013) Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK(a) of ionizable residues in proteins. In: Nucleic Acids Research, 41 (W1). W314-W321.
Bhattacharyya, Sanchari and Singh, Pranveer and Rathore, Ujjwal and Purwar, Mansi and Wagner, Denise and Arendt, Heather and DeStefano, Joanne and LaBranche, Celia C and Montefiori, David C and Phogat, Sanjay and Varadarajan, Raghavan (2013) Design of an Escherichia coli expressed HIV-1 gp120 fragment Immunogen that binds to b12 and induces broad and potent neutralizing antibodies. In: Journal of Biological Chemistry, 288 (14). pp. 9815-9825.
Mallajosyula, Vamsee Aditya V and Citron, Michael and Lu, Xianghan and ter Meulen, Jan and Varadarajan, Raghavan and Liang, Xiaoping (2013) In vitro and in vivo characterization of designed immunogens derived from the CD-helix of the stem of influenza hemagglutinin. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81 (10). pp. 1759-1775.
Shembekar, Nachiket and Mallajosyula, Vamsee Aditya V and Mishra, Arpita and Yeolekar, Leena and Dhere, Rajeev and Kapre, Subhash and Varadarajan, Raghavan and Gupta, Satish Kumar (2013) Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the `Sa' Antigenic Site. In: PLOS ONE, 8 (1).
Reichenwallner, Joerg and Chakour, Mohammed and Indu, S and Varadarajan, Raghavan and Trommer, Wolfgang E (2013) Maltose Binding Protein Is Partially Structured in Its Molten Globule State. In: APPLIED MAGNETIC RESONANCE, 44 (8). pp. 983-995.
Tripathi, Arti and Dewan, Pooja C and Barua, Bipasha and Varadarajan, Raghavan (2012) Additional role for the ccd operon of F-plasmid as a transmissible persistence factor. In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109 (31). pp. 12497-12502.
Gautam, Saurabh and Dubey, Priyanka and Singh, Pranveer and Kesavardhana, S and Varadarajan, Raghavan and Gupta, Munishwar N (2012) Smart polymer mediated purification and recovery of active proteins from inclusion bodies. In: Journal of Chromatography A, 1235 . pp. 10-25.
Gautam, Saurabh and Dubey, Priyanka and Singh, Pranveer and Varadarajan, Raghavan and Gupta, Munishwar N (2012) Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning. In: Analytical Biochemistry, 430 (1). pp. 56-64.
Varadarajan, Raghavan and Sharma, Deepak and Chakraborty, Kausik and Patel, Mayuri and Citron, Michael and Sinha, Prem and Yadav, Ramkishor and Rashid, Umar and Kennedy, Sarah and Eckert, Debra and Geleziunas, Romas and Bramhill, David and Schleif, William and Liang, Xiaoping and Shiver, John (2005) Characterization of gp120 and its Single-Chain Derivatives, $gp120-CD4_D_1_2$ and gp120-M9: Implications for Targeting the $CD4_i$ Epitope in Human Immunodeficiency Virus Vaccine Design. In: Journal of Virology, 79 (3). pp. 1713-1723.
Flint, Jasper and Aghera, Nilesh K and Varadarajan, Raghavan and Jaswal, Sheila (2019) Application of Numerical Simulations to Extract Protein Folding Parameters from Hydrogen Exchange Mass Spectrometry Experiments under Native Conditions. In: BIOPHYSICAL JOURNAL, 116 (3, 1). 334A-335A.
Tawfik, Dan S and Varadarajan, Raghavan (2016) Editorial overview: Engineering and design. In: CURRENT OPINION IN STRUCTURAL BIOLOGY, 39 . V-VI.
Jain, Pankaj C and Patel, Siddharth and Kumar, Prasanth and Varadarajan, Raghavan (2016) Structural and Mechanistic Insights Derived from Saturation Mutagenesis of CcdB. In: BIOPHYSICAL JOURNAL, 110 (3, 1). 42A.
Rathore, Ujjwal and Saha, Piyali and Kesavardhana, Sannula and Kumar, Aditya A and Mascola, John R and Varadarajan, Raghavan (2014) N-linked Glycosylation of HIV-1 core gp120 is Not Required for Native Trimer Formation or Viral Infectivity. In: PROTEIN SCIENCE, 23 (1).
