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Profile Details
Subject Matter Expertise
Services
Work Experience
Assistant Professor
SASTRA University
December 2019 - Present 
Senior Scientist
VivagenDX Labs
July 2019 - Present
Assistant Professor
Jaypee University of Information Technology
September 2015 - June 2019
Postdoctoral Research Associate
Rice University
September 2012 - June 2014
Postdoctoral Research Associate
University of Wisconsin Madison
October 2011 - September 2012
Postdoctoral Research Associate
Iowa State University
July 2009 - September 2011
Research Assistant
Jawaharlal Nehru University
October 2008 - February 2009
Education
Ph.D
Jawaharlal nehru university
July 2003 - July 2008
PhD (Center for Computational Biology and Bioinformatics)
Jawaharlal Nehru University
2003 - 2008
PG Diploma in Bioinformatics (Center for Computational Biology and Bioinformatics)
Jawaharlal Nehru University
2002 - 2003
M.Sc. Microbial Gene Technology (Microbial Technology)
Madurai Kamaraj University
2000 - 2002
B.Sc (Microbiology)
University of Madras
1997 - 2000
Certifications
- Certification details not provided.
Publications
JOURNAL ARTICLE
Alexandar SP, Yennamalli RM, Ulaganathan V(2022). Coarse grained modelling highlights the binding differences in the two different allosteric sites of the Human Kinesin EG5 and its implications in inhibitor design . Computational biology and chemistry.
Mhade S, Panse S, Tendulkar G, Awate R, Narasimhan Y, Kadam S, Yennamalli RM, Kaushik KS(2021). AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to <i>Corynebacterium striatum</i>, an Emerging Pathogen . Frontiers in cellular and infection microbiology.
Chatterjee J, Coe RA, Acebron K, Thakur V, Yennamalli RM, Danila F, Lin HC, Balahadia CP, Bagunu E, Padhmapreiya POS, et al.(2021). Identification of a low CO2 responsive mutant from chemical mutagenesis of Setaria viridis shows that reduced carbonic anhydrase severely limits C4 photosynthesis . Journal of experimental botany.
Pal P, Modi M, Ravichandran S, Yennamalli R, Priyadarshini R(2021). DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus . Frontiers in microbiology.
Sanjay Singh, Ragothaman M. Yennamalli, Manish Gupta, Harish Changotra(2020). Identification of nsSNPs of transcription factor E2F1 predisposing individuals to lung cancer and head and neck cancer . Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 821. p. 111704. Elsevier {BV}
Poonam Katoch, Kinam Gupta, Ragothaman M. Yennamalli, Jitendraa Vashistt, Gopal Singh Bisht, Rahul Shrivastava(2020). Random insertion transposon mutagenesis of Mycobacterium fortuitum identified mutant defective in biofilm formation . Biochemical and Biophysical Research Communications. Elsevier {BV}
Pulkit Anupam Srivastava, Eric L. Hegg, Brian G. Fox, Ragothaman M. Yennamalli(2020). PreDSLpmo: A neural network-based prediction tool for functional annotation of lytic polysaccharide monooxygenases . Journal of Biotechnology. 308. p. 148--155. Elsevier {BV}
Deepa Teotia, Mariam Gaid, Shashank S. Saini, Aparna Verma, Ragothaman M. Yennamalli, Satyajeet P. Khare, Kiran Ambatipudi, Javid Iqbal Mir, Till Beuerle, Robert Hänsch, et al.(2019). Cinnamate‐CoA ligase is involved in biosynthesis of benzoate‐derived biphenyl phytoalexin in Malus × domestica ‘Golden Delicious’ cell cultures . The Plant Journal. Wiley
Singh D, Soni S, Khan S, Sarangi AN, Yennamalli RM, Aggarwal R, Veerapu NS(2019). Genome-wide mutagenesis of hepatitis C virus reveals genome ability to overcome detrimental mutations . Journal of virology.
Singaraju GS, Sagar A, Kumar A, Samuel JS, Hazra JP, Sannigrahi MK, Yennamalli RM, Ashish F, Rakshit S(2019). Structural basis of the strong cell-cell junction formed by cadherin-23 . The FEBS journal.
Vijay Singh Gondil, Taru Dube, Jiban J. Panda, Ragothaman M. Yennamalli, Kusum Harjai, Sanjay Chhibber (2019). Comprehensive evaluation of chitosan nanoparticle based phage lysin delivery system; a novel approach to counter S. pneumoniae infections . International Journal of Pharmaceutics.
Chauhan D, Srivastava PA, Ritzl B, Yennamalli RM, Cava F, Priyadarshini R(2019). Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1 . Frontiers in microbiology.
Poonam, Ragothaman M. Yennamalli, Gopal S. Bisht, Rahul Shrivastava(2019). Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions . 3 Biotech. 9. (4). Springer Science and Business Media {LLC}
Deepika Chauhan, Pulkit A. Srivastava, Vidushi Agnihotri, Ragothaman M. Yennamalli, Richa Priyadarshini(2019). Structure and function prediction of arsenate reductase from Deinococcus indicus DR1 . Journal of Molecular Modeling. 25. (1). Springer Science and Business Media {LLC}
Mansi Arora, Ragothaman M. Yennamalli, Taner Z. Sen(2018). Application of Molecular Simulations Toward Understanding Cellulase Mechanisms . BioEnergy Research. 11. (4). p. 850--867. Springer Nature
Arora R, Bharval P, Sarswati S, Sen TZ, Yennamalli RM(2018). Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region . Journal of molecular graphics & modelling.
Kumar A, Mehta V, Raj U, Varadwaj PK, Udayabanu M, Yennamalli RM, Singh TR(2018). Computational and in-vitro validation of natural molecules as potential Acetylcholinesterase inhibitors and neuroprotective agents . Current Alzheimer research.
Shukla, A., Yennamalli, R.M., Singh, T.R.(2018). Network and structure based inference of functional single nucleotide polymorphisms associated with the TGFβ1 gene and its role in colorectal cancer (CRC) . Gene Reports. 11. p. 131-142.
Nancy Singh, Sunil Datt Sharma, Ragothaman M. Yennamalli(2017). Modified S-transform as a tool to identify secondary structure elements in RNA . Bio-Algorithms and Med-Systems. 0. (0). Walter de Gruyter {GmbH}
Chauhan D, Srivastava PA, Yennamalli RM, Priyadarshini R(2017). Draft Genome Sequence of Deinococcus indicus DR1, a Novel Strain Isolated from a Freshwater Wetland . Genome announcements.
Chauhan, D., Srivastava, P.A., Yennamalli, R.M., Priyadarshini, R.(2017). Draft genome sequence of Deinococcus indicus DR1, a novel strain isolated from a freshwater wetland . Genome Announcements. 5. (31). p. e00754-17.
Vij, A., Yennamalli, R.M., Changotra, H.(2017). Non-synonymous single nucleotide polymorphisms of ATG5 destabilize ATG12–ATG5/ATG16L1 complex: An enzyme with E3 like activity of ubiquitin conjugation system . Meta Gene. 13. p. 38-47.
Jones, D.C., Zheng, W., Huang, S., Du, C., Zhao, X., Yennamalli, R.M., Sen, T.Z., Nettleton, D., Wurtele, E.S., Li, L.(2016). A Clade-specific arabidopsis gene connects primary metabolism and senescence . Frontiers in Plant Science. 7. (JULY2016).
Chauhan, M., Yennamalli, R.M., Garlapati, V.K.(2016). Biochemical characterization and molecular modeling of a unique lipase from Staphylococcus arlettae JPBW-1 . Engineering in Life Sciences. 16. (8). p. 762-768.
Chang, C.-Y., Lohman, J.R., Cao, H., Tan, K., Rudolf, J.D., Ma, M., Xu, W., Bingman, C.A., Yennamalli, R.M., Bigelow, L., et al.(2016). Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus . Biochemistry. 55. (36). p. 5142-5154.
Huang, T., Chang, C.-Y., Lohman, J.R., Rudolf, J.D., Kim, Y., Chang, C., Yang, D., Ma, M., Yan, X., Crnovcic, I., et al.(2016). Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027 . Journal of Antibiotics. 69. (10). p. 731-740.
Gautam, L.K., Yennamalli, R.M., Rathore, J.S.(2016). Implication on the function of novel Xn-relE toxin structure of xenorhabdus nematophila using homology modeling . Current Bioinformatics. 11. (3).
Cao, H., Tan, K., Wang, F., Bigelow, L., Yennamalli, R.M., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Joachimiak, A., Kharel, M.K., et al.(2016). Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate . Structural Dynamics. 3. (3).
Singh, S., Michalska, K., Bigelow, L., Endres, M., Kharel, M.K., Babnigg, G., Yennamalli, R.M., Bingman, C.A., Joachimiak, A., Thorson, J.S., et al.(2015). Structural characterization of cals8, a tdp-α-d-glucose dehydrogenase involved in calicheamicin aminodideoxypentose biosynthesis . Journal of Biological Chemistry. 290. (43). p. 26249-26258.
Weerth, R.S., Michalska, K., Bingman, C.A., Yennamalli, R.M., Li, H., Jedrzejczak, R., Wang, F., Babnigg, G., Joachimiak, A., Thomas, M.G., et al.(2015). Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution . Proteins: Structure, Function and Bioinformatics. 83. (2). p. 383-388.
Auldridge, M.E., Cao, H., Sen, S., Franz, L.P., Bingman, C.A., Yennamalli, R.M., Phillips, G.N., Mead, D., Steinmetz, E.J.(2015). LucY: A versatile new fluorescent reporter protein . PLoS ONE. 10. (4).
Ilgu, M., Fulton, D.B., Yennamalli, R.M., Lamm, M.H., Sen, T.Z., Nilsen-Hamilton, M.(2014). An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures . RNA. 20. (6). p. 815-824.
Book, A.J., Yennamalli, R.M., Takasuka, T.E., Currie, C.R., Phillips, G.N., Fox, B.G.(2014). Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases . Biotechnology for Biofuels. 7. (1).
Elshahawi, S.I., Ramelot, T.A., Seetharaman, J., Chen, J., Singh, S., Yang, Y., Pederson, K., Kharel, M.K., Xiao, R., Lew, S., et al.(2014). Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19 . ACS Chemical Biology. 9. (10). p. 2347-2358.
Yennamalli, R., Arangarasan, R., Bryden, A., Gleicher, M., Phillips Jr., G.N.(2014). Using a commodity high-definition television for collaborative structural biology . Journal of Applied Crystallography. 47. (3). p. 1153-1157.
Wang, F., Zhou, M., Singh, S., Yennamalli, R.M., Bingman, C.A., Thorson, J.S., Phillips, G.N.(2013). Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis . Proteins: Structure, Function and Bioinformatics. 81. (7). p. 1277-1282.
Yennamalli, R.M., Rader, A.J., Kenny, A.J., Wolt, J.D., Sen, T.Z.(2013). Endoglucanases: Insights into thermostability for biofuel applications . Biotechnology for Biofuels. 6. (1).
Rader, A.J., Yennamalli, R.M., Harter, A.K., Sen, T.Z.(2012). A rigid network of long-range contacts increases thermostability in a mutant endoglucanase . Journal of Biomolecular Structure and Dynamics. 30. (6). p. 628-637.
Khan, S.N., Yennamalli, R., Subbarao, N., Khan, A.U.(2011). Mitoxantrone Induced Impediment of Histone Acetylation and Structural Flexibility of the Protein . Cell Biochemistry and Biophysics. 60. (3). p. 209-218.
Yennamalli, R.M., Rader, A.J., Wolt, J.D., Sen, T.Z.(2011). Thermostability in endoglucanases is fold-specific . BMC Structural Biology. 11.
Yennamalli, R.M., Wolt, J.D., Sen, T.Z.(2011). Dynamics of endoglucanase catalytic domains: Implications towards thermostability . Journal of Biomolecular Structure and Dynamics. 29. (3). p. 509-526.
Kampmann, T., Yennamalli, R., Campbell, P., Stoermer, M.J., Fairlie, D.P., Kobe, B., Young, P.R.(2009). In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses . Antiviral Research. 84. (3). p. 234-241.
Vashist, J., Vishvanath, Kapoor, R., Kapil, A., Yennamalli, R., Subbarao, N., Rajeswari, M.R.(2009). Interaction of nalidixic acid and ciprofloxacin with wild type and mutated quinolone-resistance-determining region of DNA gyrase a . Indian Journal of Biochemistry and Biophysics. 46. (2). p. 147-153.
Das, S., Yennamalli, R.M., Vishnoi, A., Gupta, P., Bhattacharya, A.(2009). Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains . Journal of Biosciences. 34. (3). p. 397-404.
Yennamalli, R., Subbarao, N., Kampmann, T., McGeary, R.P., Young, P.R., Kobe, B.(2009). Identification of novel target sites and an inhibitor of the dengue virus E protein . Journal of Computer-Aided Molecular Design. 23. (6). p. 333-341.
Mueller, D.S., Kampmann, T., Yennamalli, R., Young, P.R., Kobe, B., Mark, A.E.(2008). Histidine protonation and the activation of viral fusion proteins . Biochemical Society Transactions. 36. (1). p. 43-45.
Khan, S.N., Islam, B., Yennamalli, R., Zia, Q., Subbarao, N., Khan, A.U.(2008). Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin . Journal of Pharmaceutical and Biomedical Analysis. 48. (4). p. 1096-1104.
Khan, S.N., Islam, B., Yennamalli, R., Sultan, A., Subbarao, N., Khan, A.U.(2008). Interaction of mitoxantrone with human serum albumin: Spectroscopic and molecular modeling studies . European Journal of Pharmaceutical Sciences. 35. (5). p. 371-382.
PREPRINT
Sankar Mahesh, Deepa Sethi, Richa Priyadarshini, Ragothaman M. Yennamalli (2021). Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes .
OTHER
Chauhan, Deepika; Srivastava, Pulkit Anupam; Agnihotri, Vidushi; Yennamalli, Ragothaman M; Priyadarshini, Richa (2019). Arsenate Reductase (ArsC) of Deinococcus indicus DR1 . modelarchive.org.
Singaraju GS, Kumar A, Samuel JS, Sagar A, Hazra JP, Sannigrahi MK, Yennamalli RM, Ashish FNU, Rakshit S(2017). Molecular mechanism of cell-cell adhesion mediated by cadherin-23 .
Yennamalli, Ragothaman;Chauhan, Mamta;Garlapati, Vijay Kumar (2016). Staphylococcus aureus Capsular Polysaccharide D . modelarchive.org.
Gautam, Lalit Kumar;Yennamalli, Ragothaman M;Rathore, Jitendra Singh (2016). Xenorhabdus nematophila RelE antitoxin . modelarchive.org.
Gautam, Lalit Kumar;Yennamalli, Ragothaman M;Rathore, Jitendra Singh (2016). Xenorhabdus nematophila RelE toxin . modelarchive.org.
Book, Adam J.;Yennamalli, Ragothaman M.;Takasuka, Taichi E.;Currie, Cameron R.;Phillips Jr., George N.;Fox, Brian G. (2014). Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases . modelarchive.org.
Book, Adam J.;Yennamalli, Ragothaman M.;Takasuka, Taichi E.;Currie, Cameron R.;Phillips Jr., George N.;Fox, Brian G. (2014). Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases . modelarchive.org.
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