Welcome to

Yennamalli Lab

Ragothaman M. Yennamalli, Ph.D

Assistant Professor-III
PhD (2008), Jawaharlal Nehru University, India

Dr. Yennamalli is a computational biologist with a more than a decade of experience in predictive modelling and biomolecular simulation projects. Dr. Yennamalli’s skills involve machine learning, systems biology, molecular docking, molecular dynamics simulation, coarse grained modelling, data mining, data analytics, and molecular modelling. He has contributed to multiple diverse projects that focus on basic and applied sciences. His experience in computational structural biology is critical in finding answers to bigger questions in life. After the completion of his PhD degree from the prestigious Jawaharlal Nehru University, he gained more experience as a Post Doctoral Research Associate at Iowa State University, University of Wisconsin-Madison, and at Rice University, USA. In 2018, he was featured in the Early-Career Researcher series of Communications Biology (Nature Publications)

Current Position

  • Assistant Professor-III SASTRA Deemed to be University, Thanjavur, Tamil Nadu

Previous Positions

  • Assistant Professor at Jaypee University of Information Technology , Waknaghat, Himachal Pradesh.

  • Postdoctoral Research Associate in the Laboratory of Prof. George N. Phillips, Jr. at Rice University, Houston, Texas.

  • Postdoctoral Research Associate in the Laboratory of Prof. George N. Phillips, Jr. at the University of Wisconsin-Madison Madison, Wisconsin.

  • Postdoctoral Research Associate in the lab of Dr. Taner Z. Sen, Iowa State University, Ames, Iowa.

  • Research Assistant in the lab of Prof. Alok Bhattacharya, Jawaharlal Nehru University, New Delhi.

  • Ph.D. Student (Thesis advisor: Dr. Naidu Subbarao), Jawaharlal Nehru University, New Delhi (2003–2008)

Teaching



Courses taught at:


Rice University

  • BIOC 115 Freshman Seminar in Local Biology Research (Fall 2013 and Spring 2014)
  • BIOC 482 Structural Biology, Teaching Assistant (Spring 2014)



Jaypee University of Information Technology

  • 10B11BI211 Structural Biology (Spring 2018, Spring 2017, Spring 2016)
  • 10B17BI271 Structural Biology Lab (Spring 2018, Spring 2017, Spring 2016)
  • 15B11BI421 Programming Languages for Bioinformatics (Spring 2018, Spring 2017, Spring 2016)
  • 15B17BI472 Programming Languages for Bioinformatics Lab (Spring 2018, Spring 2017, Spring 2016)
  • 14B11BI372 Linux Lab (Fall 2018, Fall 2017, Fall 2016)
  • 15B11BI511 Structural Bioinformatics (Fall 2018, Fall 2017, Fall 2016, Fall 2015)
  • 15B11BI571 Structural Bioinformatics Lab (Fall 2018, Fall 2017, Fall 2016, Fall 2015)
  • 14B1WBI733 Clinical Data Management Systems (Fall 2016)
  • 14B1WBI732 Computational Systems Biology (Fall 2017, Fall 2016, Fall 2015)
  • 16B11BI611 Computer Aided Drug Design (Spring 2018, Spring 2019)
  • 16B17BI671 Computer Aided Drug Design Lab (Spring 2018, Spring 2019)



SASTRA Deemed to be University

  • BBTDBT612 and MBTDBT612 Systems Biology (Spring 2020)
  • Practical Machine Learning-Value Added Course (Spring 2020)
  • BBIDBI703R01 Systems Biology (Fall 2020)
  • INT529 Big Data Analytics in Genomics (Fall 2020)

Our Interest

Welcome to the lab of Dr. Ragothaman M. Yennamalli at SASTRA Deemed to be University, Thanjavur. We are part of School of Chemical and Biotechnology.

Current work – The Yennamalli lab works on interdisciplinary research combining techniques of Computational modeling, Systems Biology, Machine learning, and Structural Bioinformatics. Some of the current areas of research are:

  • Carbohydrate-Active enZymes (CAZymes) – their molecular function and dynamics
  • Lytic Polysaccharide Monooxygenases (LPMO) – structural analysis and dynamics
  • Comparative genomics of Deinococcus genomes
  • Transglutaminase and their involvement in celiac disease


Publications

Original Investigations

  1. Yennamalli RM, Srivastava PA, Sarswati S, Garlapati VK. Recombinant production and Molecular Docking studies of Casoplatelin, a bioactive peptide. The Open Biotechnology Journal. 14: 84-92.
  2. Singh S, Yennamalli RM, Gupta M, Changotra H. (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: 111704.
  3. Srivastava PA, Hegg EL, Fox BG, Yennamalli RM*. (2020) PreDSLpmo: a neural network-based prediction tool for functional annotation of lytic polysaccharide monooxygenases. Journal of Biotechnology. 308:148-155.
  4. (*Corresponding Author)
  5. Gondil VS, Dube T, Panda JJ, Yennamalli RM, Harjai K, Chhibber S. (2020) Comprehensive evaluation of chitosan nanoparticle based phage lysin delivery system; a novel approach to counter S. pneumoniae infections. International Journal of Pharmaceutics.573: 118850.
  6. Katoch P, Gupta K, Yennamalli RM, Vashistt J, Bisht GS, Shrivastava R. (2020) Random insertion transposon mutagenesis of Mycobacterium fortuitum identified mutant defective in biofilm formation. Biochemical and Biophysical Research Communications. 521(4): 991-996.
  7. Singh D, Soni S, Khan S, Sarangi A, Yennamalli RM, Aggarwal R, Veerapu NS.(2020) Full-genome mutant libraries of hepatitis C virus reveal genome plasticity for replication. Journal of Virology. 94(3): e01327-19.
  8. Teotia D, Gaid M, Saini SS, Verma A, Yennamalli RM, Khare SP, Ambatipudi K, Mir JI, Hänsch R, Partha Roy P, Agrawal PK, Beerhues L, Sircar D. (2019) Cinnamate:CoA-ligase is involved in benzoate-derived biphenyl phytoalexin biosynthesis in Malus×domestica 'Golden Delicious' cell cultures. The Plant Journal. 100(6): 1176-1192.
  9. 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. 10:1449.
  10. Poonam, Yennamalli RM, Bisht GS, Shrivastava R. (2019) Ribosomal Maturation Factor (RimP) is essential for Survival of Nontuberculous Mycobacteria Mycobacterium fortuitum under In vitro Acidic Stress Conditions. 3Biotech. 9(4):127.
  11. Arora R, Bharval P, Sarswati S, Sen TZ, Yennamalli RM* (2019) Structural Dynamics of Lytic Polysaccharide Monoxygenases reveals a Highly Flexible Substrate Binding Region. . Journal of Molecular Graphics and Modelling. 88:1-10.
  12. (*Corresponding Author)
  13. Kumar A, Mehta V, Raj U, Varadwaj PK, Malairaman U, Yennamalli RM, Singh TR. (2019) Computational and in-vitro validation of natural molecules as potential Acetylcholinesterase inhibitors and neuroprotective agents. Current Alzheimer Research. 16(2): 116-127.
  14. Chauhan D, Srivastava PA, Agnihotri V, Yennamalli RM*, Priyadarshini R*. (2019) Structure and Function Prediction of Arsenate Reductase from Deinococcus indicus DR1.Journal of Molecular Modeling. 25(1):15.
  15. (*Co-Corresponding Authors)
  16. Panigrahi PP, Singla R, Bansal A, Junior MC, Jaitak V, Yennamalli RM, Singh TR. (2018) In silico Screening and Molecular Interaction Studies of Tetrahydrocannabinol and its Derivatives with Acetylcholine Binding Protein. Current Chemical Biology. 12 (2): 181-190
  17. Shukla A, Yennamalli RM* Singh TR*. (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: 131-142. (*Co-Corresponding Authors)
  18. Singh N, Sharma SD, Yennamalli RM*(2017) Modified S-transform as a tool to identify secondary structure elements in RNA. Bio-Algorithms and Med-Systems 13(4):187-193.
  19. (*Corresponding Author)
  20. 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. 5(31): e00754-17.
  21. Vij A, Yennamalli RM, 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. MetaGene 13: 38-47.
  22. Chang CY, Lohman JR, Cao H, Tan K, Rudolf JD, Ma M, Xu W, Bingman CA, Yennamalli RM, Bigelow L, Babnigg G, Yan X, Joachimiak A, Phillips GN Jr, Shen B. (2016) Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase that Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate in Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus. Biochemistry. 55 (36):5142-5154.
  23. Jones DC, Zheng W, Huang S, Du C, Zhao X, Yennamalli RM, Sen TZ, Nettleton D, Wurtele ES, Li L. (2016) A clade-specific Arabidopsis gene connects primary metabolism and senescence. Frontiers in Plant Science. 7: 983.
  24. Gautam LK, Yennamalli RM*, Rathore JS*. (2016) Implication on the function of novel Xn-relE toxin structure of Xenorhabdus nematophila using Homology modeling. Current Bioinformatics. 12 (6):535-542. (*Co-Corresponding author)
  25. Huang T, Chang CY, Lohman J, Rudolf J, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN Jr. (2016) Crystal Structure of SgcJ, An NTF2-Like Superfamily Protein Involved in Biosynthesis of the 9-Membered Enediyne Antitumor Antibiotic C-1027. The Journal of Antibiotics. 69(10):731-740.
  26. Chauhan M*, Yennamalli RM*, Garlapati VK. (2016) Biochemical and Molecular Characterization of a unique lipase from Staphylococcus arlettae JPBW1. Engineering in Life Sciences 16(8):762–768 (* Equal authors)
  27. Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson J, Phillips. GN, Jr. (2016) Structural Dynamics of a Methionine γ-Lyase for Calicheamicin Biosynthesis: Rotation of the Conserved Tyrosine Stacking with Pyridoxal Phosphate Structural Dynamics. 3, 034702
  28. Singh S, Michalska K, Bigelow L, Endres M, Kharel MK, Babnigg G, Yennamalli RM, Bingman CA, Joachimiak A, Thorson JS, Phillips GN Jr. (2015) Structural Characterization of CalS8, a TDP-alpha-D-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis. Journal of Biological Chemistry. 290(43):26249-26258.
  29. Auldridge ME, Cao H, SenS, FranzLP, Bingman CA, Yennamalli RM, Phillips GN Jr, Mead D, Steinmetz EJ. (2015) LucY: a versatile new fluorescent reporter protein. PLOS One. 10(4):e0124272
  30. Weerth RS, Michalska K, Bingman CA, Yennamalli RM, Li H, Jedrzejczak R, Wang F, Babnigg G, Joachimiak A, Thomas MG, Phillips GN Jr. (2015) Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35Å resolution. Proteins: Structure, Function, and Bioinformatics. 83(2):383-388.
  31. Book AJ*, Yennamalli RM*, Takasuka TE*, Currie CR, Phillips GN, Fox BG. (2014) Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases. Biotechnology for Biofuels. 7:109 (*Equal authors)
  32. Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S, Yennamalli RM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN Jr, Thorson JS. (2014) Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19. ACS Chemical Biology. 9(10):2347-2358.
  33. Yennamalli RM, Arangarasan R, Bryden A, Gleicher M, Phillips GN. (2014) Using commodity HDTV for Collaborative Structural Biology. Journal of Applied Crystallography. 29: 47 (Pt 3): 1153-1157.
  34. Ilgu M, Fulton BD, Yennamalli RM, Lamm MH, Sen TZ, Nilsen-Hamilton M. (2014) An Adaptable Pentaloop Defines a Robust Neomycin-B RNA Aptamer with Conditional Ligand Bound Structures. RNA. 20(6): 815-824.
  35. Wang F, Zhou M, Singh S, Yennamalli RM, Bingman CA, Thorson JS, Phillips GN Jr. (2013) Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis.Proteins: Structure, Function, and Bioinformatics. 81(7): 1277-1282.
  36. Rader AJ, Yennamalli RM, Harter AK, Sen TZ. (2012) A rigid network of long-range contacts increases thermostability in a mutant endoglucanase. Journal of Biomolecular Structure and Dynamics. 30(6): 628-637
  37. Yennamalli RM, Wolt JD, Sen TZ. (2011) Dynamics of endoglucanase catalytic domains: Implications towards thermostability. Journal of Biomolecular Structure and Dynamics. 29(3): 509-526.
  38. Yennamalli RM, Rader AJ, Wolt JD, Sen TZ. (2011) Thermostability in Endoglucanases is Fold-specific. BMC Structural Biology. 11:10.
  39. Khan SN, Yennamalli RM, Subbarao N, Khan AU. (2010) Mitoxantrone Induced Impediment of Histone Acetylation and Structural Flexibility of the Protein. Cell Biochemistry and Biophysics 60(3): 209-218.
  40. Hambarde S, Yennamalli RM, Subbarao N, Chandna S. (2010) Predictive inference on cytoplasmic and mitochondrial thioredoxin peroxidases in the highly radioresistant Lepidopteran insect Spodoptera frugiperda. Bioinformation. 4(9):399-404.
  41. Yennamalli RM*, Das S*, Vishnoi A*, Gupta P, Bhattacharya A. (2009) Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains. Journal of Biosciences. 34(3):397-404. (*Equal authors)
  42. Kampmann T, Yennamalli RM, Campbell P, Stoermer MJ, Fairlie DP, Kobe B, Young PR. (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):234-241.
  43. Vashist J, Vishvanath, Kapoor R, Kapil A, Yennamalli RM, Subbarao N, Rajeswari MR. (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):147-153.
  44. Yennamalli RM, Subbarao N, Kampmann T, McGeary RP, Young PR, 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):333-341.
  45. Khan SN, Islam B, Yennamalli RM, Zia Q, Subbarao N, Khan AU. (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):1096-1104.
  46. Khan SN, Islam B, Yennamalli RM, Sultan A, Subbarao N, Khan AU. (2008) Interaction of mitoxantrone with human serum albumin: spectroscopic and molecular modeling studies. European Journal of Pharmaceutical Sciences. 35(5):371-382.
  47. Yennamalli RM, Sultan A, Subbarao N, Khan AU. (2008) Interaction of mitoxantrone with human serum albumin: spectroscopic and molecular modeling studies. European Journal of Pharmaceutical Sciences. 35(5):371-382.
  48. Mueller DS, Kampmann T, Yennamalli RM, Young PR, Kobe B, Mark AE. (2008) Histidine protonation and the activation of viral fusion proteins. Biochemical Society Transactions. 36(Pt 1):43-45.

Pre-Print

  1. 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. bioRxiv 208272

Reviews and Commentaries

  1. Arora M, Sen TZ, Yennamalli RM. (2018) Application of molecular simulations toward understanding cellulase mechanisms. BioEnergy Research. 11 (4): 850-867.
  2. Srivastava PA, Kalra S, Yennamalli RM. (2017) Structural Bioinformatics and Big Data Analytics: A mini-review. International Journal of Computational Biology 6 (1): 25-30.
  3. Yennamalli RM, Kalra S, Srivastava PA, Garlapati VK. (2017) Computational Tools and Resources for CRISPR/Cas 9 Genome Editing Method: Mini Review. MOJ Proteomics and Bioinformatics 5(4): 00164.
  4. Yennamalli RM, Rader AJ, Kenny AJ, Wolt JD, Sen TZ. (2013) Endoglucanases: Insights into Thermostability for Biofuel Applications. Biotechnology for Biofuels 6:136.

Book Chapters

  1. Sharma A, Yennamalli RM. (2020) Docking Strategies. In Bhatt AK, Bhatia RK, Bhalla TC. Basic Biotechniques for Bioprocess and Bioentrepreneurship. Elsevier publications. [ISBN: 9780128161098]
  2. Martin HI, Agnihotri V, Yennamalli RM, Aurijit Sarkar (2020) Methods of protein and drug interaction. In Bhatt AK, Bhatia RK, Bhalla TC. Basic Biotechniques for Bioprocess and Bioentrepreneurship. Elsevier publications. [ISBN: 9780128161098]
  3. Yennamalli RM. (2019) Protein Design. In: Ranganathan, S., Gribskov, M., Nakai, K. and Schönbach, C. (eds.), Encyclopedia of Bioinformatics and Computational Biology, vol. 3, pp. 644–651. Oxford: Elsevier. [ISBN: 9780128096338]
  4. Srivastava PA, Yennamalli RM. (2019) OMIC Technologies in Bioethanol Production: An Indian Context. In Rintu Banerjee, Garlapati Vijay Kumar, and S.P. Jeevan Kumar, OMICS-based Approaches for Plant Biotechnology (1st, pp. 217-243). Austin, USA: Wiley-Scrivener Publishing House. [ISBN: 9781119509936]

Members

Undergraduates

Ayshwarya Nagarajan

Sankar Mahesh

Sruthi Suresh

Shashank Ravichandran

Yatindra Pravanan

Alumni of Yennamalli Lab

Priya Bharval

2017

Sheena Sarswati

2017

Nancy Singh

2017

Radhika Arora

2018

Mansi Arora

2018

Pulkit Anupam Srivastava

2019

Resources

Contact

Ragothaman M Yennamalli, Ph.D.
Assistant Professor
Department of Bioinformatics,
School of Chemical and Biotechnology,
SASTRA Deemed to be University,
Tirumalaisamudram,
Thanjavur – 613401.
INDIA
Email: [email protected]