Y.M. Ragothaman
Y.M. Ragothaman
Associate Professor
Centre/School/Special Centre
School of Computational and Integrative Sciences
Room No
39
Email
ragothaman[at]mail[dot]jnu[dot]ac[dot]in, ragothaman[at]jnu[dot]ac[dot]in, ragothaman[at]gmail[dot]com
Personal Webpage
https://yennamalli-lab.in/
Qualifications

Ph.D. (Computational Biology and Bioinformatics), Jawaharlal Nehru University (2008)
Advanced Post Graduate Diploma (Bioinformatics), Jawaharlal Nehru University (2003)
M.Sc. (Microbial Gene Technology), Madurai Kamaraj University (2002)

Areas of Interest/Specialization

Carbohydrate-Active enZymes (CAZymes) – their molecular function and dynamics
Lytic Polysaccharide Monooxygenases (LPMO) – structural analysis and dynamics
Comparative genomics of Bos genomes
Comparative genomics of Deinococcus genomes
Human Transglutaminase2 and their involvement in celiac disease

Experience

Associate Professor, School of Computational and Integrative Sciences, Jawaharlal Nehru University (2018-Present)
Senior Assistant Professor-II, SASTRA Deemed to be University, India (2025-2026)
Senior Assistant Professor-I, SASTRA Deemed to be University, India (2024-2025)
Assistant Professor-III, SASTRA Deemed to be University, India (2019-2024)
Honorary Fellow, Department of Biochemistry, University of Wisconsin-Madison, USA (2012-2015, 2018-2019)
Assistant Professor-II, Dept. of Biotechnology and Bioinformatics, Jaypee University of Information Technology, India (2015-2019)

Awards & Honours
  • Biophysical Society Ambassador for India – Seventh Cohort (2026-2028)
  • Manuscript featured on the cover of Journal of Biological Chemistry (2025)
  • Chair, Publications Committee, International Society for Computational Biology (ISCB) (2022-Present)
  • Executive Committee member of Asia-Pacific Bioinformatics Network (APBioNET) (2024-Present)
  • Travel Award for ISMB2024 from EvolCompGen, Montreal, Canada (2024)
  • Featured in Biophysical Society Bulletin as Biophysicist in Profile, March Issue (2024)
  • Outstanding volunteer service to the International Society for Computational Biology in 2023
  • Mid-Career Travel Award, Biophysical Society, USA (2024)
  • Co-organizer for Young Investigators' Meet (YIM 2024), IISER Bhopal (2024)
  • Featured in Nature Communications Biology series on early career researchers. (2018)
  • Bioenergy-Awards for Cutting Edge Research (B-ACER) fellowship, Indo-U.S. Science and Technology Forum (IUSSTF) (2018)
  • Endeavour Australia Cheung Kong award for Asian scholars (2006)
  • Jawaharlal Nehru University – The University of Queensland student exchange award (2004)
  • Gold Medal for high scores in Physics and Chemistry High School examination (1997)
  • Silver Medal at National Children’s Science Congress (1996)
  • Associate Editor, Computational and Structural Biotechnology Journal
  • Associate Editor, Bioinformatics and Biology Insights
  • Special Issue Editor of Biophysical Journal “Applications of Coarse-Grained and Multiscale Modeling” (2024)
  • Editorial Board, BMC Bioinformatics
  • Editorial Board, Scientific Reports
  • Early Career Researcher Review Board, Protein Science
International Collaboration/Consultancy

Collaborations with USDA-ARS and University of Regina, Canada.

Best Peer Reviewed Publications

Google Scholar Profile: http://bit.ly/RY_google_scholar 

PubMed profile: https://pubmed.ncbi.nlm.nih.gov/?term=yennamalli&sort=pubdate 

  1. Thambiraja M, Iyengar SK, Satishkumar B, Kavuru SR, Katari A, Singh D, Onteru SK* and Yennamalli RM* (2026) Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome. Scientific Reports. 16, 11005 (*Corresponding Authors)

  2. Yennamalli RM and Tama F. (2026) Applications of coarse-grained and multiscale modelling. Biophysical Journal 125(2): E1-E4.

  3. Agarwal R, Biswas K, Agrawal A, Shankar NN, Kundu S, Roy D, Son DH, Yennamalli RM, Lee DK, Bhunia A, Roy S (2025) SA-XV, a 15-amino acid fragment of host defense peptide S100A12, targets mitochondria, and is protective against fungal infections.Journal of Biological Chemistry, 310(10): 110743.

  4. Senthilkumar S, Mahesh S, Jaisankar S, Yennamalli RM. (2025) Surface exposed and charged residues drive thermostability in Fungi. Proteins: Structure, Function, and Bioinformatics. 93(1):226-240. Included in the special issue “Macromolecular Form and Function in the GN Ramachandran Centenary Year”.

  5. Saha D, Kothari S, Kulkarni SD, Thambiraja M, Yennamalli RM*, Das DK*. (2024) Genetic heterogeneity and respiratory chain enzyme analysis in pediatric Indian patients with mitochondrial disorder: Report of novel variants in POLG1 gene and their functional implication using molecular dynamic simulation. Mitochondrion 76:101870. (*Corresponding Authors)

  6. Modi M, Thambiraja M, Cherukat A, Yennamalli RM and Priyadarshini R. (2024) Structure predictions and functional insights into Amidase_3 domain containing N-acetylmuramyl-L-alanine amidases from Deinococcus indicus DR1. BMC Microbiology 24:101.

  7. Ravichandran S, Avatapalli S, Narasimhan Y, Yennamalli RM*, Kaushik KS*. (2022) 'Targeting the Search': An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets. Frontiers in Cellular and Infection Microbiology 12:1020391. (*Corresponding Authors) 

  8. 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 (AMPs) for biofilm studies (Biofilm-AMP), and a case study of its application to Corynebacterium striatum, an emerging pathogen. Frontiers in Cellular and Infection Microbiology 11:803774. (*Corresponding Authors)

  9. 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.

  10. Singaraju GS, Sagar A, Kumar A, Samuel JS, Hazra JP, Sannigrahi MK, Yennamalli RM, Ashish, Rakshit S. (2020) Structural Basis of the Strong Cell-Cell Junction Formed by cadherin-23. The FEBS Journal. 287 (11): 2328-2347.

Recent Peer Reviewed Journals/Books

  1. Marimuthu VKD, Matheswaran K, Thambiraja M, Onteru SK*, Yennamalli RM* (2026) Meta-Analysis of Transcriptomic Datasets Reveals Key Immune Gene Profiles and Signaling Pathways in Bos taurus. Animal Genetics. 57:e70117.

  2. Roshan M, Vats A, Bajwa KK, Moses T, Singh D, Yennamalli RM*, Onteru SK*. (2025) Comparative Transcriptome profiling of Peripheral Blood Mononuclear Cells suggests Protocadherin 1 (PCDH1) as a distinctive innate immunity signature in Sahiwal, Tharparkar and Gir compared to Karan Fries cattle. Developmental and Comparative Immunology. 173: 10552 (*Corresponding Authors)

  3. Thambiraja M, Karthikeyan PP, Sezen M, Senthilkumar S, Singh D, Onteru SK*, Yennamalli RM* ImmFinder: A Fully Connected Neural Network approach for predicting the immune genes in livestock. OMICS: A Journal of Integrative Biology. 29(11):551-559. (*Corresponding Authors)

Review articles

  1. Ranganathan S, Mahesh S, Suresh S, Nagarajan A, Sen TZ, Yennamalli RM. (2022) Experimental and Computational studies of Cellulases as Bioethanol enzymes. Bioengineered. 13(5): 14028-14046.

  2. Arora M, Sen TZ, Yennamalli RM. (2018) Application of molecular simulations toward understanding cellulase mechanisms. BioEnergy Research. 11 (4): 850-867.

  3. Yennamalli RM, Rader AJ, Kenny AJ, Wolt JD, Sen TZ. (2013) Endoglucanases: Insights into Thermostability for Biofuel Applications. Biotechnology for Biofuels 6:136.

Edited Books/Special Issues

Special Issue on “Applications of Coarse-Grained and Multiscale Modeling” Biophysical Journal https://www.cell.com/biophysj/issue?pii=S0006-3495(25)X0004-7 

Webservers/Databases/Resources developed

https://predlpmo.in/

https://deinococcus.in/

https://b-amp.karishmakaushiklab.com/ 

GitHub Repositories: https://github.com/raghuyennamalli 

Patents (if any)

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