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Dr. Sona Charles

Dr. Sona Charles
Name Dr. Sona Charles
Designation Scientist
Division Crop Improvement and Biotechnology
Qualification Ph.D.
Specialisation Agricultural Bioinformatics
Contact sonacharlesicar@gmail.com
Areas of Interest Computational Biology, Development of algorithms for omics data analysis, Development of AI based models

  1. Dilkush F, Sarathambal C, Charles S, Peter B, Praveena R, Prasath D. Antagonistic bacterial endophytes from gingers and their metabolite-mediated interactions against Pythium soft rot. Curr Microbiol. 2025 Nov 20;83(1):34.

  2. Ravindran P, Sheeja TE, Anees K, Srinivasan V, Leela NK, Charles S, George P, Abraham A, Payatatti VKI, Subila KP, Anushree M, Dinesh R. Zinc solubilizing rhizobacteria as bioinoculant for turmeric: transcriptomic insights into acid stress adaptation, zinc mobilization and growth promotion. World J Microbiol Biotechnol. 2025 Nov 5;41(11):435.

  3. Charles S, Kaprakkaden A, Duraisamy P, Thotten Elampilay S, Arif S. Letter: Integrating omics for future-ready plant science: reflections from the National Symposium on Recent Trends in Omics in Plant Biology, held in Kozhikode, India. OMICS. 2025 Aug 8.

  4. Charles S, Kaprakkaden A, Duraisamy P, Thotten Elampilay S, Arif S. Letter: Integrating omics for future-ready plant science: reflections from the National Symposium on Recent Trends in Omics in Plant Biology, held in Kozhikode, India. OMICS. 2025 Sep;29(9):473–474.

  5. Rincy KM, Fayad MA, Charles S, Praveena R, Eapen SJ. The fungal endophyte Pochonia chlamydosporia boosts growth and defence in black pepper (Piper nigrum L.): insights from transcriptomics and functional studies. Rhizosphere. 2025; (Advance online publication).

  6. Dinesh R, Sreena CP, Sheeja TE, Sona C, Kumar IPV, Anusree M, Alagupalamuthirsolai M, Jayarajan K, Sajith V. Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil. J Hazard Mater. 2025 Mar 5;485:136885.

  7. Charles S, Subeesh A, Natarajan J. Tree based models for classification of membrane and secreted proteins in heart. J Proteins Proteomics. 2024;15(2):147–157.

  8. Fayad MA, Charles S, Shelvy S, Sheeja TE, Sangeetha K, Angadi UB, Tandon G, Iquebal MA, Jaiswal S, Kumar D. Whole genome based identification of BAHD acyltransferase gene involved in piperine biosynthetic pathway in black pepper. J Biomol Struct Dyn. 2024 Feb 12;1–13.

  9. Charles S, Natarajan J. Identification of key gene modules and novel transcription factors in Tetralogy of Fallot using machine learning and network topological features. Medinformatics. 2023 Oct 10;1(1):27–34.

  10. Dinesh R, Sreena CP, Sheeja TE, Charles S, Srinivasan V, Jayarajan K, Sajith V, Subila KP, Haritha P. Soil polluted with nano ZnO reveals unstable bacterial communities and decoupling of taxonomic and functional diversities. Sci Total Environ. 2023 Sep 1;889:164285.

  11. Raghavan D, Patinharekkara SC, Elampilay ST, Payatatti VKI, Charles S, Veeraraghavan S, Kadiyalath J, Vandana S, Purayil SK, Prasadam H, Anitha SJ. New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide. Ecotoxicol Environ Saf. 2023 Sep 15;263:115222.

  12. Dinesh R, Sreena CP, Sheeja TE, Charles S, Srinivasan V, Sajith V, Subila KP, Haritha P. Metagenomics indicates abundance of biofilm-related genes and horizontal transfer of multidrug-resistant genes among bacterial communities in nano zinc oxide polluted soil. Sci Total Environ. 2023 Feb 10;859(Pt 1):160032.

  13. Sarathambal C, Jeevalatha A, Sivaranjani R, Biju CN, Charles S, Srinivasan V, et al. Arbuscular mycorrhizal colonization alters biochemical, molecular defense responses and root exudate composition against Phytophthora capsici infection in black pepper. Rhizosphere. 2023;25:100651.

  14. Charles S, Sreekumar J, Natarajan J. Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot. J Bioinform Comput Biol. 2022 Aug;20(4):2240004.

  15. George JK, Fayad MA, Shelvy S, Sheeja TE, Eapen SJ, Charles S, Rai A, Kumar D. Dataset of de novo hybrid berry transcriptome profiling and characterization of Piper species (Piper nigrum and Piper longum) using Illumina and Nanopore sequencing. Data Brief. 2022 May 11;42:108261.

  16. Charles S, Natarajan J. Integrated regulatory network based on lncRNA-miRNA-mRNA-TF reveals key genes and sub-networks associated with dilated cardiomyopathy. Comput Biol Chem. 2021 Jun;92:107500.

  17. Ahmad SF, Mehrotra A, Charles S, Ganai NA. Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi. Gene. 2021;799:145809.

  18. Vidya V, Prasath D, Snigdha M, Gobu R, Sona C, et al. Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.). PLOS ONE. 2021;16(10):e0259146.

  19. Charles S, Natarajan J. Two-way network construction and analysis of mRNA, miRNA and lncRNA reveals critical regulators and regulatory modules in cardiovascular diseases. Genes Genomics. 2020 Aug;42(8):855–867.

  20. Jadhav PR, Soni KB, Sona Charles, Alex S. An in silico phylogenetic analysis and homology modelling of coat protein of banana bract mosaic virus. J Pharmacogn Phytochem. 2018;7(5):1957–1962.

  21. James P, Baby B, Charles S, Nair LS, Nazeem PA. Computer aided gene mining for gingerol biosynthesis. Bioinformation. 2015 Jun 30;11(6):316–321.

  22. James P, Girijadevi R, Charles S, Pillai MR. MethFinder – a software package for prediction of human tissue-specific methylation status of CpG islands. Bioinformation. 2013;9(1):61–64.

Awards by Professional Bodies

  1. Qualified CSIR-JRF-NET, AIR-54.

  2. Qualified DBT-JRF.

  3. Open Bioinformatics Foundation Event Fellowship for attending the Great Lakes Bioinformatics Conference 2021.

  4. James Taylor Fellowship 2021 for attending the Galaxy Community Conference 2021.

  5. InCoB Fellowship 2022.

  6. Women in Biology Excellence Award by Bioclues, 2025.

Copyrights

  1. Black Pepper Drought Transcriptome Database. (Application No.: 29356/2024-CO/SW; Date of Filing: 20/09/2024)

PI

  1. Development of data-driven pipelines and tools for multiple high throughput sequencing data from spices (2022-2025) (Institute Funded)

Co-PI

  1. Genomics-assisted identification of trait-specific markers for major biotic and abiotic stresses and development of core collections of black pepper (2021–2026). Funded by ICAR.

  2. Integrating whole genome resequencing, transcriptome sequencing and genome-wide association analysis for allele mining of yield and quality traits in black pepper and cardamom (2024–2027). Funded by NASF.

  3. National Network Project on Crop Bioinformatics (2024–2029). Funded by DBT.

Book Chapters 
 

  1. Charles S, Telukunta KK, Joshi D, Rajagopal S, Singh H. Standard operating procedures for effective Galaxy workflows. In: Suravajhala PN, Bizzaro JW, editors. Next-Generation Sequencing: Standard Operating Procedures and Applications. 1st ed. CRC Press; 2025.

  2. Charles S, Subeesh A, Dhanya VG, Malathi VM. Opportunities and prospects of artificial intelligence in plant genomics. In: Chaudhary A, Sethi SK, Verma A, editors. Unraveling New Frontiers and Advances in Bioinformatics. Springer; 2024.

  3. Charles S, Lopus M. Bioinformatics tools and resources for plant transcriptomics. In: Chen JT, editor. Bioinformatics for Plant Research and Crop Breeding. 2024.

  4. Malathi VM, Lakshmi MA, Charles S. Chapter 4: Applications of genomics and transcriptomics approaches for biotic stress tolerance in crops. In: Prakash CS, editor. Principles and Practices of Omics and Genome Editing for Crop Improvement. Springer Nature; 2022.

  5. Janardanan S, Charles S. Chapter 23: Omics in tuber crops: cassava and sweet potato. In: Rout GR, Peter KV, editors. Omics in Horticultural Crops. Academic Press; 2022. p. 527–543.

  6. Pandey MK, Srinivasa Rao Ch, Ratna Prabha, Sahu S, Charles S, Supriya P, Yuvaraj I, Balakrishnan M, Soam SK, Mangrauthia SK. Application of bioinformatics in climate smart agriculture. In: Pandey MK, Srinivasa Rao Ch, editors. Climate Change and Indian Agriculture: Challenges and Adaptation Strategies. ICAR-National Academy of Agricultural Research Management; 2020.

  7. Ratna Prabha, Sahu S, Charles S, Supriya P, Yuvaraj I, Balakrishnan M, Soam SK, Mangrauthia SK. Role of genomics in agriculture in age of climate change. In: Pandey MK, Srinivasa Rao Ch, editors. Climate Change and Indian Agriculture: Challenges and Adaptation Strategies. ICAR-National Academy of Agricultural Research Management; 2020.
     

Review Article

  1. Charles S, Natarajan J. Transcriptomic approaches in understanding SARS-CoV-2 infection. In: Hameed S, Fatima Z, editors. Integrated Omics Approaches to Infectious Diseases. Springer; 2021.