Dr. Sona Charles

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Name	Dr. Sona Charles
Designation	Scientist (Senior Scale)
Discipline	Agricultural BioInformatics
Qualification	PhD Bioinformatics
Specialisation	Genomics and transcriptomics, Next Generation Sequencing
Contact	sona.charles@icar.gov.in, sonacharlesicar@gmail.com
Areas of Interest	Next Generation Sequencing, Genomics, Gene Networks and Systems Biology, Applications of machine learning to molecular biology.

Vertical Tabs

Research Publications

Research Publications:

Rincy K., M., Fayad, M. A., Charles, S., Praveena, R., & Eapen, S. J. (2025). The Fungal Endophyte Pochonia chlamydosporia Boosts Growth and Defence in Black Pepper (Piper nigrum L.): Insights from Transcriptomics and Functional Studies. Rhizosphere. Advance online publication. https://doi.org/10.1016/j.rhisph.2025.101139

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. doi: 10.1016/j.scitotenv.2022.160032. Epub 2022 Nov 10. PMID: 36370776.

Raghavan D, Patinharekkara SC, Elampilay ST, Payatatti VKI, Charles S, Veeraraghavan S, et al. New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide. Ecotoxicol Environ Saf [Internet]. 2023;263:115222. Available from: https://www.sciencedirect.com/science/article/pii/S0147651323007261
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. doi: 10.1016/j.scitotenv.2022.160032. Epub 2022 Nov 10. PMID: 36370776.
Raghavan D, Patinharekkara SC, Elampilay ST, Payatatti VKI, Charles S, Veeraraghavan S, et al. New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide. Ecotoxicol Environ Saf [Internet]. 2023;263:115222. Available from: https://www.sciencedirect.com/science/article/pii/S0147651323007261
R. Dinesh, C.P. Sreena, T.E. Sheeja, I.P. Vijesh Kumar, R. Praveena, Sona Charles, V. Srinivasan, K. Jayarajan, V. Sajith, K.P. Subila, P. Haritha (2023) Soil polluted with nano ZnO reveals unstable bacterial communities and decoupling of taxonomic and functional diversities. Science of The Total Environment. 889: 164285
George JK, Fayad MA, Shelvy S, Sheeja TE, Eapen SJ, Sona C, 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
Vidya V, Prasath D, Snigdha M, Gobu R, Sona C, Maiti CS. Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.). PLoS One. 2021, 16(10):e0259146
Ahmad S.F, Mehrotra A, Sona C, & Ganai NA. Analysis of selection signatures reveals important insights into the adaptability of high-altitude Indian sheep breed Changthangi. Gene, 2021, 799, 145809.
Sona C, Natarajan J. Integrated regulatory network based on lncRNA-miRNA-mRNA-TF reveals key genes and sub-networks associated with dilated cardiomyopathy. Computational Biology and Chemistry. 2021 92, 107500
Sona C and Natarajan J. Computational meta-analysis of transcriptome in Tetrology of Fallot reveals dysregulated hubs and pathways. F1000Research 2020, 9(ISCB Comm J):730
Sona C, Natarajan J. Two way network construction and analysis of mRNA, miRNA and lncRNA reveals critical regulators and regulatory modules in cardiovascular diseases. Genes and Genomics 42(8):855-867 2020
Jadhav PR, Soni KB, Sona C, Alex S. An in silico phylogenetic analysis and homology modelling of coat protein of banana bract mosaic virus. Journal of Pharmacognosy and Phytochemistry 2018 7 (5) 1957- 1962
P. James, B. Baby, Sona C, LS Nair, PA Nazeem. Computer aided gene mining for gingerol biosynthesis. Bioinformation. 2015 Jun 30;11(6):316-21. doi: 10.6026/97320630011316.
Santhi WS, Rajalekshmi P, Sona C, Anurup KG, Girijadevi R, Ramachandran S, Jissa VT, Sebastian P, Pillai MR.Oncogenic microRNAs as biomarkers of oral tumorigenesis and minimal residual disease.Oral Oncol. 2013 Feb 1. pii: S1368-8375(13)00007-9. doi:10.1016/j.oraloncology.2013.01.001
James P, Girijadevi R, Sona C, Pillai MR. MethFinder - A software package for prediction of human tissue-specific methylation status of CpG islands. Bioinformation. 9(1): 064- 067
Ramachandran S, Venugopal A, Satisha K, Girijadevi R, Sona C, Chandran NSP, Mullassari A, Pillai MR and Kartha CC. Proteomic Profiling of High Glucose Primed Monocytes Identifies Cyclophilin A as a Potential Secretory Marker of Inflammation in Type 2 Diabetes. Proteomics. 12: 2808–2821
Girijadevi R, James P, Sona C, Sreedhar JV, Rajalekshmi P, Ramachandran S, Raveendran D,Ramadas K, Pillai MR. OrCa-dB: A complete catalogue of Oral Cancer. Oral Oncol. Oral Oncol. (2012) 48(6):e19.
Girijadevi R, Sona C, Pillai MR. Comprehensive Patterns in microRNA Regulation of Transcription Factors during Tumor Metastasis. J. Cell Biochem. (2011) 112: 2210–2217
Dinesh R, Sreena CP, Sheeja TE, Sona C, 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. doi: 10.1016/j.scitotenv.2022.160032.

Sona C, 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. doi: 10.1142/S0219720022400042. Epub 2022 Aug 3. PMID: 35918793.

Book Chapters

Charles S, KK. Telukunta, Joshi D, Rajagopal S, Singh H. Standard Operating Procedures for Effective Galaxy Workflows. In: Suravajhala, P.N., & Bizzaro, J.W. (Eds.). (2025). Next-Generation Sequencing: Standard Operating Procedures and Applications (1st ed.). CRC Press. https://doi.org/10.1201/9781003354062
Charles, S. and Lopus, M. (2024). Bioinformatics Tools and Resources for Plant Transcriptomics. In Bioinformatics for Plant Research and Crop Breeding, J.-T. Chen (Ed.). https://doi.org/10.1002/9781394209965.ch10
Charles, S., Subeesh, A., Dhanya, V.G., Malathi, V.M. (2024). Opportunities and Prospects of Artificial Intelligence in Plant Genomics. In: Chaudhary, A., Sethi, S.K., Verma, A. (eds) Unraveling New Frontiers and Advances in Bioinformatics. Springer, Singapore. https://doi.org/10.1007/978-981-97-7123-3_5
Sona C, J Natarajan. Transcriptomic Approaches in Understanding SARS-CoV-2 Infection Integrated Omics Approaches to Infectious Diseases, 221
Ratna Prabha*, Sarika Sahu*, Sona Charles*, P. Supriya*, I. Yuvaraj*, M. Balakrishnan, S.K. Soam, Satendra K. Mangrauthia, Manish K. Pandey and Ch. Srinivasa Rao. Role of Genomics in Agriculture in Age of Climate Change. Climate Change and Indian Agriculture: Challenges and Adaptation Strategies, ICAR-National Academy of Agricultural Research Management, Hyderabad, Telangana, India. pp-1-22. (*equal authorship)
Ratna Prabha*, Sarika Sahu*, Sona Charles*, P. Supriya*, I. Yuvaraj*, M. Balakrishnan, S.K. Soam, Satendra K. Mangrauthia, Manish K. Pandey and Ch. Srinivasa Rao. Application of Bioinformatics in Climate Smart Agriculture. Climate Change and Indian Agriculture: Challenges and Adaptation Strategies, ICAR-National Academy of Agricultural Research Management, Hyderabad, Telangana, India. pp-1-22. (*equal authorship)
Janardanan, S., & Sona C. (2022). Chapter 23 - Omics in tuber crops: Cassava and sweet potato (G. R. Rout & K. V. B. T.-O. in H. C. Peter (eds.); pp. 527–543). Academic Press. https://doi.org/https://doi.org/10.1016/B978-0-323-89905-5.00021-5
Malathi, V.M., Lakshmi, M.A., Sona C. (2022). The Applications of Genomics and Transcriptomics Approaches for Biotic Stress Tolerance in Crops. In: Prakash, C.S., Fiaz, S., Fahad, S. (eds) Principles and Practices of OMICS and Genome Editing for Crop Improvement. Springer

Conference Presentations

Sona C, Sreekumar J Sequence based prediction of Phytophthora- Host interaction using machine learning methods. Great Lakes Bioinformatics Conference 2021
Sona C, Jeyakumar N. Integrated regulatory network based on lncRNA-miRNA-mRNA-TF reveals key genes and sub-networks associated with Dilated Cardiomyopathy. Intelligent Systems in Molecular Biology-2020 (Poster)
Sona C, Jeyakumar N. Computational meta-analysis of transcriptome in Tetrology of Fallot reveals dysregulated hubs and pathways. Bioinformatics Community Conference-2020 (BCC2020) (Poster)
Sona C, Jeyakumar N. Network based Decoding of Long Noncoding RNA- Disease Association Modules in Cardiovascular Diseases. International Conference on Biotechnology and Bioinformatics (ICBB)- 2017 (Oral Presentation)
Harikumar KB, Charles S. A computational based approach to analysis of MicroRNA and transcription factor co-regulatory networks in pancreatic cancer. 32nd Annual Convention of Indian Association for Cancer Research (Poster)
S Charles, Girijadevi R, Pillai MR. Revelation of Transcription Factor-microRNA Regulating Networks in Human Stem Cells. International Conference on Stem Cells and Cancer-2012 (Poster)
Suseela GK and Charles S. Tagging Pest Resistance Genes in Rice. In Proceedings of Annam National Seminar on Health, Food and Agrobiodiversity- Changing Paradigms 12-14 February 2010, Kozhikode, India. (Oral Presentation)
Sona Charles, Fayad MA, Krishnamurthy KS, Sheeja TE and Johnson K George. De-novo and reference based transcriptome assembly of Piper nigrum reveals novel genes and transcripts in drought tolerance. 21st International Conference in Bioinformatics 2022 (21-23 November 2022)
M.A. Fayad, Sona Charles, S. Shelvy and T.E. Sheeja. Identification of BAHD Acyltransferase Gene Involved In Piperine Biosynthetic Pathway. National Conference on Enhancing Competitiveness in Horticulture

Through Technology Innovations (17-18 November 2022)

Awards

Awards:

Women in Biology Excellence Award in Bioinformatics by Bioclues Organization- 2025
Post-Graduate Indira Gandhi Scholarship (2008-10)
2nd Rank Holder in MSc Bioinformatics PG course (University of Kerala) (2008-10)
CSIR-JRF- AIR-54
DBT-JRF- Category I
Shortlisted candidate (as one among 28) in Biotechnology/ Biochemical Engineering category for the Commonwealth Fellowship tenable in the UK-2017
GATE- 2017 (XL) AIR- 196
First Prize in oral presentation at the International Conference on Biosciences and Bioinformatics-2017 conducted by Bharathiar University, Coimbatore held during 14-16th December, 2017
ARS (Agricultural Bioinformatics)- 2017, AIR- 5
Open Bioinformatics Foundation Event Fellowship for attending Great Lakes Bioinformatics Conference 2021
James Taylor Fellowship 2021 for attending Galaxy Community Conference 2021
InCoB Fellowship 2022

Research Projects

Research Projects:

Biotech. XVI (813): Development of data-driven pipelines and tools for multiple high throughput sequencing data from spices (2022-2025) [Ms Sona Charles]