Scientist IV
Ph.D: Jawaharlal Nehru University, New Delhi
Postdoctoral Fellow: University of Virginia, Charlottesville, USA
- 91-11-26741612,14,17 Ext. - 217
- shailesh@nipgr.ac.in , shailesh.97@gmail.com
Profile
Research Area
Bioinformatics, Genomics, Multi-omics data analysis, Machine Learning (ML), Intelligence (AI), and Plant Biotechnology
Research Interests
In planta, we are exploring the generation and function of novel components (e.g., non-coding RNAs and genes) of genome regulatory circuits by using both computational and experimental approaches. For this purpose, we are using multi-omics datasets, and our choice of molecules includes Transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs), ribosomal RNA-derived fragments (e.g. rRFs), long non-coding RNAs, Fusion transcripts, and novel gene family in legume crops. In addition to this, we are also developing tools and databases for plant genomics research.
Transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs)
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression at the epigenetic, transcriptional, and post-transcriptional levels in the living system. Transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) are distinct group of regulatory RNAs, have been reported in all three domains of life, derived from the endonucleolytic cleavage of precursor tRNAs (pre-tRNAs) or mature tRNAs. tncRNAs includes well-known shorter tRNA-derived RNA fragments (~12 to 30 nucleotides [nt]) popularly termed as tRFs or tDRs, and longer tRNA halves or tRHs (~30 to 40 nt). In planta, we are trying to understand their generation and function of tncRNAs including their expression in different tissues, and different stress conditions.
Fusion transcripts
Fusion transcripts, also known as “chimeric transcripts”, can be generated because of chromosomal rearrangements at DNA level or by trans-splicing or intergenic cis splicing at RNA level. Gene fusion is believed to be a major factor for controlling morphology, physiology, and phenotypic character in plants as well as a major contributor for adaptive evolution. Fusion transcripts may code for proteins, or may act as long non-coding RNAs, and playing a major role in the genome regulation. We are exploring these novel molecules to understand their generation and function in plants with special focus on different traits for the development of improved verities.
Development of webservers, databases, and computational pipelines
We are analysing multi-omics datasets by developing our own pipelines/methodologies, and web-servers. We are also using Machine Learning, Deep Learning and Artificial Intelligence to decipher the biology of different biomolecules. Further, we are also presenting our results in form of user friendly databases.
Professional & Academic Background
2017- till date
Staff Scientist: National Institute of Plant Genome Research (NIPGR), New Delhi, India
2015-2017
Postdoctoral Research Associate: University Of Virginia, Charlottesville, VA, USA
2014-2015
Research Scientist: Sir Ganga Ram Hospital, New Delhi, India
2009-2014
Ph.D.: Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh, India, awarded by JNU, New Delhi
Scientific Contributions/ Recognitions
Elected Member: National Academy of Sciences India (NASI), 2022
Selected for SAKURA Exchange Program in Science for Indian Young officers, JAPAN (January 21-27, 2018) by Department of Biotechnology (DBT), India
Visiting scientist: Guangxi medical university and Guilin Medical University, China (October-November 2017).
Associate editor: PloS one and BMC Bioinformatics.
Web-servers, Databases, and Tools
GitHub Page:┬аhttps://github.com/skbinfo
PFGPred: A stack ensemble classifier for the identification of fusion genes in plants (www.nipgr.ac.in/PFGPred)
PlantXBot: Plant Genomics Chatbot (www.nipgr.ac.in/PlantXBot)
AquaaG:┬аA Comprehensive Pipeline for Quality Assessment and Annotation of Genomes┬а(www.nipgr.ac.in/
PbtRF:┬аA tRNA-Derived Fragments Database for Biotic Conditions┬а(http://www.nipgr.ac.in/PbtRFdb)
athisomiRDB:┬аA comprehensive database of Arabidopsis isomiRs┬а(https://www.nipgr.ac.in/athisomiRDB)
ANNInter:┬аArabidopsis ncRNA-ncRNA interactions (NNIs) networks database┬а(https://www.nipgr.ac.in/ANNInter/)
PFusionDB:┬аPlant Fusion Database┬а( www.nipgr.ac.in/PFusionDB)
smAMPsTK:┬аA toolkit to unravel the smORFome encoding AMPs of plant species( www.nipgr.ac.in/smAMPsTK)
rsRNAfinder:┬аA tool toidentify and annotate ribosomal RNA-derived small RNAs (rsRNAs)(www.nipgr.ac.in/rsRNAfinder)
Cotton non-coding RNAs Atlas:(www.nipgr.ac.in/CoNCRAtlas/)
PTPAMP:┬аPrediction Tool for Plant-derived Antimicrobial Peptides┬а(http://www.nipgr.ac.in/PTPAMP/)
PtncRNAdb:┬аPlant transfer RNA-derived non-coding RNAs (tncRNAs) database┬а(https://nipgr.ac.in/PtncRNAdb)
MedProDB:┬аMediator Protein Database┬а(http://www.nipgr.ac.in/MedProDB/)
AlnC:┬аAn extensive database of long non-coding RNAs (lncRNAs) in Angiosperms┬а(http://www.nipgr.ac.in/AlnC)
tncRNA:┬аA pipeline for the identification of tRNA-derived small ncRNAs (tncRNAs) from high throughput sequencing data┬а(http://www.nipgr.ac.in/tncRNA)
PlantPepDB: A database of plant peptides having different functions and therapeutic activities┬а(http://www.nipgr.ac.in/PlantPepDB/)
PtRNAdb: A database containing information of tRNA genes┬а(http://www.nipgr.ac.in/PtRNAdb/)
AtFusionDB: A Database of Fusion Transcripts in┬аArabidopsis thaliana┬а(http://www.nipgr.ac.in/AtFusionDB/)
PVsiRNAdb: Plant Virus siRNA Database┬а(http://www.nipgr.ac.in/PVsiRNAdb/)
PtRFdb: Plant transfer RNA-derived fragments database┬а(http://www.nipgr.ac.in/PtRFdb/)
Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer┬а(https://webs.iiitd.edu.in/raghava/cancertope/)
CancerDr: Cancer Drug Resistance Database.┬а(https://webs.iiitd.edu.in/raghava/cancerdr/)
PCMDB: Pancreatic cancer methylation database.┬а(https://webs.iiitd.edu.in/raghava/pcmdb/).
Publications
Citations of the publications:Google Scholar
A) Corresponding Author
Mukherjee K, AT Vivek, Hamid F, Bisht N,┬аKumar S*.┬аPlantXbot: an LLm-guided intelligent chatbot suite to query plant biological databases.┬аSoftwareX, 35,102891 (2026).┬аPMID:┬а
Zahra S, Gangwar R, Tiwari S, Biswas DK, SIngh A, and┬аKumar S*.┬аAbiotic Stress-Mediated Modulation of the tncRNome: Unraveling tRNA-Derived RNA Networks in Plant Adaptive Responses.┬аJournal of Plant Growth Regulation┬а(2026).┬аhttps://doi.org/10.1007/
Hamid F, Mukherjee K, Chaudhary S, Kaushik L,┬аKumar S*.┬аPFGPred: A stack ensemble classifier for the identification of fusion genes in plants,┬аDNA Research,┬аdsag005 (2026).┬аPMID:┬а42261622
Bisht B, Mayilraj S, Kaur N,┬аKumar S*.┬аUncovering the Biosynthetic Potential of┬аAmycolatopsis: New Insights into Glycopeptide Antibiotic and Polyketide Gene Clusters,┬аJournal of Applied Microbiology, lxag134 (2026).┬аPMID:┬а42258184
Shukla J, Mukherjee K, Sahu N, Kumar S*. AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes. MethodsX 16:103955. PMID: 42199883
Vivek┬аAT,┬аKiran┬аH,┬аSahu┬аN,┬аKal
Vivek AT,┬аBhatia M,┬аSahu N,┬аKalakoti G,┬аKaushik L,┬аMukherjee K,┬аKumar S*.┬а┬аAraNSdb: a dedicated database of stress-responsive non-coding RNAs in┬аArabidopsis thaliana.┬а3 Biotech.┬а16, 90 (2026).┬аPMID:┬а41710470
Hamid F, Arora S,┬аKumar S*. Breaking and making genes: the genesis of novel traits in plants.┬аNew Phytol.┬а249:2746-2759.┬аPMID:┬а4
┬аHamid F, Zahra S, Kumar S*. Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea. Front. Plant Sci.┬а16:1677098.┬а(2025)┬аPMID:┬а41245461
Bisht N, Mayilraj S,┬аKumar S*, Kaur N, Identification of NRPS and type II PKS biosynthetic gene cluster (s) encoding decaplanin and kigamicin from Amycolatopsis regifaucium DSM 45072T,┬аFEMS Microbiology Letters, Volume 372, 2025, fnaf049.┬аPMID:40388313
Swain SP, Bisht N and┬аKumar S*. Comprehensive study of tRNA-derived fragments in plants for biotic stress responses.┬аFunct Integr Genomics┬а25, 70 (2025).┬аPMID:┬а40131555
Chitkara P, Singh A, Gangwar R, Bhardwaj R, Zahra S, Arora S, Hamid F, Arya A, Sahu S, Chakraborty S, Ramesh M and┬аKumar S*. The landscape of fusion transcripts in plants: a new insight into genome complexity.┬аBMC Plant Biol 24, 1162 (2024).┬аPMID:┬а39627690.
Vivek AT, Sahu N, Kalakoti G,┬аKumar S*. ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana.┬аComputational Biology and Chemistry, 2025,115:108328.PMID:┬а39754835.
Arora S, Hamid F,┬аKumar S*. Fusion transcripts in plants: hidden layer of transcriptome complexity.┬аTrends in Plant Science┬а30(3):229-231 (2025).┬аPMID:┬а39753389.┬а
Vivek AT, Arya A, Swain SP,┬аKumar S*. athisomiRDB: A comprehensive database of Arabidopsis isomiRs,┬аDatabase (2024), Volume 2024, baae115.┬аPMID:39514415
Arya A, Arora S, Hamid F,┬аKumar S*. PFusionDB: a comprehensive database of plant-specific fusion transcripts.┬а3 Biotech┬а14, 282 (2024). PMID:39479298
Kalakoti G, Vivek AT, Kamboj A, Singh A, Chakraborty S,┬аKumar S*. Comprehensive profiling of rRNA-derived small RNAs in Arabidopsis thaliana using rsRNAfinder pipeline.┬аMethodsX┬а12:102494 (2024).┬аPMID:┬а38089152
Swain SP, Ahamad S, Samarth N, Singh S, Gupta D,┬аKumar S*. In silico studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from Mycobacterium tuberculosis.┬аJournal of Biomolecular Structure and Dynamics,┬а42(20), 10950-10964 (2024).┬аPMID:┬а37728544
Jaiswal M &┬аKumar S*. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species.┬аJournal of Biomolecular Structure and Dynamics.┬а42(13):6600-6612 (2024).┬аPMID:37464885
Singh A, At V, Gupta K, Sharma S,┬аKumar S*. Long non-coding RNA and microRNA landscape of two major domesticated cotton species.┬аComput Struct Biotechnol J.┬а21:3032-3044 (2023).┬аPMID:┬а3726640
Chakraborty S, Gangwar R, Zahra S,Poddar N, Singh A and┬аKumar S*. Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes.┬аSci Rep┬а13, 5914 (2023).┬аPMID:┬а37041245
Zahra S, Singh A,┬аand┬аKumar S*. tncRNA Toolkit: a pipeline for convenient identification of RNA (tRNA)-derived non-coding RNAs.┬аMethodsX, 10:101991 (2023).┬аPMID:┬а36632599
Poddar N, Deepika D, Chitkara P, Singh A* and┬аKumar S*.Molecular and expression analysis indicate the role of CBL interacting protein kinases (CIPKs) in abiotic stress signaling and development in chickpea.┬аSci Rep┬а12, 16862 (2022).┬аPMID:┬а36207429
Jaiswal M, Singh S and┬аKumar S*.┬аPTPAMP: Prediction Tool for Plant-derived Antimicrobial Peptides.┬аAmino Acids┬а55, 1-17 (2023). PMID:┬а35864258
Chakraborty S, Soudararajan P, and┬аKumar S*. Genome-wide identification, characterization, and expression profiling of 14-3-3 genes in legumes. Plant Biotechnol Rap.┬а16, 579тАУ597 (2022). Link:┬аhttps://doi.org/10.1007/
Singh A, Zahra S, Das D,┬аand┬аKumar S*. PtRNAdb: A web resource of Plant tRNA genes from a wide range of plant species.┬а3 Biotech┬а12, 185 (2022).┬аPMID:┬а35875176
Deepika D, Poddar N,┬аKumar S*┬аand Singh A.* Molecular characterization reveals the involvement of calcium dependent protein kinases in abiotic stress signaling and development in chickpea (Cicer arietinum).┬аFront. Plant Sci.┬а2022, 13:831265.┬аPMID:┬а35498712
Zahra S, Bhardwaj R, Sharma S, Singh S and┬аKumar S.* PtncRNAdb: Plant transfer RNA-derived non-coding RNAs (tncRNAs) database.┬а3 Biotech, 12,┬а105 (2022).┬аPMID:┬а35462956
Chitkara P, Poddar N, Singh A and┬аKumar S.* BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development.┬аPlant Biotechnol Rep.┬а16, 369-388 (2022).┬аhttps://doi.org/10.1007/s11816-022-00752-2
Singh A, Zahra S, Poddar N and┬аKumar S.*┬аTransfer RNA-derived non-coding RNAs (tncRNAs): hidden regulation of plants transcriptional regulatory circuits.┬аComputational and Structural Biotechnology Journal┬а19:5278-5291 (2021).┬аPMID:┬а34630945
Bhardwaj R, Thakur JK* and┬аKumar S*.┬а MedProDB: A database of Mediator proteins.┬аComputational and Structural Biotechnology Journal┬а19:4165-4176 (2021).┬аPMID:┬а34527190
Singh A, Vivek AT and┬аKumar S*.(2021)┬а AlnC: An extensive database of long non-coding RNAs in angiosperms. PLoS ONE 16(4): e0247215.┬аPMID:┬а33852582
Vivek AT and┬аShailesh Kumar*.┬аComputational methods for annotation of plant regulatory non-coding RNAs using RNA-seq.┬аBriefings in Bioinformatics┬а22(4):bbaa322┬а(
Das D, Jaiswal M, Khan F N, Ahamad S and┬аKumar S*. PlantPepDB: A manually curated plant peptide database.┬аScientific reports. 10:2194(2020) PMID:┬а32042035
Vivek AT, Zahra S, and┬аKumar S*.┬аFrom current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants.┬аMethods┬а83:30-37 (2020).┬аPMID:┬а31669354. (Review Article)
Singh A, Zahra S, Das D and┬аKumar S*.┬аAtFusionDB: A Database of Fusion Transcripts in┬аArabidopsis thaliana.┬аDatabase,┬аVolume 2019, 2019, bay135 (2019).┬аPMID:┬а30624648
Gupta N, Zahra S, Singh A and┬аKumar S.*┬аPVsiRNAdb: A Database for Plant Exclusive Viral-derived small interfering RNAs.┬аDatabase.┬аVolume 2018, 2018 bay105 (2018).┬аdoi.org/10.1093/
Gupta N, Singh A, Zahra S and┬аKumar S.*┬аPtRFdb: a database for plant transfer RNA-derived fragments.┬аDatabase.┬аVolume 2018, 2018, bay063 (2018).┬аdoi: 10.1093/database/bay063┬аPMID:┬а
B) First Author Publications
Kumar S, Razzaq SK, Vo AD, Gautam M, Li H: Identifying fusion transcripts using next generation sequencing.┬аWiley Interdisciplinary Reviews: RNA 2016, 7:811тАУ823.┬а(Cover Image)┬аPMID:┬а27485475
Kumar S, Vo AD, Qin F, Li H: Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data.┬аScientific reports┬а2016, 6:21597.┬аPMID:┬а26862001
Kumar S, Vikram S, Raghava GPS: Genome Annotation of┬аBurkholderia┬аsp. SJ98 with Special Focus on Chemotaxis Genes.┬аPLoS ONE 2013, 8:e70624.┬аPMID:┬а23940608
Kumar S, Kushwaha H, Bachhawat AK, Raghava GPS, Ganesan K: Genome sequence of the oleaginous red yeast┬аRhodosporidium toruloides┬аMTCC 457.┬аEukaryotic cell 2012,11:1083тАУ4.┬аPMID:┬а22858828
Kumar S, Randhawa A, Ganesan K, Raghava GPS, Mondal AK: Draft genome sequence of salt-tolerant yeast┬аDebaryomyces hansenii┬аvar. hansenii MTCC 234.┬аEukaryotic cell 2012,11:961тАУ2.┬аPMID:┬а22744717
Kumar S, Subramanian S, Raghava GPS, Pinnaka AK: Genome sequence of the marine bacterium┬аMarinilabilia salmonicolor┬аJCM 21150T.┬аJournal of bacteriology 2012, 194:3746.┬аPMID:┬а22740671
Kumar S, Vikram S, Subramanian S, Raghava GPS, Pinnaka AK: Genome sequence of the halotolerant bacterium┬аImtechella halotolerans┬аK1T.┬аJournal of bacteriology 2012, 194:3731.┬аPMID:┬а22740661
Kumar S, Vikram S, Raghava GPS: Genome sequence of the nitroaromatic compounddegrading Bacterium┬аBurkholderia┬аsp. strain SJ98.┬аJournal of bacteriology 2012, 194:3286.┬аPMID:┬а22628512
Vikram S,┬аKumar S, Subramanian S, Raghava GPS: Draft genome sequence of the nitrophenol-degrading actinomycete┬аRhodococcus imtechensis┬аRKJ300.┬аJournal of bacteriology 2012, 194:3543.┬аPMID:┬а22689233
Kumar S, Kaur N, Singh NK, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аStreptomyces gancidicus┬аStrain BKS 13-15.┬аGenome announcements, 1:e0015013.┬аPMID:┬а23599292
Kumar S, Bala M, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аRhodococcus triatomae┬аStrain BKS 15-14.┬аGenome announcements, 1:e0012913.┬аPMID:┬а23538907
Bala M,┬аKumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аRhodococcus ruber┬аStrain BKS 20-38.┬аGenome announcements, 1:e0013913. (Equal Contribution)┬аPMID:┬а23558535
Kumar S, Kaur C, Kimura K, Takeo M, Raghava GPS, Mayilraj S: Draft Genome Sequence of the Type Species of the Genus┬аCitrobacter,┬аCitrobacter freundii┬аMTCC 1658.┬аGenome announcements 2013, 1.┬аPMID:┬а23405287
Kaur N,┬аKumar S, Bala M, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аAmycolatopsis decaplanina┬аStrain DSM 44594T.┬аGenome announcements, 1:e0013813. (Equal Contribution)┬аPMID:┬а23558534
Singh NK,┬аKumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аAcinetobacter baumannii┬аStrain MSP4-16.┬аGenome announcements, 1:e0013713. (Equal Contribution)┬аPMID:┬а23558533
Bala M,┬аKumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of┬аRhodococcus qingshengii┬аStrain BKS 20-40.┬аGenome announcements, 1:e0012813. (Equal Contribution)┬аPMID:┬а23538906
Vikram S,┬аKumar S, Vaidya B, Pinnaka AK, Raghava GPS: Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium┬аArthrobacter┬аsp. Strain SJCon.┬аGenome announcements, 1:e0005813. (Equal Contribution)┬аPMID:┬а23516196
Kaur N,┬аKumar S, Mayilraj S: Genome sequencing and annotation of┬аAmycolatopsis vancoresmycina┬аstrain DSM 44592T.┬аGenomics Data 2014, 2:16тАУ17. (Equal Contribution)┬аPMID:┬а26484057
Kimura K,┬аKumar S, Takeo M, Mayilraj S: Genome sequencing, annotation of┬аCitrobacter freundii┬аstrain GTC 09479.┬аGenomics Data 2014, Dec; 2: 40тАУ41┬а. (Equal Contribution)┬аPMID:┬а26484065
C) As Collaborator / Contributor / Co-author
Xinrui Shi et al. Kumar S. and Li Hui*.UBA1-CDK16: A female-specific chimeric RNA emerging through evolution and involved in immune regulation.Sci. Adv.12,eadz9784(2026). PMID: 4
Prabhakaran S, AT Vivek, Gokul B.S, Bhavya S, Kanchan B.M.S,┬аShailesh K, Abinaya M. Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of UтАЩs genomes.┬аPlant Gene, 42, 2025, 100497.┬аLink:┬аhttps://doi.org/10.1016/
Yadav B, Sardar S, Yadav A, Kumari A, Gautam M, Mandlik R, Arora S,┬аKumar S, Jewaria PK, Sonah H, Deshmukh R, Chinnusamy V, Ram H. A CRISPR-Cas9 library to target putative redundant gene sets facilitates their functional exploration in grain development in rice.┬аBMC Plant Biol. 2025 Nov 22;25(1):1769. doi: 10.1186/s12870-025-07769-z.┬аPMID:┬а41275110
Kumari S, et al., Thum T,┬аKumar S, and Gupta SK, The RNA-binding protein Quaking is essential for cardiac homeostasis and function by regulating Morf4l2 splicing, Journal of Molecular and Cellular Cardiology, 2025,┬аttps://doi.org/10.1016/
Singh S, Gaur A, Sharma RK, Kumari R, Prakash S, Kumari S, Chaudhary AD, Prasun P, Pant P, Hunkler H, Thum T, Jagavelu K, Bharati P, Hanif K, Chitkara P,┬аKumar S, Mitra K, Gupta SK. Musashi-2 causes cardiac hypertrophy and heart failure by inducing mitochondrial dysfunction through destabilizing Cluh and Smyd1 mRNA.┬аBasic Res Cardiol. 2023 Nov 3;118(1):46. PMID:37923788
Saxena H, Negi H, Keshan R, Chitkara P,┬аKumar S, Chakraborty A, Roy A, Singh IK, Singh A. A comprehensive investigation of lipid-transfer proteins from Cicer arietinum disentangles their role in plant defense against┬аHelicoverpa armigera-infestation.┬аFront Genet, 2023. 14:1195554. PMID:37456660
Ankit A, Singh A, Kumar S and┬аSingh A*┬а(2023) Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K+) deficiency response in two contrasting chickpea cultivars.┬аFrontiers in Plant Science. 13:1054821.
Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh AK, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, E Scheffler B, Ozias Akins P, Dutta Sharma R, Bandyopadhyay K, Gaur V,┬аKumar S, Sinharoy S. Microscopic and transcriptomic analyses of Dalbergoid legume peanut reveal a divergent evolution leading to Nod Factor dependent epidermal crack-entry and terminal bacteroid differentiation.┬аMol Plant Microbe Interact. 35(2):131-145.┬аPMID:┬а34689599
Singh S, Qin F,┬аKumar S, Elfman J, Lin E,┬аPham L, Yang A and Li H (2019)┬аThe Landscape of Chimeric RNAs in Non-Diseased Tissues and Cells.┬а┬аNucleic acids research 2020; 48(4):1764-1778┬аPMID:┬а31965184
Wu P, Yang S, Singh S, Qin F,┬аKumar S,┬аWang L, Ma D and Li H: The Landscape and Implications of Chimeric RNAs in Cervical Cancer.┬аEBioMedicine 2018┬аOct 31. pii: S2352-3964(18)30477-8. doi: 10.1016/j.ebiom.2018.10.059.┬аPMID:┬а30389505
Huang R,┬аKumar S, Li H: Absence of Correlation between Chimeric RNA and Aging.┬аGenes 2017, 8: 386.┬аPMID:┬а29240691
Xie Z, Babiceanu M,┬аKumar S, Jia Y, Qin F, Barr FG, Li H: Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma.┬аProceedings of the National Academy of Sciences (PNAS) of the United States of America 2016, 113:13126тАУ13131.┬аPMID:┬а27799565
Dhanda SK, Vir P, Singla D, Gupta S,┬аKumar S, Raghava GPS: A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of┬аMycobacterium tuberculosis.┬аPLOS ONE 2016, 11:e0153771.┬аPMID:┬а27096425
Babiceanu M, Qin F, Xie Z, Jia Y, Lopez K, Janus N, Facemire L,┬аKumar S, Pang Y, Qi Y, Lazar IM, Li H: Recurrent chimeric fusion RNAs in non-cancer tissues and cells.┬аNucleic acids research 2016, 44:2859тАУ72.┬аPMID:┬а26837576
Gupta S, Chaudhary K, Dhanda SK, Kumar R,┬аKumar S, Sehgal M, Nagpal G, Raghava GPS: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.┬аPLOS ONE 2016, 11:e0166372.┬аPMID:┬а27832200
Nagpal G, Sharma M,┬аKumar S, Chaudhary K, Gupta S, Gautam A, Raghava GPS: PCMdb: Pancreatic Cancer Methylation Database.┬аScientific reports 2014, 4:4197.┬аPMID:┬а24569397
Kumar R, Chaudhary K, Gupta S, Singh H,┬аKumar S, Gautam A, Kapoor P, Raghava GPS: CancerDR: cancer drug resistance database.┬аScientific reports 2013, 3:1445.┬аPMID:┬а23486013
Vikram S, Pandey J,┬аKumar S, Raghava GPS: Genes involved in degradation of paranitrophenol are differentially arranged in form of non-contiguous gene clusters in┬аBurkholderia┬аsp. strain SJ98.┬аPloS one 2013, 8:e84766.┬аPMID:┬а24376843
Singh SV, Kumar N, Singh SN, Bhattacharya T, Sohal JS, Singh PK, Singh AV, Singh B, Chaubey KK, Gupta S, Sharma N,┬аKumar S, Raghava GPS: Genome Sequence of the тАЬIndian Bison TypeтАЭ Biotype of┬аMycobacterium avium┬аsubsp.┬аparatuberculosis┬аStrain S5.┬аGenome announcements 2013, 1.┬аPMID:┬а23469332
Book Chapter
Hamid, F., Aftab, S., Shree, T.,┬аKumar, S*.┬а(2026).┬аValidation of Plant Fusion Peptides Using Proteomics Data. In: Lynch, S., Li, H. (eds) Chimeric RNAs. Methods in Molecular Biology, vol 3024. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-
Shree, T.,┬аKumar, S*.┬а(2026).┬аAtFusionDB: A Comprehensive Database of Fusion Transcripts in Model Plant┬аArabidopsis thaliana.┬аIn: Lynch, S., Li, H. (eds) Chimeric RNAs. Methods in Molecular Biology, vol 3024. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-
Arora, S., Aftab, S., Shree, T., Kumar, S*. (2026). Identification of tRNA-Derived Fragments in Legumes. In: Jain, M., Garg, R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2977. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4820-9_15
Arora, S., Hamid F., Singh, S., Verma, D., Kumar, S*. Transfer RNA-derived fragments: A new frontier in plant stress adaptation, In: Jen-Tsung Chen (eds), Functional RNAs in Plants, Academic Press, 2026, 411-424, https://doi.org/10.1016/B978-0-443-33341-5.00026-4
Hamid, F., Arora, S., Chitkara, P.,┬аKumar, S*. (2024). A Protocol for the Detection of Fusion Transcripts Using RNA-Sequencing Data. In: Azad, R.K. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 2812. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-0716-3886-6_14
Vivek, A.T.,┬аKumar, S*. (2024). Identification of Virus-Derived Small Interfering RNAs (vsiRNAs) from Infected sRNA-Seq Samples. In: Azad, R.K. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 2812. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-0716-3886-6_17
Singh, A., Zahra, S., Arora, S., Hamid, F.,┬аKumar, S*. (2024). In Silico Identification of tRNA Fragments, Novel Candidates for Cancer Biomarkers, and Therapeutic Targets. In: Azad, R.K. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 2812. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-0716-3886-6_21
Narayan, A., Pahwa, B.,┬аKumar, S*.┬а(2022). Computational Tools and Databases for Fusion Transcripts: Therapeutic Targets in Cancer. In: Singh, S. (eds) Systems Biomedicine Approaches in Cancer Research. Springer, Singapore.┬аhttps://doi.org/10.1007/978-981-19-1953-4_6
Narayan A, Chitkara P,┬аKumar S*. (2022). Updates on Genomic Resources for Crop Improvement. In: Wani, S.H., Kumar, A. (eds) Genomics of Cereal Crops.┬аSpringer Protocols Handbooks. Humana, New York, NY.┬аhttps://doi.org/10.1007/978-1-0716-2533-0_2
Narayan A and┬аKumar S*. (2022) Identification of novel RNAs in plants with the help of next-generation sequencing technologies. Bioinformatics in Agriculture,┬аAcademic Press, 177-189, doi:┬аhttps://doi.org/10.1016/B978-0-323-89778-5.00018-0
Narayan A, Zahra S, Singh A,┬аKumar S*. In Silico Methods for the Identification of Viral-Derived Small Interfering RNAs (vsiRNAs) and Their Application in Plant Genomics.┬аMethods Mol Biol.┬а2022;2408:71-84. doi: 10.1007/978-1-0716-1875-2_4. PMID:35325416.
Mandal M, Poddar N,┬аKumar S.*┬а(2022) Identification of Novel Noncoding RNAs in Plants by Big Data Analysis. In: Singh S. (eds) Machine Learning and Systems Biology in Genomics and Health.┬аSpringer, Singapore.┬аhttps://doi.org/10.1007/978-981-16-5993-5_7
Narayan A, Singh A, and┬аKumar S.*┬аUnderstanding Microbiome Science through Big Data analysis.┬а(eds).┬аIn: Singh S. (eds).┬аMetagenomics Systems Biology.┬аSpringer, Singapore.┬аhttps://doi.org/10.1007/978-981-15-8562-3_3
Vivek A.T., and┬аKumar S.*┬а(2020). Genomics approaches in Plant Stress Research. In. Khan, Singh, and Poor (eds).┬аImproving Abiotic Stress Tolerance in Plants. CRC Press/Taylor & Francis Group┬аDOI: 10.1201/9780429027505-16.
Jaiswal M, Zahra S and┬аKumar S.*┬а(2020). Bioinformatics tools for Epitope Prediction. In: Singh S. (eds).┬аSystems and Synthetic Immunology. Springer, Singapore┬аhttps://doi.org/10.1007/978-981-15-3350-1_4
Singh A and┬аKumar S.*┬а(2019). Study of Plant Exclusive Virus-Derived Small Interfering RNAs. In: Kumar S., Egbuna C. (eds)┬аPhytochemistry: An in-silico and in-vitro Update. Springer,Singapore.┬аhttps://doi.org/10.1007/978-981-13-6920-9_29.
Zahra S and┬аKumar S.*┬а(2019). PtRFdb: Plant tRNA-Derived Fragments Database. In: Kumar S., Egbuna C. (eds)┬аPhytochemistry: An in-silico and in-vitro Update. Springer,Singapore.┬аhttps://doi.org/10.1007/978-981-13-6920-9_27.
Singh A, Zahra S, and┬аKumar S.*┬а(2019). In-Silico Tools in Phytochemical Research. In: Kumar S., Egbuna C. (eds)┬аPhytochemistry: An in-silico and in-vitro Update. Springer,Singapore.┬аhttps://doi.org/10.1007/978-981-13-6920-9_19.
Narayan A, Singh A, and┬аKumar S.*┬а(2019). Protein Homology Modeling in Phytochemical Research. In: Kumar S., Egbuna C. (eds)┬аPhytochemistry: An in-silico and in-vitro Update. Springer, Singapore.┬аhttps://doi.org/10.1007/978-981-13-6920-9_24.
┬аZahra S, Singh A and Kumar S.*┬а(2018). Synthetic Probes, Their Applications and Designing. In: Singh S. (eds)┬аSynthetic Biology (Omics Tools and Their Applications). Springer, Singapore┬аhttps://doi.org/10.1007/978-981-10-8693-9_11.
Kumar S┬аand Li H. (2017) ┬аIn silico┬аdesigning of Anticancer Peptides.┬а In: Lazar I., Kontoyianni M., Lazar A. (eds)┬аProteomics for Drug Discovery. Methods in Molecular Biology, vol 1647. Humana Press, New York, NY┬аhttps://doi.org/10.1007/978-1-4939-7201-2_17.
Current Members
Dr. A T Vivek
Project Scientist - I
- vivek37373@nipgr.ac.in
Dr. Rohit Kumar
Project Scientist -I
Dr. Shilpa Sri Pushan
Project Scientist - I
- shilpasripushan@gmail.com
Dr. Sneha Tiwari
Research Associate-I
- sneha23@nipgr.ac.in
Ms.Simran
Ph.D. Student
- simran@nipgr.ac.in
Ms. Fiza Hamid
Ph.D. Student
- fiza@nipgr.ac.in
Ms. Sheetal Singh
Ph.D. Student
- sheetalsingh@nipgr.ac.in
Ms. Gayathri Sunil
i3c BRIC - RCB PhD Scholar
Ms. Ashu
PhD Student
Mr. Ankur Singh
Young Professional-II
Mr. Ananya Sourav
Project Assistant
- ananyasourav@nipgr.ac.in
Mr. Love Kaushik
Project Associate- I
List of Ph. D. Students
Ajeet Singh
2022
Thesis: Computational approaches to study the long non-coding RNAs (IncRNAs) and fusion transcripts in plants
Shafaque Zahra
2023
Thesis: Computational approaches to study the transfer RNA-derived fragments (tRFs) in plants
Mohini Jaiswal
2023
Thesis: Computational approaches to study plant-derived peptides having biological activities
AT Vivek
2024
Thesis: Insights into regulatory non-coding RNAs in plants using big data