National Institute of Plant Genome Research
Digital India   Azadi Ka Amrit Mahotsav     
 
    Dr. Shailesh Kumar
    (M.Sc. & Ph.D., Jawaharlal Nehru University, New Delhi)
    Staff Scientist III, Laboratory #202,
    National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067
    Tel: +91-11-26735217
    Fax: +91-11-26741658
    E-mail: shailesh@nipgr.ac.in
 Research Area
Bioinformatics, Genomics, Big data analysis, Machine Learning (ML), Deep Learning, Artificial Intelligence (AI), and Plant Biotechnology
 Professional & Academic Background
Staff Scientist III (July 2020- Present): National Institute of Plant Genome Research (NIPGR), New Delhi, India
Staff Scientist II (May 2017- June 2020): National Institute of Plant Genome Research (NIPGR), New Delhi, India
Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA
Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India
Ph.D. (2009-2014): 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.
 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.

 Group Members
Dr. Rashmi GangwarProject Scientist-I
Ajeet SinghPh.D. Student
Shafaque ZahraPh.D. Student
A. T. VivekPh.D. Student
Mohini JaiswalPh.D. Student
Srija ChakrabortySenior Research Fellow (SRF)
Rohan BhardwajProject Associate- I
Pragya ChitkaraProject Associate- I
Akila S.Project Associate- I
 Web Resources, Databases and Tools (Developed/Contributed)
PTPAMP: Prediction Tool for Plant-derived Antimicrobial Peptides (http://www.nipgr.ac.in/PTPAMP/)
PtncRNAdb: Plant transfer RNA-derived non-coding RNAs (tncRNAs) database (https://nipgr.ac.in/PtncRNAdb)
MedProDB: Mediator Protein Database (http://www.nipgr.ac.in/MedProDB/)
AlnC: An extensive database of long non-coding RNAs (lncRNAs) in Angiosperms (http://www.nipgr.ac.in/AlnC)
tncRNA: A pipeline for the identification of tRNA-derived small ncRNAs (tncRNAs) from high throughput sequencing data (http://www.nipgr.ac.in/tncRNA)
PlantPepDB: A database of plant peptides having different functions and therapeutic activities (http://www.nipgr.ac.in/PlantPepDB/)
PtRNAdb: A database containing information of tRNA genes (http://www.nipgr.ac.in/PtRNAdb/)
AtFusionDB: A Database of Fusion Transcripts in Arabidopsis thaliana (http://www.nipgr.ac.in/AtFusionDB/)
PVsiRNAdb:Plant Virus siRNA Database (http://www.nipgr.ac.in/PVsiRNAdb/)
PtRFdb: Plant transfer RNA-derived fragments database (http://www.nipgr.ac.in/PtRFdb/)
Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (https://webs.iiitd.edu.in/raghava/cancertope/)
CancerDr: Cancer Drug Resistance Database. (https://webs.iiitd.edu.in/raghava/cancerdr/).
PCMDB: Pancreatic cancer methylation database. (https://webs.iiitd.edu.in/raghava/pcmdb/).
OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/).
MtbVeb: A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (https://webs.iiitd.edu.in/raghava/mtbveb/).

 Publications

Citations of the publications:Google Scholar
A) Corresponding Author
Jaiswal M, Singh S and Kumar S*. PTPAMP: Prediction Tool for Plant-derived Antimicrobial Peptides. Amino Acids. PMID: 35864258
Chakraborty S, Soudararajan P, and Kumar S*. Genome-wide identification, characterization, and expression profiling of 14-3-3 genes in legumes. Plant Biotechnol Rep (2022). In Press
Singh A, Zahra S, Das D and Kumar S*. PtRNAdb: A web resource of Plant tRNA genes from a wide range of plant species. 3 Biotech (2022). 12, 185 (2022). PMID: 35875176
Deepika D, Poddar N, Kumar S* and Singh A.* Molecular characterization reveals the involvement of calcium dependent protein kinases in abiotic stress signaling and development in chickpea (Cicer arietinum). Front. Plant Sci. 2022, 13:831265. PMID: 35498712
Zahra S, Bhardwaj R, Sharma S, Singh S and Kumar S.* PtncRNAdb: Plant transfer RNA-derived non-coding RNAs (tncRNAs) database. 3 Biotech, 12, 105 (2022). PMID: 35462956
Chitkara P, Poddar N, Singh A and Kumar S.* BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development. Plant Biotechnol Rep. 16, 369-388 (2022). https://doi.org/10.1007/s11816-022-00752-2
Singh A, Zahra S, Poddar N and Kumar S.* Transfer RNA-derived non-coding RNAs (tncRNAs): hidden regulation of plants transcriptional regulatory circuits. Computational and Structural Biotechnology Journal. Volume 19, 2021, Pages 5278-5291. PMID: 34630945
Bhardwaj R, Thakur JK* and Kumar S*.  MedProDB: A database of Mediator proteins. Computational and Structural Biotechnology Journal Volume 19, 2021, Pages 4165-4176. PMID: 34527190
Singh A, Vivek AT and Kumar S*.(2021)  AlnC: An extensive database of long non-coding RNAs in angiosperms. PLoS ONE 16(4): e0247215. PMID: 33852582
Vivek AT and Shailesh Kumar*. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Briefings in Bioinformatics, Volume 22, Issue 4, July 2021, bbaa322, https://doi.org/10.1093/bib/bbaa322 PMID: 33333550. (Review Article)
Das D, Jaiswal M, Khan F N, Ahamad S and Kumar S*. PlantPepDB: A manually curated plant peptide database. Scientific reports 10:2194(2020) PMID: 32042035
Vivek AT, Zahra S, and Kumar S*. From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants. Methods; 2020 Nov 1;183:30-37. PMID: 31669354. (Review Article)
Singh A, Zahra S, Das D and Kumar S.* AtFusionDB: A Database of Fusion Transcripts in Arabidopsis thaliana. Database (2018). Database (Oxford).Volume 2018 Jan 1. doi.org/10.1093/database/bay135. PMID: 30624648
Gupta N, Zahra S, Singh A and Kumar S.* PVsiRNAdb: A Database for Plant Exclusive Viral-derived small interfering RNAs. Database (2018). Database (Oxford).Volume 2018 Jan 1. doi.org/10.1093/database/bay105. PMID: 30307523
Gupta N, Singh A, Zahra S and Kumar S.* PtRFdb: a database for plant transfer RNA-derived fragments. Database (2018). Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay063 PMID: 29939244
B) First Author Publications
Kumar S, Razzaq SK, Vo AD, Gautam M, Li H: Identifying fusion transcripts using next generation sequencing. Wiley Interdisciplinary Reviews: RNA 2016, 7:811–823. (Cover Image) PMID: 27485475
Kumar S, Vo AD, Qin F, Li H: Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Scientific reports 2016, 6:21597. PMID: 26862001
Kumar S, Vikram S, Raghava GPS: Genome Annotation of Burkholderia sp. SJ98 with Special Focus on Chemotaxis Genes. PLoS ONE 2013, 8:e70624. PMID: 23940608
Kumar S, Kushwaha H, Bachhawat AK, Raghava GPS, Ganesan K: Genome sequence of the oleaginous red yeast Rhodosporidium toruloides MTCC 457. Eukaryotic cell 2012,11:1083–4. PMID: 22858828
Kumar S, Randhawa A, Ganesan K, Raghava GPS, Mondal AK: Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234. Eukaryotic cell 2012,11:961–2. PMID: 22744717
Kumar S, Subramanian S, Raghava GPS, Pinnaka AK: Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. Journal of bacteriology 2012, 194:3746. PMID: 22740671
Kumar S, Vikram S, Subramanian S, Raghava GPS, Pinnaka AK: Genome sequence of the halotolerant bacterium Imtechella halotolerans K1T. Journal of bacteriology 2012, 194:3731. PMID: 22740661
Kumar S, Vikram S, Raghava GPS: Genome sequence of the nitroaromatic compounddegrading Bacterium Burkholderia sp. strain SJ98. Journal of bacteriology 2012, 194:3286. PMID: 22628512
Vikram S, Kumar S, Subramanian S, Raghava GPS: Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300. Journal of bacteriology 2012, 194:3543. PMID: 22689233
Kumar S, Kaur N, Singh NK, Raghava GPS, Mayilraj S: Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. Genome announcements, 1:e0015013. PMID: 23599292
Kumar S, Bala M, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14. Genome announcements, 1:e0012913. PMID: 23538907
Kumar S, Kaur C, Kimura K, Takeo M, Raghava GPS, Mayilraj S: Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658. Genome announcements 2013, 1. PMID: 23405287
Bala M, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38. Genome announcements, 1:e0013913. (Equal Contribution) PMID: 23558535
Kaur N, Kumar S, Bala M, Raghava GPS, Mayilraj S: Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T. Genome announcements, 1:e0013813. (Equal Contribution) PMID: 23558534
Singh NK, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16. Genome announcements, 1:e0013713. (Equal Contribution) PMID: 23558533
Bala M, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40. Genome announcements, 1:e0012813. (Equal Contribution) PMID: 23538906
Vikram S, Kumar S, Vaidya B, Pinnaka AK, Raghava GPS: Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon. Genome announcements, 1:e0005813. (Equal Contribution) PMID: 23516196
Kaur N, Kumar S, Mayilraj S: Genome sequencing and annotation of Amycolatopsis vancoresmycina strain DSM 44592T. Genomics Data 2014, 2:16–17. (Equal Contribution) PMID: 26484057
Kimura K, Kumar S, Takeo M, Mayilraj S: Genome sequencing, annotation of Citrobacter freundii strain GTC 09479. Genomics Data 2014, Dec; 2: 40–41 . (Equal Contribution) PMID: 26484065
C) As Collaborator / Contributor / Co-author
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, Kumar 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. Mol Plant Microbe Interact. 35(2):131-145. PMID: 34689599
Singh S, Qin F, Kumar S, Elfman J, Lin E, Pham L, Yang A and Li H (2019) The Landscape of Chimeric RNAs in Non-Diseased Tissues and Cells.  Nucleic acids research 2020; 48(4):1764-1778 PMID: 31965184
Wu P, Yang S, Singh S, Qin F, Kumar S, Wang L, Ma D and Li H: The Landscape and Implications of Chimeric RNAs in Cervical Cancer. EBioMedicine 2018 Oct 31. pii: S2352-3964(18)30477-8. doi: 10.1016/j.ebiom.2018.10.059. PMID: 30389505
Huang R, Kumar S, Li H: Absence of Correlation between Chimeric RNA and Aging. Genes 2017, 8: 386. PMID: 29240691
Xie Z, Babiceanu M, Kumar S, Jia Y, Qin F, Barr FG, Li H: Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma. Proceedings of the National Academy of Sciences (PNAS) of the United States of America 2016, 113:13126–13131. PMID: 27799565
Dhanda SK, Vir P, Singla D, Gupta S, Kumar S, Raghava GPS: A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PLOS ONE 2016, 11:e0153771. PMID: 27096425
Babiceanu M, Qin F, Xie Z, Jia Y, Lopez K, Janus N, Facemire L, Kumar S, Pang Y, Qi Y, Lazar IM, Li H: Recurrent chimeric fusion RNAs in non-cancer tissues and cells. Nucleic acids research 2016, 44:2859–72. PMID: 26837576
Gupta S, Chaudhary K, Dhanda SK, Kumar R, Kumar S, Sehgal M, Nagpal G, Raghava GPS: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer. PLOS ONE 2016, 11:e0166372. PMID: 27832200
Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GPS: PCMdb: Pancreatic Cancer Methylation Database. Scientific reports 2014, 4:4197. PMID: 24569397
Kumar R, Chaudhary K, Gupta S, Singh H, Kumar S, Gautam A, Kapoor P, Raghava GPS: CancerDR: cancer drug resistance database. Scientific reports 2013, 3:1445. PMID: 23486013
Vikram S, Pandey J, Kumar S, Raghava GPS: Genes involved in degradation of paranitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98. PloS one 2013, 8:e84766. PMID: 24376843
Singh SV, Kumar N, Singh SN, Bhattacharya T, Sohal JS, Singh PK, Singh AV, Singh B, Chaubey KK, Gupta S, Sharma N, Kumar S, Raghava GPS: Genome Sequence of the “Indian Bison Type” Biotype of Mycobacterium avium subsp. paratuberculosis Strain S5. Genome announcements 2013, 1. PMID: 23469332
D) Book Chapters
Narayan A, Chitkara P, Kumar S*. (2022). Updates on Genomic Resources for Crop Improvement. In: Wani, S.H., Kumar, A. (eds) Genomics of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2533-0_2
Narayan A and Kumar S*. (2022) Identification of novel RNAs in plants with the help of next-generation sequencing technologies. Bioinformatics in Agriculture, Academic Press, 177-189, doi: https://doi.org/10.1016/B978-0-323-89778-5.00018-0
Narayan A, Zahra S, Singh A, Kumar S*. In Silico Methods for the Identification of Viral-Derived Small Interfering RNAs (vsiRNAs) and Their Application in Plant Genomics. Methods Mol Biol. 2022;2408:71-84. doi: 10.1007/978-1-0716-1875-2_4. PMID:35325416.
Mandal M, Poddar N, Kumar S.* (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. Springer, Singapore. https://doi.org/10.1007/978-981-16-5993-5_7
Narayan A, Singh A, and Kumar S.* Understanding Microbiome Science through Big Data analysis. (eds). In: Singh S. (eds). Metagenomics Systems Biology. Springer, Singapore. https://doi.org/10.1007/978-981-15-8562-3_3
Vivek A.T., and Kumar S.* (2020). Genomics approaches in Plant Stress Research. In. Khan, Singh, and Poor (eds). Improving Abiotic Stress Tolerance in Plants. CRC Press/Taylor & Francis Group DOI: 10.1201/9780429027505-16.
Jaiswal M, Zahra S and Kumar S.* (2020). Bioinformatics tools for Epitope Prediction. In: Singh S. (eds). Systems and Synthetic Immunology. Springer, Singapore https://doi.org/10.1007/978-981-15-3350-1_4
Singh A and Kumar S.* (2019). Study of Plant Exclusive Virus-Derived Small Interfering RNAs. In: Kumar S., Egbuna C. (eds) Phytochemistry: An in-silico and in-vitro Update. Springer,Singapore. https://doi.org/10.1007/978-981-13-6920-9_29.
Zahra S and Kumar S.* (2019). PtRFdb: Plant tRNA-Derived Fragments Database. In: Kumar S., Egbuna C. (eds) Phytochemistry: An in-silico and in-vitro Update. Springer,Singapore. https://doi.org/10.1007/978-981-13-6920-9_27.
Singh A, Zahra S, and Kumar S.* (2019). In-Silico Tools in Phytochemical Research. In: Kumar S., Egbuna C. (eds) Phytochemistry: An in-silico and in-vitro Update. Springer,Singapore. https://doi.org/10.1007/978-981-13-6920-9_19.
Narayan A, Singh A, and Kumar S.* (2019). Protein Homology Modeling in Phytochemical Research. In: Kumar S., Egbuna C. (eds) Phytochemistry: An in-silico and in-vitro Update. Springer, Singapore. https://doi.org/10.1007/978-981-13-6920-9_24.
Zahra S, Singh A and Kumar S.* (2018). Synthetic Probes, Their Applications and Designing. In: Singh S. (eds) Synthetic Biology (Omics Tools and Their Applications). Springer, Singapore https://doi.org/10.1007/978-981-10-8693-9_11.
Kumar S and Li H. (2017)  In silico designing of Anticancer Peptides.  In: Lazar I., Kontoyianni M., Lazar A. (eds) Proteomics for Drug Discovery. Methods in Molecular Biology, vol 1647. Humana Press, New York, NY https://doi.org/10.1007/978-1-4939-7201-2_17.