National Institute of Plant Genome Research
Digital India     
 
    Dr. Shailesh Kumar, Ph.D.
    Staff Scientist II, Bioinformatics Laboratory #202
    National Institute of Plant Genome Research (NIPGR), New Delhi
    Tel:  91-11-26735217
    Fax:  91-11-26741658
    E-mail: shailesh@nipgr.ac.in, shaileshgenome@gmail.com
 Openings in the Lab
Every year we have several open positions in our laboratory.
  1. Two supporting staff position (JRF/SRF or RA level)
  2. One summer trainee position for B.Sc./B.Tech student (2-3 months)
  3. Two trainee positions for M.Sc/M.Tech students (6-10 months)
  4. Two trainee positions for M.Sc/M.Tech students (6 months with Salary of INR 10,000 p.m.)
  5. Postdoctoral Fellows
For more details please email me at shailesh@nipgr.ac.in
 Research Area
Bioinformatics, Genomics and Big data analysis
 Research Interests
My research group is exploring several new areas in plant genome research including identification, characterization and validation of novel molecules by analysing high throughput sequencing datasets. Our choice of molecules includes transfer RNA-derived fragments (e.g. tRFs), fusion transcripts, circular RNAs and ribosomal RNA-derived fragments (e.g. rRFs). In addition to this, we are also developing in silico tools, pipelines, web-servers and databases for biological research community.

Study of Transfer RNA-derived fragments (e.g. tRFs) in Plants

Transfer RNA-derived fragments or tRFs is a novel class of 15-28 nucleotides length small non-coding RNAs, generated by endonucleolytic cleavage of both mature and precursor tRNAs. Current understanding of the plant tRFs indicates that these sRNAs originate from 5' end (i.e. tRF-5) and 3' end (i.e. tRF-3) of mature tRNAs; and precursor tRNAs (i.e. tRF-1). In plants, there is an enhancement of tRFs generation in case of different biotic and abiotic stress conditions. Initial reports suggests that both Dicer-dependent and Dicer-independent pathways involved in tRFs generation. Reports also suggests that tRFs have role in both transcription and translation repression. In a nutshell, It is very import class of molecule to study in plants. Now, the key is "when" and "where" to look for such events. We are trying to understand the role of tRFs, biogenesis and their mode of action.

Study of Fusion transcripts in Plants

We are also exploring the area of fusion transcripts in plants. Chimeric transcripts may either act as long non-coding RNAs or can encode novel chimeric proteins. Advancement in the high-throughput technologies has led to the accumulation of enormous sequencing data, which has eased the understanding of the molecular mechanism behind this complex event, and its implications are being attempted to be elucidated in eukaryotic organisms including plants. Negligible information available for the chimeric transcripts in plants. We have to understand their role, mode of generation and functional mechanism in plants.

Development of webservers, databases and computational pipelines for plant research

Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies.
 Group Members
Shafaque ZahraPh.D. Student
Ajeet SinghPh.D. Student
A. T. VivekPh.D. Student
Mohini JaiswalPh.D. Student
Mustafa Raza Research Associate (RA)
Meghna Agrawal Junior Research Fellow (JRF)
Durdam Das Junior Research Fellow (JRF)
Anukriti Ghosh Junior Research Fellow (JRF)
 Professional & Academic Background
Staff Scientist II (May 2017- present): 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. Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India
M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India
B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India
 Awards and Fellowships
Junior and Senior Research Fellowship (2009-2014) : Council of Scientific and Industrial Research (CSIR), New Delhi, India
GATE (Graduate Aptitude Test in Engineering) : Qualified in years 2008 and 2009
 Scientific Contributions/ Recognitions
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: Journal of Translational Medicine and BMC Bioinformatics.
Editorial Board Member of Journal: Theoretical Biology and Medical Modelling.
Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals.
 Web Resources, Databases and Tools (Developed/Contributed)
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 (http://www.imtech.res.in/raghava/cancertope/)
GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/).
Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/).
CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/).
PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/).
Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/).
Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/)
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. (http://crdd.osdd.net/raghava/mtbveb/).

 Publications

A) Peer reviewed publications
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
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.
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.
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.
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.
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.
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.
Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GPS: PCMdb: Pancreatic Cancer Methylation Database. Scientific reports 2014, 4:4197.
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.
Kumar S, Vikram S, Raghava GPS: Genome Annotation of Burkholderia sp. SJ98 with Special Focus on Chemotaxis Genes. PLoS ONE 2013, 8:e70624.
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.
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.
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.
Kumar S, Subramanian S, Raghava GPS, Pinnaka AK: Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. Journal of bacteriology 2012, 194:3746.
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.
Kumar S, Vikram S, Raghava GPS: Genome sequence of the nitroaromatic compounddegrading Bacterium Burkholderia sp. strain SJ98. Journal of bacteriology 2012, 194:3286.
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.
B) Review articles
Vivek A.T., 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 (In Press).
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)
C) Genome Announcement Publications
Kumar S, Kaur N, Singh NK, Raghava GPS, Mayilraj S: Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. Genome announcements, 1:e0015013.
Kumar S, Bala M, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14. Genome announcements, 1:e0012913.
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.
Bala M, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38. Genome announcements, 1:e0013913. (Equal Contribution)
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)
Singh NK, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16. Genome announcements, 1:e0013713. (Equal Contribution)
Bala M, Kumar S, Raghava GPS, Mayilraj S: Draft Genome Sequence of Rhodococcus qingshengii Strain BKS 20-40. Genome announcements, 1:e0012813. (Equal Contribution)
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.
Kaur N, Kumar S, Mayilraj S: Genome sequencing and annotation of Amycolatopsis vancoresmycina strain DSM 44592T. Genomics Data 2014, 2:16–17.
Kimura K, Kumar S, Takeo M, Mayilraj S: Genome sequencing, annotation of Citrobacter freundii strain GTC 09479. Genomics Data 2014, Dec; 2: 40–41 .
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.
D) Book Chapters
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.