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Mukesh Jain

Mukesh Jain
Mukesh Jain
Professor
Centre/School/Special Centre
School of Computational and Integrative Sciences
Room No
21
Off. Phone
011-26704686
Email
mjain[at]jnu[dot]ac[dot]in , mjainanid[at]gmail[dot]com
Personal Webpage
http://ccbb.jnu.ac.in/mjain
Qualifications

Ph.D. (Plant Molecular Biology), University of Delhi (2006)

M.Sc. (Biotechnology), Kurukshetra University (2001)

Areas of Interest/Specialization

Plant Biology – Functional and Translational Genomics

Chromatin Biology and Epigenomics
Gene/Genome Regulation, Regulatory Network Analysis

Abiotic Stress, Seed Development

Experience

 

Professor, SC&IS, Jawaharlal Nehru University (2018-Present)

Dean, SC&IS, Jawaharlal Nehru University (February 2022-February 2024)

Chief Coordinator, Communication & Information Services, JNU, New Delhi (May 2020-May 2022).

Associate Professor, SC&IS, Jawaharlal Nehru University (2015-2018)
Staff Scientist II-IV, National Institute of Plant Genome Research, New Delhi (2008-2015)
Visiting Scientist, University of Georgia, Georgia (2011-2012)
Assistant Professor, GGS Indraprastha University, New Delhi (2007-2008)
Research Scientist, Centre for Plant Molecular Biology, New Delhi (2006-2007)

Awards & Honours

Fellow, Indian National Science Academy, New Delhi (2026); Fellow, National Academy of Agricultural Sciences, New Delhi (2016); Fellow, National Academy of Sciences India, Allahabad (2015); Associate Fellow, National Academy of Agricultural Sciences, New Delhi (2011-2015); Associate Fellow, Indian Academy of Sciences, Bangalore (2007-2012)
Editor/Associate/Academic/Review Editor - `The Plant Genome` (2022 onwards); `BMC Plant Biology` (2021 onwards); `Journal of Plant Growth Regulation` (2021 onwards); `Scientific Reports` NPG (2015 onwards); `PLoS ONE` (2014 onwards); `Frontiers in Plant Science` (2014-2019); `Molecular Breeding` (2013-2018); `BMC Research Notes` (2010-2020)


Tata Innovation Fellowship 2018-19 from DBT; Haryana Vigyan Ratna Award 2019 from DST-Haryana; National Bioscience Award 2016 from DBT; Rajib Goyal Prize in Life Sciences 2014-2015 from Kurukshetra University, Annual Eminence Award from Rawal Institutions, 2014; NASI-Scopus Young Scientist Award, 2012; Young Scientist Award from the National Academy of Agricultural Sciences, 2011-2012; Prof. B.K. Bachhawat Memorial Young Scientist Lecture Award from NASI, 2012; Haryana Yuva Vigyan Ratna Award from the Haryana State Council for Science & Technology, 2010-11; Anil Kumar Bose Memorial Award from the Indian National Science Academy, 2011; Young Scientist Platinum Jubilee Award from the National Academy of Sciences India (NASI), 2009; Young Scientist Award from the Indian Science Congress Association, 2007-08; Indian National Science Academy (INSA) medal for Young Scientist, 2007; Professor LSS Kumar Memorial Award, 2007; Innovative Young Biotechnologists Award (IYBA), 2006; University Medal Kurukshetra University, 2001

DBT-CREST Fellowship Award for 2010-2011 from the Department of Biotechnology; BOYCAST Fellowship for 2010-2011 from the Department of Science & Technology (not availed); Biography listed in the Marquis Who`s Who in the World 2010 and 2012 editions; Certificate of Recognition as Genomics Pioneer (2008) from Ocimum Biosolutions in association with OBBeC; Visiting Scientist at The Institute for Genomic Research, Rockville, MD for the Rice Genome Annotation workshop (2007); Junior and Senior Research Fellowships from CSIR (February 2002-September 2006) 

International Collaboration/Consultancy
Best Peer Reviewed Publications

View Complete List

  • Sahil R, Pal V, Kharat AS, Jain M. (2025) A multi-omics meta-analysis of rhizosphere microbiome reveals growth-promoting marker bacteria at different stages of legume development. Plant, Cell & Environment, doi: https://doi.org/10.1111/pce.15429.

  • Rajkumar MS, Tembhare K, Garg R, Jain M. (2024) Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars. The Plant Journal 119, 2063-2079. doi: http://doi.org/10.1111/tpj.16864.

  • Dwivedi A, Singh V, Anwar K, Pareek A, Jain M. (2023) Integrated transcriptome, proteome and metabolome analyses revealed auxiliary carbohydrate metabolism augmenting drought tolerance in rice. Plant Physiology and Biochemistry 201, 107849. doi: 10.1016/j.plaphy.2023.107849.

  • Rajkumar MS, Garg R†, Jain M†. (2022) Genome-wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress. Physiologia Plantarum 174, e13611. doi: 10.1111/ppl.13611. †Joint corresponding author

  • Jain M, Bansal J, Rajkumar MS, Garg R. (2022) An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea.  Communications Biology 5, 1106. doi: 10.1038/s42003-022-04083-4.

  • Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. (2021) Draft genome and transcriptome analyses of wild halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. Physiologia Plantarum 173, 1309-1322. doi: 10.1111/ppl.13284.

  • Rajkumar MS, Gupta K, Khemka N, Garg R, Jain M. (2020) DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea. Communications Biology 3, 340. doi: 10.1038/s42003-020-1059-1.

  • Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. (2020) Draft genome and transcriptome analyses of wild halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. Physiologia Plantarum doi: 10.1111/ppl.13284.

  • Singh U, Khemka N, Rajkumar MS, Garg R, Jain M. (2017) PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Research DOI: 10.1093/nar/gkx866.

  • Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. (2017) Global transcriptome and co-expression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea. The Plant Journal 91, 1088-1107. doi: 10.1111/tpj.13621.

  • Jain M*, Moharana KC, Shankar R, Kumari R, Garg R* (2014) Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnology Journal 12, 253-264.

  • Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Sharma P, Kant C, Yadav M, Yadav G, Bhatia S, Tyagi AK, Chattopadhyay D. (2013) Draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). The Plant Journal 74, 715-729.

  • Singh VK, Garg R, Jain M. (2013) A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnology Journal 11, 691-701.

  • Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M (2012). Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnology Journal 10, 690-702.

  • Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiology 156, 1661-1678. 

Recent Peer Reviewed Journals/Books

Review articles

  • Sahil R, Jain M (2025). Selenobacteria: The unsung friends of plants. Trends in Plant Science doi: 10.1016/j.tplants.2025.03.017

  • Garg R, Sahu SK, Jain M (2025). Single same-cell multiome for dissecting key plant traits. Trends in Plant Science 30, 128-130. doi: 10.1016/j.tplants.2024.10.008

  • Singh V, Jain M. (2022) Recent advancements in CRISPR-Cas toolbox for imaging applications. Critical Reviews in Biotechnology 42, 508-531. doi: 10.1080/07388551.2021.1950608.

  • Jain M, Garg R. (2021) Enhancers as potential targets for engineering abiotic stress tolerance in crop plants. Physiologia Plantarum 173, 1382-1391. doi: 10.1111/ppl.13421.

  • Kumar V, Jain M. (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66: 47-57.

  • Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6, doi: 10.3835/plantgenome2013.04.0011.

 

Edited Books/Special Issues

  • Book on “Legume Genomics: Methods and Protocols - Second Edition”, Methods in Molecular Biology (Eds.) Jain M, Garg R, (2026) Springer Science+Business Media LLC, New York, USA. Vol 2977, pp 1-303 (ISBN 978-1-0716-4819-3; ISBN 978-1-0716-4820-9 for eBook)

  • E-book/Special Issue on “Abiotic Stress: Molecular Genetics and Genomics, Volume II”, Frontiers in Plant Science (2022) Eds. Jain M, Garg R, Varshney RK, Subudhi PK. Frontiers Media SA https://www.frontiersin.org/research-topics/27165/abiotic-stress-molecular-genetics-and-genomics-volume-ii pp 1-464 (ISBN 978-2-83251-541-9).

  • Book on “Legume Genomics: Methods and Protocols”, Methods in Molecular Biology (Eds.) Garg R, Jain M. (2020) Springer Science+Business Media LLC, New York, USA Vol 2107, pp 1-406 (ISBN 978-1-0716-0234-8).

  • Book on “Pulse Improvement-Physiological, Molecular and Genetic Perspectives”, (Eds.) Wani SH, Jain M (2019). Springer, Cham; Springer Nature Switzerland AG pp 1-241. (ISBN 978-3-030-01742-2). https://doi.org/10.1007/978-3-030-01743-9

  • E-book and Special Issue on “Abiotic Stress: Molecular Genetics and Genomics”, Frontiers in Plant Science (December 2014) Eds. Jain M, Garg R, Varshney RK. Frontiers Media SA pp 1-101. (ISBN 978-2-88919-359-2) http://journal.frontiersin.org/researchtopic/1863/abiotic-stress-molecular-genetics-and-genomics 

 

Webservers/Databases/Resources developed

Hosted at JNU

1. Chickpea Gene Expression Atlas Database: CaGEA (http://tgsbl.jnu.ac.in/CaGEA) A web resource for mining/downloading full-length transcriptome sequence data (protein-coding and lncRNAs), functional annotation (gene description, PFam domain and gene ontology), tissue-specific expression profiles and co-expression network of all chickpea transcripts.

2. PLncPRO: Plant Long Non-coding RNA Prediction via Random Forest Model (http://ccbb.jnu.ac.in/plncpro) A standalone tool based on machine learning random forest algorithm for prediction of long non-coding RNAs in plants and animals.

3. Plant G-Quadruplex Database: (PlantG4DB, http://ccbb.jnu.ac.in/PlantG4DB) A web resource for mining/downloading various information about G-quadruplexes in different plant species.

4. Chickpea SNP Discovery Project: (http://ccbb.jnu.ac.in/Casnp) SNP and InDel data among 18 chickpea genotypes with contrasting seed size/weigh.

5. Oryza coarctata Genome: (http://ccbb.jnu.ac.in/ory-coar) Draft genome sequence and annotation of Oryza coarctata (wild halophyte rice) genome.

6. Morus indica Genome: (http://tgsbl.jnu.ac.in/MindGP) Draft genome sequence and annotation of Morus indica (Indian mulberry) genome.

 

Hosted at NIPGR, New Delhi

NGS QC Toolkit: Next Generation Sequencing Quality Control Toolkit - A toolkit comprised of user-friendly stand-alone tools for the quality check (QC) and filtering of next generation sequencing (NGS) data. (https://github.com/mjain-lab/NGSQCToolkit)

Chickpea Transcriptome Database: (CTDB) A web resource for mining/downloading sequence data, functional annotation (gene description, domain and gene ontology) and tissue-specific expression profiles of chickpea transcriptome. (http://www.nipgr.ac.in/ctdb.html)

Rice Stress-Responsive Transcription Factor Database: (RiceSRTFDB) A web resource for comprehensive information (genomic features, expression profiles, cis-regulatory elements and Tos17 mutants) for rice transcription factors

PlantRGS: Plant Reference Gene Server - A web server for the identification of most suitable candidate reference gene(s) with minimum expression variance for quantitative gene expression studies in plants.

Chickpea MicroSatellite Database: (CMsDB) A database for mining of microsatellites in desi and kabuli chickpea genomes and polymorphic microsatellites between desi/kabuli chickpea types along with their annotation and primer sequences.

Other Resources:

Rice SNP Discovery: SNP and InDel data among rice accessions with contrasting response to abiotic stresses.

Catharanthus Transcriptome: Transcriptome sequence, functional annotation, gene expression and microsatellite data.

Saffron Transcriptome: Transcriptome sequence, functional annotation, gene expression and microsatellite data.

Porteresia Transcriptome: Transcriptome sequence and functional annotation data.

Chickpea Genome Analysis Project (CGAP): Draft genome sequence and annotation of desi chickpea (http://www.nipgr.ac.in/CGAP)

Patents (if any)
  • Nucleic acid sequences encoding glutathione S-transferases associated with abiotic stress responses in plants (2009). [Indian patent application (2302/DEL/2009) filed on November 9, 2009]. Inventor: Jain M
  • Nucleic acid sequences involved in floral transition in rice and uses thereof (2007). [Indian patent application (158/DEL/2007) filed on January 25, 2007]. Inventors: Khurana JP, Tyagi AK, Nijhawan A, Sharma P, Jain M
  • Topoisomerase 6 genes from rice for conferring stress tolerance in plants (2006). [Indian patent application (1844/DEL/2006) filed on August 17, 2006]. Inventors: Khurana JP, Tyagi AK, Jain M