Publications

Edited Books

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) https://link.springer.com/book/10.1007/978-1-0716-4820-9


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).



Abiotic Stress: Molecular Genetics and Genomics
(ISBN 978-2-88919-359-2)


Pulse Improvement: Physiological, Molecular and Genetic Perspectives
(ISBN 978-3-030-01742-2)


Legume Genomics: Methods and Protocol
(ISBN 978-1-0716-0235-5)













Review articles

  • Garg R, Jain M (2026). Single-cell multi-omics atlases unlock cellular mysteries. Trends in Plant Science doi: https://doi.org/10.1016/j.tplants.2025.12.011
  • Sen MK†, Roy A, Mondal SK, Hamouzova, Jain M† (2026) RNA-directed DNA methylation: epigenome-guided herbicide-tolerant crop management. Journal of Experimental Botany https://doi.org/10.1093/jxb/erag094 †Joint corresponding author
  • Anand R, Sahil R, Jain M, Maurya GK, Khrat AS (2025). Plant-based diet as a precursor to human gut diversity. The Journal of Nutrition 156, 101251. doi: 10.1016/j.tjnut.2025.11.020
  • Sahil R, Jain M (2026). A multi-omics approach for microbiome data analysis in legumes. Methods in Molecular Biology 2977, 181-196.
  • Sahil R, Jain M (2026). A computational pipeline for the identification of RNA virome in legumes. Methods in Molecular Biology 2977, 197-204.
  • Banerjee AK, Jain M, Garg R (2026). Large-scale identification of transposon insertion polymorphisms in leguminous plants from paired-end WGS data. Methods in Molecular Biology 2977, 15-28.
  • Sahil R, Jain M (2025). Selenobacteria: The unsung friends of plants. Trends in Plant Science 30, 915-917. 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
  • Jain M (2024). Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities. Current Opinion in Plant Biology 82, 102662. doi: 10.1016/j.pbi.2024.102662.
  • Garg R, Subudhi PK, Varshney R, Jain M (2023). Abiotic Stress: Molecular genetics and genomics. Frontiers in Plant Science 13, 1101139. doi: 10.3389/fpls.2022.1101139.
  • 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.
  • Kandhol N, Jain M†, Tripathi DK†. (2022) Nanoparticles as potential hallmark of drought stress tolerance in plants: A systematic overview. Physiologia Plantarum 174, e13665. Doi: 10.1111/ppl.13665 †Joint corresponding author
  • 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.
  • Chennakesavulu K, Singh H, Trivedi P, Jain M, Yadav SR. (2021) State-of-the-art in CRISPR technology and engineering drought, salinity, and thermo-tolerant crop plants. Plant Cell Reports doi: 10.1007/s00299-021-02681-w.
  • Ghangal R, Singh VK, Khemka N, Rajkumar MS, Garg R, Jain M (2020). Updates on genomic resources in chickpea for crop improvement. Methods in Molecular Biology 2107, 19-33.
  • Khemka N, Singh U, Dwivedi A, Jain M (2020). Machine-learning based annotation of long non-coding RNAs using PLncPRO. Methods in Molecular Biology 2107, 253-260.
  • Kumar V, Jain M. (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66, 47-57. doi: 1093/jxb/eru429.
  • Jain M. (2015) Function genomics of abiotic stress tolerance in plants: A CRISPR approach. Frontiers in Plant Science 6, 375. doi: 10.3389/fpls.2015.00375.
  • Garg R, Varshney R, Jain M (2014). Molecular genetics and genomics of abiotic stress responses. Frontiers in Plant Science 5, 398. doi: 10.3389/fpls.2014.00398.
  • Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6, doi: 10.3835/plantgenome2013.04.0011.
  • Garg R, Jain M (2013). RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069, 43-58.
  • Jain M (2013). Emerging role of metabolic pathways in abiotic stress tolerance. Journal of Plant Biochemistry & Physiology
  • Jain M (2012). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional Genomics 2, 63-70.
  • Jain M (2011). A next generation approach to the characterization of a non-model plant transcriptome. Current Science 101, 1435-1439.

Book Chapters/Proceedings/Reports
  • Khandelwal R, Jain M (2018). Genome engineering tools for functional genomics and crop improvement in legumes. In: Wani SH, Jain M (eds.), Pulse Improvement - Physiological, Molecular and Genetic Perspectives, Springer Nature Switzerland AG pp 219-234. ISBN 978-3-030-01742-2.
  • Gupta V, Jain M, Reddy CRK (2017). Macroalgal functional genomics: A missing area. In: Kumar M, Ralph P (eds.), Systems Biology of Marine Ecosystems, Springer pp 3-12. ISBN 978-3-319-62092-3.
  • Sharma E, Sharma R, Borah P, Jain M., Khurana JP (2015). Emerging roles of auxin in abiotic stress responses. In: Pandey GK (eds.), Elucidation of Abiotic Stress Signaling in Plants: A Functional Genomic Perspective, Springer ISBN 978-1-4939-2210-9.
  • Bhattacharjee A, Jain M. (2013). Transcription factor mediated abiotic stress signaling in rice. In: Pandey GK (eds.), Plant Stress - Stress-Mediated Signaling in Plants, Global Science Books, Academic Press, Japan. 7, 16-25.
  • Patel R, Jain M. (2013). NGS QC Toolkit: A Platform for quality control of next generation sequencing data. In: Nelson K (ed.), Encyclopedia of Metagenomics: SpringerReference, Springer-Verlag Berlin Heidelberg, DOI: 10.1007/SpringerReference_304214.
  • Bhattacharjee A, Jain M. (2013). Homeobox genes as potential candidates for crop improvement under abiotic stress. In: Tuteja N, Gill SS (eds.), Plant Acclimation to Environmental Stress, Springer Science+Business Media, New York, USA, pp 163-176.
  • Tyagi AK, Khurana JP, Khurana P, Vij S, Jain M., Vaidhyanathan R (2007). Evolution and phylogenetic relationship of the rice genome. In: Sharma AK, Sharma A (eds.), Plant Genome: Biodiversity and Evolution (Volume IE-Phanerogam-Angiosperm), Science Publishers, New Hampshire, USA, pp 15-41.
  • Khurana JP, Jain M., Tyagi AK (2007). Auxin and cytokinin signaling component genes and their potential for crop improvement. In: Varshney RK, Tuberosa R (eds.), Genomics-Assisted Crop Improvement (Volume I-Genomics Approaches and Platforms), Springer Verlag, Germany, pp 289-314.
  • Chandra A, Jain M., Bhatt V, Vora J, Ghawna S, Ahuja PS (2007). Frontiers of plant biology research (Meeting report on ISPMB 2006). Current Science 92, 1331-1335.
  • Khurana JP, Jain M. (2007). Understanding plant reproductive pathways-molecular genetic analysis of floral induction and flower development. In: Chopra VL, Sharma RP, Bhat SR, Prasanna BM (eds.) Search for New Genes, Academic Foundation & National Academy of Agricultural Sciences, New Delhi. pp 173-195.
  • Tyagi AK, Khurana JP, Khurana P, Kapoor S, Singh VP, Singh AK, Thakur JK, Gupta V, Anand S, Vij S, Jain M., Ray S, Agarwal P, Arora R, Sharma P, Mukherjee S, Nijhawan A, Giri J, Khurana R (2007). Expression and functional analysis of rice genes involved in reproductive development and stress response. In: Brar DS, Mackill DJ, Hardy B (eds.), Rice Genetics V, International Rice Research Institute, Philippines, pp 313-330

User Login

Professor Mukesh Jain

Room No. 21
School of Computational and Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067. INDIA
Off. Phone : 91 11 26704686
Email: mjain@jnu.ac.in | mjainanid@gmail.com

Search