Publications

2025

• Targets and strategies to design soybean seed composition traits

Kumar R, Mulkey S, Shelake RM, Allen DK, Clemente TE, Stacey MG, Lorenz AJ, Stupar RM

The Plant Genome, August 2025. DOI: https://doi.org/10.1002/tpg2.70115 [PDF]

• Microalgal bioengineering for futuristic applications in synthetic and space biology

Shelake RM*,#, Khalid MA, Kim JY. (*First & #Corresponding author)

Biotechnology Advances, 84:108665, November 2025. DOI: https://doi.org/10.1016/j.biotechadv.2025.108665 [PDF]

• Protocol for assessment of CRISPR base editors and their components in Escherichia coli

Shelake RM*,#, Kim JY. (*First & #Corresponding author)

STAR protocols 6(3):103973, September 2025. DOI: https://doi.org/10.1016/j.xpro.2025.103973 [PDF]

2024

• Characterization of endophytic bacteria isolated from cotton and pigeon pea for plant health management

Waghunde RR, Shelake RM*, Italiya AP, Khunt MD, Kim JY. (*Co-first)

Journal of Mycopathological Research 62(4): 777–785, December 2024. DOI: https://doi.org/10.57023/JMycR.62.4.2024.777 [PDF]

• Application of genome editing in plant reproductive biology: recent advances and challenges

Gawande ND, Bhalla H, Watts A, Shelake RM, Sankaranarayanan S

Plant Reproduction 37: 441–462, December 2024. DOI: https://doi.org/10.1007/s00497-024-00506-w [PDF]

• Microbes enhance climate-ready crops for sustainable agriculture

Wagh SG, Shelake RM, Patil AM, Mankar S, Cerveny J. (Book chapter)

Rhizospheric interactions for abiotic stress mitigation, Cambridge Scholars Publishing, 100–122, December 2024. [PDF]

• Light signaling and plant secondary metabolites

Nawkar GM, Khare T, Kumar V, Shelake RM#. (#Corresponding author) (Book chapter)

Plant secondary metabolites and abiotic stress, Scrivener Publishing, Wiley, 623–643, October 2024. DOI: https://doi.org/10.1002/9781394186457.ch20 [PDF]

• Abiotic stress in cotton: Insights into plant responses and biotechnological solutions

Patil AM, Pawar BD, Wagh S, Shinde H, Shelake RM, Markad NR, Bhute NK, Cerveny J, Wagh RS

Agriculture 14(9): 1638, Sept 2024. DOI: https://doi.org/10.3390/agriculture14091638 [PDF]

• Heat stress and plant–biotic interactions: advances and perspectives

Shelake RM#, Wagh SG, Patil AM, Cerveny J, Kim JY. (*First & #Corresponding author)

Plants 13(15): 2022, July 2024. DOI: https://doi.org/10.3390/plants13152022 [PDF]

• Cas9 variants expand the targeting scope of base editing systems in bacteria

Shelake RM*,#, Kim JY. (*First & #Corresponding author)

The Nucleus 27: 25-37, April 2024. DOI: https://doi.org/10.1007/s13237-024-00473-7 [PDF]

• Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system

Nguyen CC, Vu TU, Shelake RM, Nguyen NT, Khanh TD, Kim WY, Kim JY. 

Molecular Breeding 44(2): 13, February 2024. DOI: https://doi.org/10.1007/s11032-024-01452-1 [PDF]

• Characterization of yield and fruit quality parameters of Vietnamese elite tomato lines generated through phenotypic selection and conventional breeding methods

Nguyen CC, Shelake RM, Vu TV, Van HT, Nguyen NT, Nguyen XC, Do VAK, Nguyen HT, Kim WY, Kim JY. 

Euphytica 220(1): 18, January 2024. DOI: https://doi.org/10.1007/s10681-023-03273-3 [PDF]

• CRISPR base editor-based targeted random mutagenesis tools for directed evolution

Shelake RM*,#, Pramanik D, Kim JY. (*First & #Corresponding author)

BMB Reports 57(1): 30–39, January 2024. DOI: https://doi.org/10.5483/BMBRep.2023-0086 [PDF]

2023

• Profiling of conserved orthologs and miRNAs for understanding their role in salt tolerance mechanism of Sesuvium portulacastrum L. 

Nikalje GC, Srivastava AK, Shelake RM, Kadam US, Hong JC, Kim JY, Nikam TD, Suprasanna P. 

Molecular Biology Reports 50: 9731–9738, October 2023. DOI: https://doi.org/10.1007/s11033-023-08892-6 [PDF]

• Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles 

Shelake RM*,#, Jadhav AM, Bhosale PB, Kim JY.  (*First & #Corresponding author)

Plant Physiology and Biochemistry 108070, October 2023. DOI: https://doi.org/10.1016/j.plaphy.2023.108070 [PDF]

• Hemibiotrophic Phytophthora infestans modulate the expression of SWEET genes in potato (Solanum tuberosum L.) 

Kardile HB, Karkute SG, Challam C, Sharma NK, Shelake RM, Kawar PG, Patil VU, Deshmukh R, Bhardwaj V, Chaurasia KN, Valluri SD. 

Plants 12(19): 3433. September 2023. DOI: https://doi.org/10.3390/plants12193433 [PDF]

• Method for producing Tomato Yellow Leaf Curled Virus (TYLCV) resistance allele using CRISPR/Cas gene scissors. 

Kim JY, Pramanik D, Shelake RM. (Patent)

Korean (KR) patent Reg. No. 10-2551529-0000. June 2023. DOI: https://doi.org/10.8080/1020210039854?urlappend=en

• Improved dual base editor systems (iACBEs) for simultaneous conversion of adenine and cytosine in the bacterium Escherichia coli

Shelake RM*,#, Pramanik D, Kim JY. (*First & #Corresponding author)

mBio (ASM, American Society for Microbiology) 14 (1): e02296-22, January 2023. DOI: https://doi.org/10.1128/mbio.02296-22 [PDF]

• Soil-plant-microbe interactions: An innovative approach towards improving soil health and plant growth

Kumar U, Shelake RM, Singh R. 2023. (Editorial)

Frontiers in Agronomy 5, 1165328. February 2023. DOI: 10.3389/fagro.2023.1165328 [PDF] 

• ROS-mediated plasmodesmal regulation requires a network of an Arabidopsis receptor-like kinase, calmodulin-like proteins, and callose synthases

Vu MH, Hyun TK, Bahk S, Jo Y, Kumar R, Thiruppathi D, Iswanto AB, Chung WS, Shelake RM#, Kim JY. (#Corresponding author) 

Frontiers in Plant Science 13:1107224, January 2023. DOI: https://doi.org/10.3389/fpls.2022.1107224 [PDF]

• Endophytes: A potential bioagent for plant disease management

Waghunde RR, Khunt MD, Shelake RM, Hiremani N, Patil VA, Kim JY. (Book chapter) 

Microbial endophytes and plant growth, Academic Press, Elsevier, 19–34, January 2023. DOI: https://doi.org/10.1016/B978-0-323-90620-3.00013-1 [PDF]

2022

• Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives

Shelake RM*,#, Kadam US, Kumar S, Pramanik D, Singh AK, Kim JY. (*First & #Corresponding author) 

Plant Communications 3 (6):100417. November 2022. DOI: 10.1016/j.xplc.2022.100417 [PDF] 

• Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars

Hinge VR, Shaikh IM, Chavhan RL, Deshmukh AS, Shelake RM, Ghuge SA, Dethe AM, Suprasanna P, Kadam US.

Scientific Reports 12 (1):7979, May 2023. DOI: 10.1038/s41598-022-11992-1 [PDF] 

• In vivo rapid investigation of CRISPR-Based base editing components in Escherichia coli (IRI-CCE): a platform for evaluating base editing tools and their components

Shelake RM*,#, Pramanik D, Kim JY. (*First & #Corresponding author)

International Journal of Molecular Sciences 23 (3):1145, January 2022. DOI: 10.3390/ijms23031145 [PDF]

2021

• IRI-CCE: A Platform for Evaluating CRISPR-based Base Editing Tools and Its Components

Shelake RM*,#, Pramanik D, Kim JY. (*First & #Corresponding author) 

bioRxiv September 2021. (Pre-print linked to https://doi.org/10.3390/ijms23031145) DOI: https://doi.org/10.1101/2021.07.25.453636 [PDF]

• Conserved opposite functions in plant resistance to biotrophic and necrotrophic pathogens of the immune regulator SRFR1 

Son GH, Moon J, Shelake RM, Vuong UT, Ingle RA, Gassmann W, Kim JY, Kim SH. 

International Journal of Molecular Sciences 22:6427, June 2021. DOI: https://doi.org/10.3390/ijms22126427 [PDF]

• Salinity stress in potato: Understanding physiological, biochemical, and molecular responses 

Chourasia N, Lal M, Tiwari R, Dev D, Kardile HB, Patil VU, Kumar A, Vanishree G, Kumar D, Bhardwaj V, Meena JK, Mangal V, Shelake RM, Kim JY, Pramanik D. 

Life 11:545, June 2021. DOI: https://doi.org/10.3390/life11060545 [PDF]

• Genome editing for plasmodesmal biology 

Iswanto ABB, Shelake RM*, Vu MH, Kim JY, Kim SH. (*Co-first author)  

Frontiers in Plant Science 12:679140, June 2021. DOI: https://doi.org/10.3389/fpls.2021.679140 [PDF]

• CRISPR/Cas9-mediated generation of pathogen-resistant tomato against Tomato yellow leaf curl virus and powdery mildew 

Pramanik D, Shelake RM*,#, Park J, Kim MJ, Hwang I, Park Y, Kim JY. (*Co-first & #Corresponding author)

International Journal of Molecular Sciences 22:1878, February 2021. DOI: https://doi.org/10.3390/ijms22041878  [PDF]

• CRISPR-mediated engineering across the central dogma in plant biology for basic research and crop improvement 

Pramanik D*, Shelake RM*,#, Kim MJ, Kim JY. (*Co-first & #Corresponding author)

Molecular Plant 14:1-24, January 2021. DOI: https://doi.org/10.1016/j.molp.2020.11.002 [PDF]

• Method for inducing reactive oxygen species-mediated base mutation of target gene

Kim JY, Shelake RM. (Patent)

Korean (KR) patent KR20200021320A. January 2021. DOI: https://doi.org/10.8080/1020180096931?urlappend=en

• Application of cereal and vegetable endophytes in plant health management

Waghunde RR, Khunt MD, Shelake RM, Pramanik D, Suthar H, Pandey P, Kim JY. (Book chapter)

Microbiomes and plant health: panoply and their applications, Elsevier, 29–51, January 2021. DOI: https://doi.org/10.1016/B978-0-12-819715-8.00002-1 [PDF]

2020

• Culturable plant-associated endophytic microbial communities from leguminous and nonleguminous crops

Waghunde RR, Khunt MD, Shelake RM, Patil VA. (Book chapter)

Advances in plant microbiome and sustainable agriculture, Springer, 83–103, August 2020. DOI: https://doi.org/10.1007/978-981-15-3208-5_4 [PDF]

• Microbes in crop production: Formulation and Application

Verma PK, Shelake RM, Sharma P, Kim JY, Das S, Kaur M. (Book chapter)

Microbial Diversity, interventions and scope, Springer, 51–73, June 2020. DOI: https://doi.org/10.1007/978-981-15-4099-8_3 [PDF]

• Virus-based replicon for plant genome editing without inserting replicon into plant genome and uses thereof

Kim JY, Van VU T, Kim J, Jeong SJ, Kim HJ, Park SJ, Tran MT, Sivankalyani V, Sung YW, Doan TH, Pramanik D, Shelake RM, Son GH. (Patent linked to 2022 US patent)

International Patent March 2020. WO/2020/055084. DOI: https://doi.org/10.8080/1020180108026?urlappend=en

2019

• Plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF): Potential biological control agents of diseases and pests 

Verma PK, Shelake RM, Sharma P, Das S, Kim JY. (Book chapter)

Microbial interventions in agriculture and environment, Vol 1. Springer, 281–311, November 2019. DOI: https://doi.org/10.1007/978-981-13-8391-5_11 [PDF]

• Evolution of plant mutagenesis tools: A shifting paradigm from random to targeted genome editing 

Shelake RM*, Pramanik D, Kim JY. (*First author)

Plant Biotechnology Reports 5(13): 423-445, October 2019. DOI: https://doi.org/10.1007/s11816-019-00562-z [PDF]

• Exploration of plant-microbe interactions for sustainable agriculture in CRISPR era

Shelake RM*, Pramanik D, Kim JY. (*First author) 

Microorganisms 7(8): 269, August 2019. DOI: https://doi.org/10.3390/microorganisms7080269 [PDF]

• Plant-microbe-metal (PMM) interactions and strategies for remediating metal ions

Shelake RM*,#, Waghunde RR, Kim JY. (*First & #Corresponding author) (Book chapter) 

Plant-metal interactions, Springer, 247–262, July 2019. DOI: https://doi.org/10.1007/978-3-030-20732-8_12 [PDF]

• Computational simulations identify pyrrolidine-2,3-dione derivatives as novel inhibitors of Cdk5/p25 complex to attenuate Alzheimer’s pathology 

Zeb A, Kim D, Alam SI, Son M, Kumar R, Rampogu R, Parameswaran S, Shelake RM, Rana RM, Parate S, Kim JY, Lee KW. 

Journal of Clinical Medicine 8: 746, May 2019. DOI: https://doi.org/10.3390/jcm8050746 [PDF]

• Carbon sequestration for soil fertility management: Microbiological perspective

Shelake RM*, Waghunde RR, Verma PP, Singh C, Kim JY. (*First author) (Book chapter)

Soil fertility management for sustainable development, Springer, 25–42, March 2019. DOI: https://doi.org/10.1007/978-981-13-5904-0_3 [PDF]

2018 & earlier

https://scholar.google.com/citations?user=lrgOB98AAAAJ&hl=en