List of Publications (Rita Sharma, Maiden Name: Rita Arora)

Research/Review Articles:

1)          Dhaka N, Jain R, Yadav A, Yadav P, Kumar N, Sharma MK, Sharma R. (2022)Transcriptome analysis reveals cell cycle-related transcripts as key determinants of varietal differences in seed size of Brassica juncea. Scientific Reports 12:11713,

2)          Duitama J, Bartely LE, Guyot RA, Sharma R Editorial: Grass Genome Evolution and Domestication. Frontiers in Plant Science. doi: 10.3389/fpls.2022.866201.

3)          Rahman F, Mishra A, Gupta A and Sharma R (2022) Spatiotemporal regulation of CRISPR/Cas9 enables efficient, precise, and heritable edits in plant genomes. Frontiers in Genome Editing. 4: 870108.

4)          Sathasivam M, Swamy BK, Krishnan K, Sharma R, Nayak, SN, Uppar DS and Hosamani R (2022) Insights into the molecular basis of hypergravity-induced root growth phenotype in bread wheat (Triticum aestivum L.). Genomics 114: 110307.

5)          Kandpal M, Dhaka N and Sharma R (2021) Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage. Physiology and Molecular Biology of Plants, I27(10), 2389-2406.

6)          Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye XY, Nguyen ND, Nijjar S, Ronald PC, Fischer RL and Zilberman D (2021) Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. PNAS, 118 (29) e2104445118.

7)          Lovell et al,. (2021) Polyploidy and genomic introgressions facilitate climate adaptation and biomass yield in switchgrass. Nature 590, 438-444.

8)          Dhaka N and Sharma R. (2021) MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey! Critical Reviews in Biotechnology, 1-15.

9)          Agarwal R, Dhaka N, Sharma R and Aman J. (2021) Genome-wide evolutionary analysis of precursor sequences of MIR156 and MIR172 family members in Brassica species. Research Journal of Biotechnology, 16 (4), 81-92.

10)       Kandpal M, Vishwakarma KKC, Krishnan KK, Chinnusamy V, Pareek A, Sharma MK and Sharma R. (2020) Gene expression dynamics of rice peduncles at the heading stage. Frontiers in Genetics, 11:584678.

11)       Vejlupkova Z, Warman C, Sharma R, Scheller HV, Mortimer JC, and Fowler, JE. (2020) No evidence for transient transformation via pollen magnetofection in several monocot species. Nature Plant, 6, 1323-1324.

12)       Shao W, Sharma R, Clausen M, Scheller H.V. (2020) Microscale thermophoresis as a powerful tool for screening glycosyltransferases involved in cell wall biosynthesis. Plant Methods 16.

13)       Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, Akther K, Sharma R, Katayose Y, Salehi-Ashtiani K, Hao T, Ronald PC, Ecker JR, Schweitzer PA, Kikuchi S, Mizuno H, Hill DE, Vidal M, Moghe GD, McCouch SR, and Yu H. (2020) A massively parallel barcoded sequencing pipeline enables generation of the first single-colony ORFeome and high-quality protein-protein interactome map for rice Proc Natl Acad Sci USA, Vol 117, 21.

14)       Singh V., Kumar N., Dwivedi A.K., Sharma R., Sharma M.K. (2020) Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. Current Genomics 21(2).

15)       Mathur S., Priyadarshini SS., Singh V., Vashisht I., Jung K.H., Sharma R., and Sharma M.K. (2020) Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. 3 Biotech, 10(3):139.

16)       Sharma R., Liang Y., Lee M Y., Pidtala V.R. Motimer J C., and Scheller H.V. (2020) Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies. BMC Research Notes, 13: 116.

17)       Dhaka N., Krishnan K., Kandpal M., Vashisht I., Pal M., Sharma MK. and Sharma R^*. (2020) Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum. Scientific Reports 10, 897.

18)       Dhaka N., Sharma S., Vashisht I., Kandpal M., Sharma MK. and Sharma R^*. (2019) Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics, 112 (2), 1598-1610.

19)       Chandran AKN., Moon S., Yoo, YH., Gho YS., Cao P., Sharma R., Sharma MK. Ronald PC and Jung KH (2019) A web-based tool for the prediction of rice transcription factor functions. Database, 2019, baz061.

20)       Kundu S^*. and Sharma R^*. (2018) Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evolutionary Biology 18 (1), 79.

21)       Dhaka N. and Sharma R^*. (2017) MicroRNAs as targets for engineering biofuel feedstock Sorghum. Plant Physiology Reports (Formerly Indian Journal of Plant Physiology) 22 (4): 484-492.

22)       Mangal M., Srivastava A., Sharma R. and Kalia P. (2017) Conservation and dispersion of genes conferring resistance to tomato begomoviruses between tomato and pepper genomes. Frontiers in Plant Science 8, 1803.

23)       Mathur S., Umakanth A.V., Tonapi V.A., Sharma R^*. and Sharma M.K^* (2017) Sweet sorghum as biofuel feedstock: recent advances and available resources. Biotechnol Biofuels 10, 146.

24)       Park CJ., Wei T., Sharma R. and Ronald P.C. (2017) Overexpression of rice auxilin-like protein, XB21 induces nectrotic lesions, up-regulates endocytosis-related genes, and confers enhanced resistance to Xanthomons oryzae pv. oryzae. Rice 10(1), 27.

25)       Dhaka N., Bhardwaj V., Sharma M.K. and Sharma R^*. (2017) Evolving Tale of TCPs: New Paradigms and Old Lacunae. Frontiers in Plant Science 8, 479.

26)       Francis A., Dhaka N., Bakshi., Jung K.H., Sharma M.K. and Sharma R^*. (2016) Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. Scientific Reports 6.

27)       Sharma R., Wungrampha W., Singh V., Pareek A. and Sharma, M.K. (2016) Halophytes as Bioenergy Crops. Frontiers in Plant Science 7: 1372.

28)       Kundu S., Sharma R^*. (2016) In silico Identification and taxonomic distribution of plant class C GH9 endoglucanases. Frontiers in Plant Science 7: 1185.

29)       Chandran A.K.N., Yoo Y.H., Cao P., Sharma R., Sharma M.K., Dardick C., Ronald P.C. and Jung K.H. (2016) Updated rice kinase database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. Rice 9:40.

30)       Harkenrider M., Sharma R., Vleesschauwer D.D., Tsao, L., Zhang X., Chern M., Canlas P., Zuo S. and Ronald P.C. (2016) Overexpression of rice Wall-Associated Kinase 25 (WAK25) alters resistance to bacterial and fungal pathogens. Plos One 11 (1):e0147310.

31)       Sharma M.K^*., Sharma R^*., Cao P., Harkenrider M., Jenkins J., Grimwood J., Zhang J., Udvardi M.K., Schmutz J. and Ronald P.C. (2016) Targeted switchgrass BAC library screening and sequence analysis identifies predicted biomass-related and stress response-related genes. BioEnergy Research, 9 (1): 109-122.^* First Co-Author

32)       Jung K.H., Cao P., Sharma R., Jain R., and Ronald, P.C. (2015) Phylogenomics databases for facilitating functional genomics in rice. Rice, 8: 26.

33)       Sharma R., Mishra M., Gupta B., Parsania C., Pareek S.L.S., and Pareek A. (2015) De Novo assembly and characterization of stress transcriptome in a salinity-tolerant variety CS52 of Brassica juncea. Plos One. 10(5):e0126783.

34)       Lao J., Sharma M.K., Sharma R., Fernandez-Nino S.M G., Schmutz J., Ronald P.C., Haezlewood J.L., and Schwessinger. (2015) Proteome profile of the endomembrance of developing coleoptiles from switchgrass (Panicum virgatum). Proteomics. 15(13): 2286-90.

35)       Sharma R., Cao P., Jung K.H., Sharma M.K. & Ronald P.C. (2013) Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. Frontiers in Plant Biotechnology. 4, 330.

36)       Nayar S., Sharma R., Tyagi, A.K. and Kapoor, S. (2013) Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis. Journal of Experimental Botany, 64 (14), 4239-4253.

37)       Sharma R., Vleesschauwer D.D., Sharma M.K. & Ronald P.C. (2013) Recent advances in dissecting stress regulatory crosstalk in rice (Review Article). Molecular Plant, 6 (2), 250-260.

38)       Park C.J^*., Sharma R^*., Lefebvre B., Canlas P.E. & Ronald P.C. (2013) The endoplasmic reticulum-quality control component SDF2 is essential for XA21-mediated immunity in rice. Plant Science, 210, 53-60. ^* First co-author

39)       Rodrigues J.A., Ruan R., Nishimura T., Sharma M., Sharma R., Ronald P.C., Fischer, R.L., Zilberman, D. (2013) Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. P.N.A.S., 110 (19), 7934-7939.

40)       Zhang J.Y., Lee Y.C., Jerez I. T., Wang M., Yin Y., Chou W.C., He J., Shen H., Pennacchio C., Lindquist E., Grimwood J., Schmutz J., Xu Y., Sharma M. K., Sharma R., Ronald P. Saha M., Dixon R., Tang Y. and Udvardi M. (2013) Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). The Plant Journal, 74 (1), 160-73.

41)       Sharma R^*., Agarwal P^*., Ray S., Deveshwar P., Sharma P., Sharma N., Nijhawan A., Jain M., Singh A.K., Singh V.P., Khurana J.P., Tyagi A.K. & Kapoor S. (2012) Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics, 12 (2),229-248. ^* First co-author

42)       Sharma M.K., Sharma R., Cao P., Jenkins J., Bartley L.E., Qualls M., Grimwood J., Schmutz J., Rokhsar D. & Ronald P.C. (2012) A genome-wide survey of switchgrass genome structure and organization. PLoS ONE, 7(4): e33892.

43)       Bennetzen J.L., Schmutz J., Wang H., Percifield R., Hawkins J., Pontaroli A.C., Estep M., Feng L., Vaughn J.N., Grimwood J., Jenkins J., Barry K., Lindquist E., Hellsten U., Deshpande S., Wang X., Wu X., Mitros T., Triplett J., Yang X., Ye C., Mauro-Herrara M., Wang L., Li P., Sharma M.K., Sharma R., Ronald P.C., Panaud O., Kellogg E.A., Bruntnell T., Doust A., Tuskan G.A., Rokhsar D. & Devos K.M. (2012) Reference genome sequence of the model plant Setaria. Nature Biotech, 30, 555-561.

44)       Varanasi P., Katsnelson J., Larson D., Sharma R., Sharma M. K., Vega-Sanchez M.E., Zemla M., Ronald P.C., Simmons B., Sing S., Adams P. and Auer M. (2012) Mechanical stress analysis as a method to understand the impact of genetically engineered rice and Arabidopsis plants. Industrial Biotechnology, 8(4) 238-244.

45)       Sharma R., Tan F., Jung K.H., Sharma M.K., Peng Z. & Ronald P.C. (2011) Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice. Plant Mol Biol, 77, 391-406.

46)       Deveshwar P., Bovill W.D., Sharma R., Able J.A. & Kapoor S. (2011) Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC Plant Biol, 11, 78.

47)       Ray S., Dansana P.K., Giri J., Deveshwar P., Arora R., Agarwal P., Khurana J.P., Kapoor S. & Tyagi A.K. (2011) Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics, 11, 157-178.

48)       Gaur R., Grover T., Sharma R., Kapoor S. & Khare S.K. (2010) Purification and characterization of a solvent stable aminopeptidase from Pseudomonas aeruginosa: Cloning and analysis of aminopeptidase gene conferring solvent stability. Process Biochemistry, 45, 757-764.

49)       Sharma M.K., Kumar R., Solanke A.U., Sharma R., Tyagi A.K. & Sharma A.K. (2010) Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato. Mol Genet Genomics, 284, 455-475.

50)       Park C.J., Lee S.W., Chern M., Sharma R., Canlas P.E., Song M.Y., Jeon J.S. & Ronald P.C. (2010) Ectopic expression of rice Xa21 overcomes developmentally controlled resistance to Xanthomonas oryzae pv. oryzae. Plant Sci, 179, 466-471.

51)       Sharma R., Kapoor M., Tyagi A.K., & Kapoor S. (2010) Comparative transcript profiling of TCP family genes provide insight into gene functions and diversification in rice and Arabidopsis. J. Plant Mol. Biol. Biotechnol., 1(1): 24-38.

52)       Sharma R., Mohan Singh R.K., Malik G., Deveshwar P., Tyagi A.K., Kapoor S. & Kapoor M. (2009) Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress. FEBS J, 276, 6301-6311.

53)       Kapoor M., Arora R., Lama T., Nijhawan A., Khurana J.P., Tyagi A.K. & Kapoor S. (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics, 9, 451.

54)       Arora R., Agarwal P., Ray S., Singh A.K., Singh V.P., Tyagi A.K. & Kapoor S. (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics, 8, 242.

55)       Agarwal P., Arora R., Ray S., Singh A.K., Singh V.P., Takatsuji H., Kapoor S. & Tyagi A.K. (2007) Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol Biol, 65, 467-485.

56)       Jain M., Nijhawan A., Arora R., Agarwal P., Ray S., Sharma P., Kapoor S., Tyagi A.K. & Khurana J.P. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol, 143, 1467-1483.

57)       Ray S., Agarwal P., Arora R., Kapoor S. & Tyagi A.K. (2007) Expression analysis of calcium-dependent protein kinase gene family during reproductive development and abiotic stress conditions in rice (Oryza sativa L. ssp. indica). Mol Genet Genomics, 278, 493-505.