1. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
2. Thakur JK, Jain M, Tyagi AK, Khurana JP (2005) Exogenous auxin enhances the degradation of a light down-regulated and nuclear-localized OSiIAA1, an
Aux/IAA protein from rice, via proteasome. Biochim. Biophys. Acta 1736: 196-205.
3. The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene
duplication. BMC Biology 3: 20.
4. Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP (2006) Structure and expression analysis of early auxin-responsive Aux/IAA gene family
in rice (Oryza sativa). Funct. Integr. Genomics 6: 47-59.
5. Jain M, Kaur N, Tyagi AK, Khurana JP (2006) Comprehensive analysis of auxin responsive GH3 gene family in rice (Oryza sativa). Funct.
Integr. Genomics 6: 36-46.
6. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by
quantitative real-time PCR. Biochem. Biophys. Res. Commun. 345 (2006) 646-651.
7. Jain M, Tyagi AK, Khurana JP (2006) Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family of
rice (Oryza sativa). Genomics 88 (2006) 360-371.
8. Jain M, Tyagi AK, Khurana JP (2006) Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice ( Oryza sativa). BMC Plant Biology 6: 1.
9. Jain M, Tyagi AK, Khurana JP (2006) Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS J. 273: 5245-5260.
10. Tyagi AK (2006) Rice genomics. Perspectives of Cytology and Genetics 12: 13-24.
11. Varshney RK, Hoisington DA, Tyagi AK (2006) Advances in cereal genomics and applications in crop breeding. Trends Biotechnol. 24: 490-497.
12. Vij S, Tyagi AK (2006) Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their
phylogenetic relationship with Arabidopsis. Mol. Genet. Genomics 276: 565-571.
13. Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, Khurana P, Khurana JP, Tyagi AK (2006) Decoding the rice genome. BioEssays 28: 421-432.
14. Agarwal P, Arora R, Ray S, Singh AK, Singh VP, Takatsuji H, Kapoor S, Tyagi AK (2007) Genome-wide identification of C2H2
zinc-finger gene family in rice and their phylogeny and expression analysis. Plant Mol. Biol. 65: 467-485.
15. Arora R, Agarwal P, Ray S, Singh A, Singh V, Tyagi AK, 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.
16. Gupta V, Khurana R, Tyagi AK (2007) Promoters of two anther-specific genes confer organ-specific expression in a stage-specific manner in transgenic
systems. Plant Cell Rep. 26: 1919-1931.
17. Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (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:
18. Jain M, Sharma P, Tyagi SB, Tyagi AK, Khurana JP (2007) Light regulation and differential tissue-specific expression of phototropin homologues from
rice (Oryza sativa ssp. indica). Plant Sci. 172: 164-171.
19. Kathuria H, Giri J, Tyagi H, Tyagi AK. Advances in transgenic rice biotechnology. Crit. Rev. Plant Sci. 26: 65-103.
20. Ray S, Agarwal P, Arora R, Kapoor S, Tyagi AK (2007) Expression analysis of calcium-dependent kinase gene family during reproductive development and
abiotic stress conditions in rice (Oryza sativa L. ssp. Indica). Mol. Genet. Genomics 278: 493-505.
21. Rice Annotation Project (2007) Curated genome annotation of Oryza sativa ssp. Japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 175-183.
22. Vij S, Tyagi AK (2007) Emerging trends in functional genomics of abiotic response in crop plants. Plant Biotech. Jour. 5: 361-380.
23. Jain M, Khurana P, Tyagi AK, Khurana JP (2008) Genome-wide analysis of intronless genes in rice and Arabidopsis. Funct. Integr. Genomics 8:
24. Jain M, Tyagi AK, Khurana JP (2008) Constitutive expression of a meiotic recombination protein gene homolog, OsTOP6A1, from rice confers
abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Rep. 27: 767-778.
25. Jain M, Tyagi AK, Khurana JP (2008) Differential gene expression of rice two-component signaling elements during reproductive development and
regulation by abiotic stress. Funct. Integr. Genomics 8: 175-180.
26. Jain M, Tyagi AK, Khurana JP (2008) Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in
rice. FEBS J. 275: 2845-2861.
27. Kapoor M, Arora R, Lama T, Nijhawan A, Khurana JP, Tyagi AK, 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.
28. Nizhawan A, Jain M, Tyagi AK, Khurana JP (2008) A genomic survey and gene expression analysis of basic leucine zipper (bZIP) transcription factor
family in rice. Plant Physiol. 146: 333-350.
29. Rice Annotation Project (2008) The rice annotation project database (RAP-DB): 2008 update. Nucl. Acids Res 36: D1028-D1033.
30. Vij S, Tyagi AK (2008). A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response. Funct.
Integr. Genomics 8: 301-307.
31. Vij S, Giri J, Dansana P. Kapoor S & Tyagi AK (2008) The receptor-like cytoplasmic kinase (OsRLCK) gene family in rice:
organization, phylogenetic relationship and expression during development and stress. Molecular Plant 1 (2008) 732-750.
32. Chaudhary N, Khurana P (2009) Vitamin E biosynthesis genes in rice: molecular characterization, expression profiling and comparative phylogenetic
analysis. Plant Sci. 177: 479-492.
33. Sharma R, Singh RKM, Malik G, Deveshwar P, Tyagi AK, Kapoor S, Kapoor M (2009) Rice cytosine DNA methyltransferases--gene expression profiling during
reproductive development and abiotic stress. FEBS J. 276: 6301-6311.
34. Singla B, Khurana JP, Khurana P (2009) Structural characterization and expression analysis of the SERK gene family in rice. Int. J. Plant Genomics ( doi:10.1155/2009/539402).
35. Anand S, Tyagi AK (2010) Characterization of a pollen-preferential gene OSIAGP from rice (Oryza sativa L. subspecies indica) coding
for an arabinogalactan-protein homolog and analysis of its promoter activity during pollen development and pollen tube growth. Transgenic Res. 19: 385-397.
36. Chaudhary N, Nijhawan A, Khurana JP, Khurana P (2010) Carotenoid biosynthesis genes in rice: Structural analysis, genome-wide expression profiling and
phylogenetic analysis. Mol. Genet. Genomics 283: 13-33.
37. Garg R, Jhanwar S, Tyagi AK, Jain M (2010) Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during
development and response to various stimuli in rice. DNA Res. 17: 353-367.
38. Raghuvanshi S, Kapoor M, Tyagi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK (2010) Rice genomics moves ahead. Mol. Breed. 26: 257-273.
39. Sharma R, Kapoor M, Tyagi AK, 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: 24-38.
40. Singh A, Giri J, Kapoor S, Tyagi AK, Pandey GK (2010) Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis
under abiotic stress conditions and reproductive development. BMC Genomics 11: 435.
41. Agarwal P, Kapoor S, Tyagi AK (2011) Transcription factors regulating the progression of monocot and dicot seed development. BioEssays 33: 189-202.
42. Chauhan H, Khurana N, Aggarwal P, Khurana P (2011) Heat shock factors in rice (Oryza sativa L.): Genome wide expression analysis during
reproductive development and abiotic stress. Mol. Genet. Genomics 286 (2011) 171-187.
43. Giri J, Vij S, Dansana PK & Tyagi AK (2011) Rice A20/AN1 zinc-finger containing stress-associated proteins (SAP1/11) and a receptor-like
cytoplasmic kinase (OsRLCK253) interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants. New Phytol. 191:
44. Mathur S, Vyas S, Kapoor S, Tyagi AK (2011) The mediator complex in plants: structure, phylogeny and expression profiling of representative genes in a
dicot (Arabidopsis thaliana) and a monocot (Oryza sativa) during reproduction and stress. Plant Physiol. 157: 1609-1627.
45. Ray S, Dansana PK, Giri J, Deveshwar P, Arora R, Agarwal P, Khurana JP, Kapoor S , Tyagi AK (2011) Modulation of transcription factor and metabolic
pathway genes in response to water-deficit stress in rice. Funct. Integr. Genomics 11: 157-178.
46. Swapna L, Khurana R, Kumar SV, Tyagi AK, Rao KV (2011) Pollen-specific expression of Oryza sativa indica pollen allergen gene (OSIPA)
promoter in rice and Arabidopsis transgenic systems. Mol. Biotechnol. 48: 49-59.
47. Garg R, Tyagi AK, Jain M (2012) Genome-wide analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice.
Plant Signal. Behav. 7: 951-956.
48. Khurana N, Chauhan H, Khurana P (2012) Cloning and expression analysis of a heat-inducible, myo-inositol-1-phosphate synthase (MIPS) gene from wheat
and its comparative analysis in rice and Arabidopsis. Plant Cell Reports 31: 237-251.
49. Khurana R, Kapoor S, Tyagi AK (2012) Anthology of anther/pollen-specific promoters and transcription factors. Crit. Rev. Plant Sci. 31: 359-390.
50. Ray S, Kapoor S, Tyagi AK (2012) Analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, NBS-Str1 and BLEC-Str8, of rice. Transgenic Res. 21: 351-366.
51. Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S (2012) Expression
dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct. Integr. Genomics 12: 229-248.
52. Giri J, Dansana PK, Kothari KS, Sharma G, Vij S, Tyagi AK (2013) SAPs as novel regulators of abiotic stress response in plants. BioEssays 35: 639-648.
53. Khurana R, Kapoor S, Tyagi AK (2013) Spatial and temporal activity of upstream regulatory regions of rice anther-specific genes in transgenic rice and Arabidopsis. Transgenic Res. 22: 31-46.
54. Khurana R, Kathuria H, Mukhopadhyay A, Kapoor S, Tyagi AK (2013) A 286 bp upstream regulatory region of a rice anther-specific gene, OSIPP3,
confers pollen-specific expression in Arabidopsis. Biotech. Lett. 35: 455-462.
55. Nayar S, Sharma R, Tyagi AK, Kapoor S (2013) Functional delineation of OsMADS29 reveals its role in embryo and endosperm development by affecting
hormone homeostasis. J Exp. Bot. 64: 4239-4253.
56. Singh A, Kanwar P, Pandey A, Tyagi AK, Sopory SK, Kapoor S, Pandey G (2013) Comprehensive genomic and expression profiling of phospholipase C gene
family during abiotic stress and development in rice. PLoS One 8: e62494.
57. Dansana PK, Kothari KS, Vij S, Tyagi AK (2014) OsiSAP1 overexpression improves water-deficit stress tolerance in transgenic rice by affecting
expression of endogenous stress related genes. Plant Cell Rep. 33: 1425-1440.
58. Gour P, Garg P, Jain R, Joshep S, Tyagi A, Raghuvanshi S (2014) Manually curated database of rice proteins. Nucl. Acids Res. 42: D1214-1221.
59. Sharma M, Singh A, Shankar A, Pandey A, Baranwal V, Kapoor S, Tyagi A, Pandey G (2014) Comprehensive expression analysis of rice Armadillo gene family
reveals their functional diversity in abiotic stress and development. DNA Res. 21: 267-283.
60. Singh A, Kanwar P, Yadav A, Mishra M, Jha S, Baranwal V, Pandey A, Kapoor S, Tyagi A, Pandey G (2014) Genome-wide expressional and functional analysis
of calcium transport elements during abiotic stress and development in rice. FEBS J. 281: 894-915.
61. Tyagi H, Jha S, Sharma M, Giri J, Tyagi AK (2014) Rice SAPs are responsive to multiple biotic stresses and overexpression of OsSAP1, an A20/AN1
zinc-finger protein, enhances the basal resistance against pathogen infection in tobacco. Plant Sci. 225: 68-76.