 |
|
|
|
|
|
| |
|
 | |  |
|
 | Dr. Mukesh Jain
Staff Scientist IV
Tel: 91-11-26741612, 14, 17 (Ext.) 182
91-11-26735182 (Direct)
Fax: 91-11-26741658
Webpage: http://mjainanid.googlepages.com
E-mail: mjain@nipgr.ac.in; mjainanid@gmail.com |
|
 | |  |
 Research Articles |
| Total number of citations = >3200 (as of October, 2015) |
 |
Garg R †, Chevala VVSN, Shankar R, Jain M †. (2015) Divergent DNA methylation patterns associated with abiotic stress responses and regulation of gene expression in rice. Scientific Reports 5, 14922; doi: 10.1038/srep14922. † Joint corresponding authors. |
|
Kumar V, Jain M (2015) The CRISPR-Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany 66: 47-57.doi: 10.1093/jxb/eru429. |
|
Singh VK, Jain M. (2015) Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean. Frontiers in Plant Science6, 918. doi: 10.3389/fpls.2015.00918 |
|
Bhattacharjee A, Ghangal R, Garg R, Jain M (2015) Genome-wide analysis of homeobox gene family in legumes: Identification, gene duplication and expression profiling. PLoS ONE. (Accepted). |
|
Jain M †, Pole AK, Singh VK, Ravikumar RL, Garg R. (2015) Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars. Molecular Breeding (accepted). DOI: 10.1007/s11032-015-0387-1. |
|
Parween S, Nawaz K, Roy, R, Pole AK, Suresh V, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D. (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Scientific Reports 5, 12806. |
|
Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M, Chattopadhyay D, Bhatia S. (2015) High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Scientific Reports 5, 13387. |
|
Verma M, Kumar V, Patel RK, Garg R, Jain M (2015) CTDB: An integrated chickpea transcriptome database for functional and applied genomics. PLoS ONE (Accepted) 10.1371/journal.pone.0136880. |
|
Parida S, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M (2015) Genome-wide development of polymorphic microsatellites in desi and kabuli chickpea for large-scale genotyping applications. Frontiers in Plant Science 6: 645. |
|
Jain M (2015) Functional genomics of abiotic stress tolerance in plants: A CRISPR approach. Frontiers in Plant Science 6, 375. doi: 10.3389/fpls.2015.00375. |
|
Ram H, Jain M, Singh A, Chattopadhyay S. (2015) Functional relationship of GBF1 with HY5 and HYH in genome-wide gene expression in Arabidopsis. Plant Molecular Biology Reporter. DOI 10.1007/s11105-015-0910-x. |
|
Singh VK, Jain M, Garg R (2015) Genome-wide analysis and expression profiling reveals diverse roles of GH3 gene family during development and abiotic stress responses in legumes. Frontiers in Plant Science 5: 789. doi: 10.3389/fpls.2014.00789. |
|
Khujuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S. (2015) Genome-wide development and validation of polymorphic genic and genomic microsatellite markers for construction of a high-density chickpea genome map. PLoS ONE. (accepted) |
|
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. *Joint corresponding authors. |
|
Jain M, Chevala VVSN, Garg R (2014) Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing. Journal of Experimental Botany (in press). |
|
Garg R. Verma M, Agarwal S, Shankar R, Majee M, Jain M (2014) Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Research. 21: 69-84. |
|
Garg R, Bhattacharjee A, Jain M (2014) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter DOI 10.1007/s11105-014-0753-x.(IF = 5.319) |
|
Verma M†, Ghangal R†, Sharma R, Sinha AK, Jain M (2014) Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling. PLoS ONE 10.1371/journal.pone.0103583 (In press). †Joint first authors. (IF = 3.730) |
|
Singh VK, Jain M (2014) Transcriptome profiling for discovery of genes involved in shoot apical meristem and flower development. Genomics Data 2, 135-138. (IF = NA) |
|
Sharma R, Sahoo A, Devendran R, Jain M (2014) Over-expression of a rice tau class glutathione S-transferase gene improves tolerance to salinity and oxidative stresses in Arabidopsis. PLoS ONE 10.1371/journal.pone.0092900. |
|
Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S, Tyagi AK, Jain M, Parida SK (2014) An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea. Molecular Breeding DOI 10.1007/s11032-014-0033-3. |
|
Ram H, Priya P, Jain M, Chattopadhyay S (2014) Genome-wide DNA binding of GBF1 is modulated by its heterodimerizing partners, HY5 and HYH. Molecular Plant. 7: 448-451. |
|
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. |
|
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. |
|
Sharma R, Priya P, Jain M (2013) Modified expression of an auxin-responsive rice CC-type glutaredoxin gene affects multiple abiotic stress responses. Planta 238: 871-884. |
|
Garg R, Jain M (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6: doi: 10.3835/plantgenome2013.04.0011. |
| Priya P, Jain M (2013) RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013, bat027. DOI: 10.1093/database/bat027. |
|
Ghangal R, Chaudhary S, Jain M, Purty RS, Sharma PC (2013) Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome. PLoS ONE 8: e72516. |
|
Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda CLL, Singh S,Jain M, Tyagi AK, Parida SK. (2013) Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Research 20: 355-374. |
|
Garg R, Jain M (2013) RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069: 43-58. |
| Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS ONE 7: e52443. DOI: 10.1371/journal.pone.0052443 |
| 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. |
| Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE 7: e30619. DOI:10.1371/journal.pone.0030619. |
| Jain M (2012). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional Genomics 2: 63-70. |
| Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012). High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research doi: 10.1093/dnares/dss018. |
| Garg R, Tyagi AK, Jain M (2012). Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice. Plant Signaling & Behavior 7: 951-956. |
| 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. Functional and Integrative Genomics 12: 229-248. |
| Patel RK, Jain M (2011). PlantRGS: A web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants. DNA Research 18: 463-470. |
| Jain M (2011). A next generation approach to the characterization of a non-model plant transcriptome. Current Science 101: 1435-1439. |
| Garg R, Jain M (2011). Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signaling & Behavior 6: 1868-1870. |
| 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. |
| Garg R, Patel RK, Tyagi AK, Jain M (2011). De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Research 18: 53-63. |
| 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 Research 17: 353-367. |
| Garg R, Sahoo A, Tyagi AK, Jain M (2010). Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochemical and Biophysical Research Communications 396: 283-288. |
| Jain M*, Ghanashyam C, Bhattacharjee A (2010). Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 11: 73. (*corresponding author). (Highly accessed article) |
| Jain M*, Khurana JP (2009). Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS Journal 276: 3148-3162. (*corresponding author) (2nd most highly cited article among FEBS Journal articles in last two years) |
| Ghanashyam C, Jain M (2009). Role of auxin-responsive genes in biotic stress responses. Plant Signaling & Behavior 4: 846-848. |
| Jain M (2009). Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice. Plant Science 176: 702-706. |
| Jain M*, Khurana JP (2008). Small RNA regulation of rice homeobox genes. Plant Signaling & Behavior 3: 1024-1025. (*corresponding author). |
| Jain M, Tyagi AK, Khurana JP (2008). Genome-wide identification, classification, evolutionary expansion, and expression analyses of homeobox genes in rice. FEBS Journal 275: 2845-2861. |
| 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 Reports 27: 767-778. |
| Jain M, Tyagi AK, Khurana JP (2008). Differential gene expression of rice two-component signaling elements during reproductive development and regulation by abiotic stress. Functional and Integrative Genomics 8: 175-180. |
| Nijhawan 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 Physiology 146: 333-350. |
| Jain M, Khurana P, Tyagi AK, Khurana JP (2008). Genome-wide analysis of intronless genes in rice and Arabidopsis. Functional and Integrative Genomics 8: 69-78. |
| 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 Physiology 143: 1467-1483. |
| Singh G, Jain M, Kulshreshtha R, Khurana JP, Kumar S, Singh P (2007). Expression analysis of genes encoding translation initiation factor 3 subunit g (TaeIF3g) and vesicle-associated membrane protein-associated protein (TaVAP) in drought tolerant and susceptible cultivars of wheat. Plant Science 173: 660-669. |
| Sehgal A, Khurana JP, Sethi M, Ara H, Jain M (2007). Organ identity of the thalloid plant body of Griffithella hookeriana and Polypleurum stylosum-Podostemoideae (Podostemaceae). Plant Systematics and Evolution 267: 93-104. |
| 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 Science 172: 164-171. |
| Jain M, Tyagi AK, Khurana JP (2006). Overexpression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS Journal 273: 5245-5260. (cover photo article) |
| Jain M, Tyagi AK, Khurana JP (2006). Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa). Genomics 88: 360-371. |
| 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. Biochemical and Biophysical Research Communications 345: 646-651. (Highly cited and second most downloaded article of BBRC in ScienceDirect) |
| 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. (Highly accessed article) |
| 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). Functional and Integrative Genomics 6: 47-59. |
| Jain M, Kaur N, Tyagi AK, Khurana JP (2006). The auxin-responsive GH3 gene family in rice (Oryza sativa). Functional and Integrative Genomics 6: 36-46. |
| 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. Biochimica et Biophysica Acta 1730: 196-205. |
| Dasgupta U, Jain M, Tyagi AK, Khurana JP (2005). Regulatory elements for light-dependent and organ-specific expression of Arabidopsis thaliana PSBO1 gene encoding 33 kDa polypeptide of the oxygen-evolving complex. Plant Science 168: 1633-1642. |
| Agarwal SM†, Jain M†, Grover A† (2005). Genomic distribution of genes encoding 68 cytoplasmic ribosomal protein families in rice. Acta Physiologiae Plantarum 27: 439-446. (†equal contribution) |
| Jain M, Tyagi SB, Thakur JK, Tyagi AK, Khurana JP (2004). Molecular characterization of a light-responsive gene, breast basic conserved protein 1 (OsiBBC1), encoding nuclear-localized protein homologous to ribosomal protein L13 from Oryza sativa indica. Biochimica et Biophysica Acta 1676: 182-192. |
|
| Book chapters/proceedings/reports |
|
Garg R, Varshney R, Jain M (2014). Molecular genetics and genomics of abiotic stress responses. Frontiers in Plant Science doi: 10.3389/fpls.2014.00398. |
|
Sharma E, Sharma R, Borah P, Jain M, Khurana JP (2014). Emerging roles of auxin in abiotic stress responses. In: Pandey GK (eds.), Elucidation of Abiotic Stress Signaling in Plants: A Functional Genomic Perspective, Springer (accepted) |
|
Jain M (2013) Emerging role of metabolic pathways in abiotic stress tolerance. J Plant Biochem Physiol 1, 108. |
| Bhattacharjee A, Jain M (2013) Transcription factor mediated abiotic stress signaling in rice. Plant Stress 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. |
|
| Patents |
| Nucleic acid sequences encoding glutathione S-transferases associated with abiotic stress responses in plants. (IPA 2302/DEL/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. |
|
|
|
|
| |
|
|
|
|
|
|
 |
|
