CURRICULUM VITAE
DR. MUKESH JAIN
Professor
School of Computational & Integrative Sciences (SCIS)
Jawaharlal Nehru University (JNU)
New Delhi – 110 067, INDIA
Phone: 91-11-26704686 (O); 91-11-26735136 (R)
Mobile: 91-9871711699
E-mail: mjain@jnu.ac.in
mjainanid@
Areas of specialization: Plant Genomics, Computational Biology and Biotechnology
Date of Birth: August 27, 1978
Permanent Address: H. No. 50, Gandhi Mandi
Panipat-132 103 (Haryana)
Phone no.: 91-180-2667479
Academic record
|Examination |Board/University |Year |Marks (%) |Subject(s) |
|Ph.D.* |University of Delhi |2002-2006 |- |Plant Molecular Biology |
|M.Sc. |Kurukshetra University |1999-2001 |79.6% |Biotechnology |
|B.Sc. |Kurukshetra University |1996-1999 |77.0% |Botany, Zoology, Chemistry |
*Thesis title: Functional analysis of genes encoding topoisomerase 6 homologues and genome-wide analysis of early auxin- and cytokinin-responsive gene families in rice (Oryza sativa)
Fellowships received
1. Tata Innovation Fellowship, Department of Biotechnology, Government of India, New Delhi (2018-19).
2. Fellow, National Academy of Agricultural Sciences (NAAS), New Delhi (2016).
3. Fellow, National Academy of Sciences India (NASI), Allahabad (2015).
4. Associate Fellow, National Academy of Agricultural Sciences, New Delhi (2011-2015).
5. Associate Fellow, Indian Academy of Sciences, Bangalore (2007-2012).
Awards/honors received
1. National Bioscience Award for Career Development 2016 from the Department of Biotechnology.
2. India Research Excellence - Citation Young Achiever Award 2017 across all disciplines from Clarivate Analytics.
3. Rajib Goyal Prize in Life Sciences 2014-2015 from Kurukshetra University, Kurukshetra.
4. Annual Eminence Award 2014 in 'Agriculture' from Rawal Institutions, Faridabad.
5. NASI-Scopus Young Scientist Award 2012 in ‘Agriculture’ from Elsevier.
6. Young Scientist Award from the National Academy of Agricultural Sciences, New Delhi for biennium (2011-2012).
7. Prof. B.K. Bachhawat Memorial Young Scientist Lecture Award (2012) from NASI.
8. Haryana Yuva Vigyan Ratna Award 2010-11 from the Haryana State Council for Science & Technology.
9. Anil Kumar Bose Memorial Award (2011) from the Indian National Science Academy.
10. Young Scientist Platinum Jubilee Award (2009) from the National Academy of Sciences India (NASI).
11. Young Scientist Award from the Indian Science Congress Association (2007-08).
12. Indian National Science Academy (INSA) medal for Young Scientist (2007).
13. Professor LSS Kumar Memorial Award (2007) from INSA.
14. Innovative Young Biotechnologists Award (IYBA) from the Department of Biotechnology, Government of India (2006).
15. University Medal for First-Class-First position in M.Sc. Biotechnology from Kurukshetra University, Kurukshetra.
Other recognition/fellowships received
1. DBT-CREST Fellowship Award for 2010-2011 from the Department of Biotechnology, Government of India, New Delhi (visiting scientist at the University of Georgia, USA).
2. BOYCAST Fellowship for 2010-2011 from the Department of Science & Technology, Government of India, New Delhi (not availed).
3. Biography listed in the Marquis Who’s Who in the World 2010 and 2012 editions.
4. Certificate of Recognition as Genomics Pioneer (2008) from the Ocimum Biosolutions in association with OBBeC.
5. Visiting Scientist at The Institute for Genomic Research, Rockville, MD for the Rice Genome Annotation workshop (2007).
6. Travel fellowship from the Department of Biotechnology, Government of India, to attend the 8th International Congress of Plant Molecular Biology held at Adelaide, Australia.
7. Junior and Senior Research Fellowships from CSIR, New Delhi (February 2002-September 2006).
8. Junior Research Fellowship from ICMR, New Delhi (not availed)
Membership of academic societies/bodies
1. Life Member, Indian Society for Plant Physiology, New Delhi (January 2019 onwards).
2. Life Member, The National Academy of Sciences India, Allahabad.
3. Founding & Life Member, Asia Pacific Bioinformatics Interaction and Networking Society (APBIAN)
4. Life Member, Indian Science Congress Association, Kolkata.
5. Fellow member, Society for Applied Biotechnology, Karnataka.
6. Life member, The Indian Botanical Society.
7. Member, The Science Advisory Board, USA.
8. Member, American Society of Plant Biologists, USA.
9. Member, Society for Experimental Biology.
10. Member, Crop Science Society of America.
11. Member, Society of Agronomy.
12. Member, Genome India International.
Appointments and professional experience
1. October 2018-Present - Professor, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi.
2. October 2015-October 2018 - Associate Professor, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi.
3. July 2014-October 2015, Staff Scientist IV, National Institute of Plant Genome Research (NIPGR), New Delhi.
4. February 2011-July 2014, Staff Scientist III, National Institute of Plant Genome Research (NIPGR), New Delhi (February 2011-July 2014).
5. April 2008-February 2011, Staff Scientist II, National Institute of Plant Genome Research (NIPGR), New Delhi (April 2008-February 2011).
6. November 2011-July 2012, Visiting Scientist (DBT-CREST Fellow), University of Georgia, Athens, Georgia, USA.
7. December 2007-April 2008, Assistant Professor, University School of Biotechnology, GGS Indraprastha University, Delhi.
8. December 2006- December 2007, Research Scientist, Centre for Plant Molecular Biology, University of Delhi South Campus, New Delhi.
9. November 2006-December 2006, Research Associate, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi.
10. February 2002- October 2006, Research Fellow, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi.
Research experience: >18 years
Webservers/Databases/Resources developed
1. PLncPRO: Plant Long Non-coding RNA Prediction via Random Forest Model ( )
A standalone tool based on machine learning random forest algorithm for prediction of long non-coding RNAs in plants and animals.
2. NGS QC Toolkit: Next Generation Sequencing Quality Control Toolkit ()
A toolkit comprised of user-friendly stand-alone tools for the quality check (QC) and filtering of next generation sequencing (NGS) data.
3. Rice Stress-Responsive Transcription Factor Database: (RiceSRTFDB, )
A web resource for comprehensive information (genomic features, expression profiles, cis-regulatory elements and Tos17 mutants) for rice transcription factors
4. Chickpea Transcriptome Database: (CTDB, )
A web resource for mining/downloading sequence data, functional annotation (gene description, domain and gene ontology) and tissue-specific expression profiles of chickpea transcriptome.
5. Plant G-Quadruplex Database: (PlantG4DB, )
A web resource for mining/downloading various information about G-quadruplexes in different plant species.
6. PlantRGS: Plant Reference Gene Server ()
A web server for the identification of most suitable candidate reference gene(s) with minimum expression variance for quantitative gene expression studies in plants.
7. Chickpea MicroSatellite Database: (CMsDB, ()
A database for mining of microsatellites in desi and kabuli chickpea genomes and polymorphic microsatellites between desi/kabuli chickpea types along with their annotation and primer sequences.
8. Other Resources:
Oryza coarctata Genome: Draft genome sequence and annotation of Oryza coarctata (wild halophyte rice) genome ()
Rice SNP Discovery: SNP data among rice accessions with contrasting response to abiotic stresses ()
Catharanthus Transcriptome: Transcriptome sequence, functional annotation, gene expression and microsatellite data ()
Saffron Transcriptome: Transcriptome sequence, functional annotation, gene expression and microsatellite data ()
Porteresia Transcriptome: Transcriptome sequence and functional annotation data ()
Chickpea Genomic Web Resource (CGWR): Chickpea genome visualization and comparative analysis ()
Chickpea Genome Analysis Project (CGAP): Draft genome sequence and annotation of desi chickpea ()
Product/Technology developed
1. Chickpea Gene Expression Microarray
A validated microarray containing 61,659 probes (representing 51,444 unique transcripts) based on the chickpea transcriptome has been developed for high-throughput gene expression studies. The microarray is commercially available from Genotypic Technology Pvt. Ltd.
Press release: Jain M, Mugasimangalam R. Genotypic, NIPGR launch chickpea microarray. November 29, 2012, Biospectrum Asia. Read more at: .
Research grants received
Research projects (ongoing)
1. "Discovery of novel enhancer regulatory elements in model/crop plants and their biotechnological applications" (April 2019 – March 2022) as Principal Investigator by the Department of Biotechnology, Government of India, New Delhi under the Tata Innovation Fellowship Programme (27.0 lakhs).
2. "Genomic Resources for Mulberry: Indian Mulberry Nuclear Genome Sequencing" under the Network project “Genetic enhancement of mulberry by genomics approaches: A multi-component network project” (June 2018 – June 2021) as Co-Principal Investigator by the Department of Biotechnology, Government of India, New Delhi (Individual component ~95 lakhs; Network project with total cost 864.71 lakhs).
3. "Regulatory impact and biotechnological implications of RNA architecture on drought stress response" (July 2018 – July 2021) as Principal Investigator by the Department of Biotechnology, Government of India, New Delhi under the National Bioscience Award for Career Development scheme (15.0 lakhs).
4. "Characterization of candidate homeobox gene associated regulatory network involved in abiotic stress responses" (February 2017 – May 2020) as Principal Investigator by the Science and Engineering Board, Department of Science & Technology, Government of India, New Delhi (46.8 lakhs).
5. "Investigating gene regulatory networks operating downstream of OsAP2/ERF-40 during rice adventitious root development" (Approved) as Co-Principal Investigator by the Science and Engineering Board, Department of Science & Technology, Government of India, New Delhi (~22.0 lakhs).
6. "Challenge Programme on Chickpea Functional Genomics" (November 2015 – November 2020) as Coordinator and Principal Investigator (Exploring transcriptome dynamics of chickpea development for candidate gene discovery and defining regulatory elements/modules) by the Department of Biotechnology, Government of India, New Delhi (Individual component ~224 lakhs; Network project with total cost 781.616 lakhs).
Research projects (completed)
7. “Functional genomics approaches in understanding the regulation of synthesis and accumulation of apocarotenoids in saffron crocus (Crocus sativus L.)” (July 2013 - March 2019) as Principal Investigator by the Department of Biotechnology, Government of India, New Delhi (Individual component 59.924 lakhs; Network project with total cost 366.648 lakhs).
8. "Understanding the role of DNA methylation under water-deficit stress in rice" (August 2016 – March 2019) as Principal Investigator (by the Jawaharlal Nehru University New Delhi under UPoE-UGC scheme (11 lakhs).
9. "Transcriptome and epigenome diversity analysis during seed development for discovery of molecular markers and gene regulatory mechanism in chickpea" (August 2013 - August 2018) as Principal Investigator by the Department of Biotechnology, Government of India, New Delhi (Individual component ~290 lakhs; Network project with total cost 1152.528 lakhs).
10. "Association and genetic mapping of loci for seed size/weight in chickpea" (August 2013 - August 2018) as Co-Principal Investigator by the Department of Biotechnology, Government of India, New Delhi (Individual component ~100 lakhs; Network project with total cost 1152.528 lakhs).
11. “Role of homeobox genes in abiotic stress responses in rice” (March 2012 - February 2015) as Principal Investigator by the Department of Science & Technology, Government of India, New Delhi (48.56 lakhs).
12. “Genomic approaches for stress tolerant chickpea” (March 2012- March 2015) as Senior Researcher funded by DST as a part of “Indo-Australian Strategic Research Fund” scheme with ICRISAT, Hyderabad (Indian component 5.25 crores). NIPGR component = 93.85 lakhs.
13. “Chickpea genome sequence analysis and its alignment to genetic map” (September 2009- September 2014) as Co-Principal Investigator funded by DBT as a part of “Next Generation Challenge Programme on Chickpea Genomics” (11.98 crores). Individual component = ~2.40 crores.
14. “Molecular genetic analyses and systems biology of auxin signaling networks in plants” (June 2007-November 2012) as Principal Investigator funded by DBT under Innovative Young Biotechnologists Award scheme (~50.0 lakhs).
15. “Understanding the cross-talk between hormone and stress signaling in Arabidopsis by functional genomics” (December 2006-December 2009) as Principal Investigator funded by DST under SERC Fast Track Proposal Scheme for Young Scientists (8.28 lakhs).
Teaching experience
➢ M.Sc./Pre-Ph.D. course work at SCIS, Jawaharlal Nehru University, New Delhi. (January 2016 onwards)
Courses: Genomics: Concepts, Methods and Applications; Genomic Data Analytics; Computational Genomics; Computational Methods for Genome & Structure; Research Methodology; Computational Biology and Bioinformatics
➢ Guest Lectures, M.Sc. course work at the Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi. (February 2019-Present)
Course taught: Omics: Genomics, Transcriptomics, Proteomics and Metabolomics
➢ Ph.D. course work at the National Institute of Plant Genome Research, New Delhi. (April 2008-October 2015)
Courses taught: Plant Genomics; Genomics and Bioinformatics
➢ B.Tech and M.Tech classes at the University School of Biotechnology, GGS Indraprastha University, Delhi. (December 2007-April 2008)
Courses taught: Bioinformatics; Advanced Bioinformatics
➢ M.Sc. classes at the Department of Biotechnology, Kurukshetra University, Kurukshetra. (August 2001-February 2002)
Courses taught: Biochemistry; Cell and Molecular Biology; Biotechniques
➢ Guest faculty for lectures on Bioinformatics at the Department of Zoology & Biotechnology, HNB Garhwal University, Srinagar, Uttrakhand. (December 2008)
Mentoring experience
Ph.D. Students: Eight [Four pursuing (three as supervisor and one as co-supervisor/advisor), one submitted, three awarded]
Post-doctoral Fellows/RA: 17 (2 pursuing)
SRF/JRF/PA: 52 (2 pursuing)
M.Sc./M.Tech./B.Tech. Student’s project/dissertation: 16
Summer Research Fellow/Trainees: 8
Editor/Reviewer
Editor: Editor ‘Peer J’ (November 2018 onwards)
Editor ‘Scientific Reports’ NPG (February 2015 onwards)
Academic Editor 'PLoS ONE' (August 2014 onwards)
Associate/Review Editor ‘Frontiers in Plant Science’ (July 2014 onwards)
Associate/Review Editor ‘Frontiers in Genetics’ (July 2014 onwards)
Associate Editor ‘BMC Research Notes’ (2010-2020)
Associate Editor ‘Molecular Breeding’ (April 2013 – September 2018)
Associate Editor, special issue in 'Frontiers in Plant Science' on Research Topic "Abiotic Stress: Molecular Genetics and Genomics"
(Edited more than 300 articles for above journals)
Reviewer (Journals): Nature Communications, Plant Cell, Genome Biology, Plant Physiology, Plant Journal, New Phytologist, Scientific Reports, Journal of Proteome Research, DNA Research, PLoS ONE, Planta, BMC Genomics, BMC Plant Biology, FEBS Journal, Bioinformatics, Molecular Genetics and Genomics, Rice, Plant Cell Reports, Journal of Plant Growth Regulation, Proteome Science, Transgenic Research, Plant Breeding, In Silico Biology, Protoplasma, The Plant Genome, Functional Plant Biology, Journal of Bioscience, Journal of Genetics, PMBP, Agricultural Research
(Reviewed more than 300 articles for above journals)
Reviewer (Project grants): Department of Biotechnology, Department of Science & Technology and Council of Scientific and Industrial Research, Government of India, New Delhi; Department of Biotechnology, Government of West Bengal; BARD - The US-Israel Agricultural Research & Development Fund; Austrian Science Fund; Competitive Research Grants Program of King Abdullah University of Science and Technology (KAUST)
Reviewer (Other): E-lessons on Bioinformatics (LSPT 409) for undergraduate students developed by Institute of Lifelong Learning under the project National Mission on Education of Ministry of Human Resource Development, Government of India; Reviewer GIAN proposals IIT-Kharagpur
Publications
Total no. of citations = >8600
Total impact factor = 360.688 (252.924 as first/corresponding author)
h-index = 40 i10-index = 76
Research articles
1. Rajkumar MS, Shankar R, Garg R, Jain M. (2020) Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars. Genomics (accepted) Preprint in 2019: BioRxiv doi: 10.1101/558064
(IF = 3.160; Citation = 0)
2. Ghangal R†, Rajkumar MS†, Garg R, Jain M. (2020) Genome-wide analysis of glutathione S-transferase gene family in chickpea suggests its role during seed development and abiotic stress. Molecular Biology Reports doi: 10.1007/s11033-020-05377-8. †Equal contribution
(IF = 2.107; Citation = 0)
3. Bhaskarla V, Zinta G, Ford R, Jain M, Varshney R, Mantri N. (2020) Comparative root transcriptomics provide insights on drought adaptation strategies in chickpea (Cicer arietinum L.). International Journal of Molecular Sciences 21, 1781; .
(IF = 4.183; Citation = 0)
4. Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. (2019) Genome-wide transcript profiling reveals an auxin-responsive transcription factor, OsAP2/ERF-40, promoting rice adventitious root development. Plant Cell Physiology 60, 2343-2355. doi: 10.1093/pcp/pcz132.
(IF = 3.929; Citation = 0)
5. Sharma E, Jain M, Khurana JP. (2019) Differential quantitative regulation of specific gene groups and pathways under drought stress in rice. Genomics 111, 1699-1712.
(IF = 3.160; Citation = 0)
6. Rajkumar MS, Garg R, Jain M. (2018) Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance. Scientific Reports 8, 16795. DOI:10.1038/s41598-018-35140-w.
(IF = 4.525; Citation = 1)
7. Chai C, Shankar R, Jain M†, Subudhi P†. (2018) Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Scientific Reports 8, 14218, DOI:10.1038/s41598-018-32513-z. †Joint corresponding author
(IF = 4.525; Citation = 3)
8. Bhatia H, Khemka N, Jain M, Garg R. (2018) Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea. Scientific Reports 8, 9704. doi: 10.1038/s41598-018-27979-w.
(IF = 4.525; Citation = 4)
9. Sharma C, Saripalli G, Kumar S, Gautam T, Kumar A, Rani S, Jain N, Prasad P, Raghuvanshi S, Jain M, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. (2018) A study of transciptome in leaf rust infected bread wheat involving seedling resistance gene Lr28. Functional Plant Biology. Doi: 10.1071/FP17326.
(IF = 2.327; Citation = 4)
10. Kaashyap M, Ford R, Kudapa H, Jain M, Edwards D, Varshney RK, Mantri N. (2018) Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea. Scientific Reports 8, 4855. Doi: 10.1038/s41598-018-23116-9.
(IF = 4.525; Citation = 10)
11. Singh U†, Khemka N†, Rajkumar MS, Garg R, Jain M. (2017) PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Research 22, e183. DOI: 10.1093/nar/gkx866. †Equal contribution
(IF = 11.147; Citation = 17)
12. Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. (2017) Global transcriptome and co- expression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size determination in chickpea. The Plant Journal 91, 1088-1107. doi: 10.1111/tpj.13621
(IF = 5.726; Citation = 30)
13. Singh VK, Kumar MR, Garg R, Jain M. (2017) Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea. Scientific Reports 7, 10895. Doi: 10.1038/s41598-017-11327-5.
(IF = 4.525; Citation = 6)
14. Bhattacharjee A, Sharma R, Jain M. (2017) Over-expression of OsHOX24 confers enhanced susceptibility to abiotic stresses in transgenic rice via modulating stress-responsive gene expression. Frontiers in Plant Science 8, 628. doi: 10.3389/fpls.2017.00628.
(IF = 4.106; Citation = 7)
15. Khemka N, Singh VK, Garg R, Jain M. (2016) Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. Scientific Reports 6, 33297. doi:10.1038/srep33297
(IF = 4.525; Citation = 30)
16. Shankar R, Bhattacharjee A, Jain M. (2016) Transcriptome analysis in different rice cultivars provides novel insights into drought and salinity stress responses. Scientific Reports 6, 23719. DOI: 10.1038/srep23719.
(IF = 4.525; Citation = 72)
17. Bhattacharjee A, Khurana JP, Jain M. (2016) Characterization of rice homeobox genes, OsHOX22 and OsHOX24, and over-expression of OsHOX24 in transgenic Arabidopsis suggest their role in abiotic stress response. Frontiers in Plant Science 7, 627. doi: 10.3389/fpls.2016.00627.
(IF = 4.106; Citation = 23)
18. Jain M, Srivastava PL, Verma M, Ghangal R, Garg R. (2016) De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Scientific Reports 6, 22456. doi: 10.1038/srep22456.
(IF = 4.525; Citation = 37)
19. Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M. (2016) Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea. Scientific Reports 6, 19228. doi: 10.1038/srep19228.
(IF = 4.525; Citation = 99)
20. Kotwal S, Kaul S, Sharma P, Shankar R, Jain M, Dhar M. (2016) De novo transcriptome analysis of medicinally important Plantago ovata using RNA-Seq. PLoS ONE 11, e0150273. doi:10.1371/journal.pone.0150273.
(IF = 2.776; Citation = 16)
21. Dixit AB, Banerjee J, Srivastava A, Tripathi M, Sarkar C, Kakkar A, Jain M, Chandra S. (2016) RNA-Seq analysis of hippocampal tissues reveals novel candidate genes for drug refractory epilepsy in patients with MTLE-HS. Genomics 107, 178-188.
(IF = 3.160; Citation = 23)
22. Ram H, Jain M, Singh A, Chattopadhyay S. (2016) Functional relationship of GBF1 with HY5 and HYH in genome-wide gene expression in Arabidopsis. Plant Molecular Biology Reporter 34, 211-220.
(IF = 1.604; Citation = 0)
23. 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.
(IF = 4.525; Citation = 102)
24. 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 10, e0119198. 10.1371/journal.pone.0119198
(IF = 2.776; Citation = 34)
25. Singh VK, Jain M. (2015) Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean. Frontiers in Plant Science 6, 918. doi: 10.3389/fpls.2015.00918
(IF = 4.106; Citation = 38)
26. Parida S, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. (2015) Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Frontiers in Plant Science 6, 645. doi: 10.3389/fpls.2015.00645
(IF = 4.106; Citation = 21)
27. Verma M, Kumar V, Patel RK, Garg R, Jain M. (2015) CTDB: An integrated chickpea transcriptome database for functional and applied genomics. PLoS ONE 10, 0136880. 10.1371/journal.pone.0136880.
(IF = 2.776; Citation = 31)
28. 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.
(IF = 4.106; Citation = 26)
29. Garg R†, Bhattacharjee A, Jain M†. (2015) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter 33, 388-400. DOI 10.1007/s11105-014-0753-x. †Joint corresponding authors.
(IF = 1.604; Citation = 59)
30. 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 35, 198. DOI: 10.1007/s11032-015-0387-1.
(IF = 1.862; Citation = 12)
31. 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.
(IF = 4.525; Citation = 83)
32. 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.
(IF = 4.525; Citation = 32)
33. 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. 10, e0125583. doi: 10.1371/journal.pone.0125583.
(IF = 2.776; Citation = 18)
34. 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. doi: 10.1111/pbi.12133. †Joint corresponding authors.
(IF = 6.84; Citation = 72)
35. Jain M†, Chevala VVSN, Garg R. (2014) Genome-wide discovery, analysis and implications of differential regulation of conserved and novel miRNAs in chickpea via deep sequencing. Journal of Experimental Botany 65, 5945-5958. doi:10.1093/jxb/eru333. †Corresponding author.
(IF = 5.36; Citation = 47)
36. Verma M†, Ghangal R†, Sharma R, Sinha AK, Jain M. (2014) Transcriptome analysis of Catharanthus roseus for gene discovery and expression profiling. PLoS ONE 9, e103583. doi: 10.1371/journal.pone.0103583. †Joint first authors.
(IF = 2.776; Citation = 36)
37. 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 salinity and submergence tolerance factors. DNA Research 21, 69-84. doi:10.1093/dnares/dst042.
(IF = 4.0; Citation = 76)
38. 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 9, e92900. doi: 10.1371/journal.pone.0092900.
(IF = 2.776; Citation = 94)
39. 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; Citation = 14)
40. 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. doi:10.1093/mp/sst143.
(IF = 10.812; Citation = 10)
41. Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G. (2014) The Chickpea Genomic Web Resource: Visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes. BMC Plant Biology 14, 315.
(IF = 3.67; Citation = 9)
42. 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 34, 241-265. DOI 10.1007/s11032-014-0033-3.
(IF = 1.862; Citation = 44)
43. 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.
(IF = 6.84; Citation = 87)
44. Jain M, Mishra 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. (Featured and cover photo article)
(IF = 5.726; Citation = 324)
45. 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.
(IF = 3.060; Citation = 31)
46. 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.
(IF = 3.683; Citation = 53)
47. 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. doi: 10.1371/journal.pone.0072516.
(IF = 2.776; Citation = 31)
48. 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.
(IF = 4.0; Citation = 113)
49. 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.
(IF = 2.776; Citation = 135)
50. 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.
(IF = 6.84; Citation = 132)
51. 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.
(IF = 2.776; Citation = 1509) paper access/download = >60,000
52. 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 19, 357-373.
(IF = 4.0; Citation = 148)
53. 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.
(IF = ~NA; Citation = 41)
54. 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.
(IF = 2.745; Citation = 39)
55. 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.
(IF = 4.0; Citation = 6)
56. Garg R, Jain M (2011). Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signaling & Behavior 6, 1868-1870.
(IF = ~NA; Citation = 10)
57. 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.
(IF = 6.305; Citation = 235)
58. 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.
(IF = 4.0; Citation = 446)
59. 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.
(IF = 4.0; Citation = 48)
60. 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.
(IF = 2.705; Citation = 146)
61. 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)
(IF = 3.501; Citation = 171)
62. 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)
(IF = 4.739; Citation = 256)
63. Ghanashyam C, Jain M (2009). Role of auxin-responsive genes in biotic stress responses. Plant Signaling & Behavior 4, 846-848.
(IF = ~NA; Citation = 80)
64. 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.
(IF = 3.785; Citation = 55)
65. Jain M*, Khurana JP (2008). Small RNA regulation of rice homeobox genes. Plant Signaling & Behavior 3, 1024-1025. (*corresponding author).
(IF = ~NA; Citation = 7)
66. 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.
(IF = 4.739; Citation = 102)
67. 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.
(IF = 3.499; Citation = 26)
68. 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.
(IF = 2.745; Citation = 26)
69. 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.
(IF = 6.305; Citation = 361)
70. 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.
(IF = 2.745; Citation = 75)
71. 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.
(IF = 6.305; Citation = 511)
72. 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.
(IF = 3.785; Citation = 12)
73. 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.
(IF = 1.585; Citation = 13)
74. 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.
(IF = 3.785; Citation = 18)
75. 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)
(IF = 4.739; Citation = 58)
[pic]
76. 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.
(IF = 3.160; Citation = 169)
77. 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)
(IF = 2.705; Citation = 963)
78. 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)
(IF = 3.67; Citation = 119)
79. 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.
(IF = 2.745; Citation = 216)
80. 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.
(IF = 2.745; Citation = 169)
81. 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.
(IF = 4.328; Citation = 29)
82. 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.
(IF = 3.785; Citation = 9)
83. 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)
(IF = 1.608; Citation = 1)
84. 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.
(IF = 4.308; Citation = 15)
Review articles
85. 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.
(IF = 1.828; Citation = 0)
86. 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.
(IF = 1.828; Citation = 0)
87. 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.
(IF = 5.36; Citation = 117)
88. 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.
(IF = 4.106; Citation = 45)
89. 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.
(IF = 4.106; Citation = 8)
90. Garg R, Jain M. (2013) Transcriptome analyses in legumes: A resource for functional genomics. The Plant Genome 6, doi: 10.3835/plantgenome2013.04.0011.
(IF = 4.042; Citation = 14)
91. Garg R, Jain M (2013). RNA-seq for transcriptome analysis in non-model plants. Methods in Molecular Biology 1069, 43-58.
(IF = 1.828; Citation = 36)
92. Jain M (2013). Emerging role of metabolic pathways in abiotic stress tolerance. J Plant Biochem Physiol (IF = 3.404; (Citation = 21)
93. Jain M (2012). Next generation sequencing technologies for gene expression profiling in plants. Briefings in Functional Genomics 2, 63-70.
(IF = 3.133; Citation = 99)
94. Jain M (2011). A next generation approach to the characterization of a non-model plant transcriptome. Current Science 101, 1435-1439.
(IF = 0.756; Citation = 42)
Book chapters/proceedings/reports
95. 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.
96. 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.
97. 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. (Citation = 25)
98. 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. (Citation = 10)
99. 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. (Citation = 12)
100. 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. (Citation = 11)
101. 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.
102. 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. (Citation = 2)
103. 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.
104. 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.
105. 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. (Citation = 3)
Edited Books
1. Book on “Legume Genomics: Methods and Protocols”, Methods in Molecular Biology (Eds.) Garg R, Jain M. (2020) Springer Science+Business Media LLC, New York, USA Vol 2107, pp 1-406 (ISBN 978-1-0716-0234-8).
2. Book on “Pulse Improvement-Physiological, Molecular and Genetic Perspectives”, (Eds.) Wani SH, Jain M (2018). Springer, Cham; Springer Nature Switzerland AG pp 1-241. (ISBN 978-3-030-01742-2).
3. E-book on “Abiotic Stress: Molecular Genetics and Genomics”, Frontiers in Plant Science (December 2014) Eds. Jain M, Garg R, Varshney RK. Frontiers Media SA pp 1-101. (ISBN 978-2-88919-359-2)
Citation details
The total number of citations of published articles according to Google Scholar and Scopus databases are more than 8600 to date. The articles have been cited in several refereed journals of high repute and impact factor, including Annual Reviews in Plant Biology, Nature, Science, Nature Genetics, Plant Cell, PNAS, NAR, Trends in Plant Science, BioEssays, Plant Physiology, Plant Journal, BMC Genomics, Plant Molecular Biology, Functional and Integrative Genomics, BMC Plant Biology, Current Opinion in Plant Biology, Journal of Experimental Botany, FEBS Journal, BBRC, Molecular Genetics and Genomics, Genomics etc. Some of the articles are in the list of most viewed/most downloaded/highly accessed articles. The current h-index and i10-index (the indexes that quantify both the actual scientific productivity and the apparent scientific impact of a scientist) is “40” and “76”, respectively, according to the Google Scholar Citations.
Patents
1. Nucleic acid sequences encoding glutathione S-transferases associated with abiotic stress responses in plants (2009). [Indian patent application (2302/DEL/2009) filed on November 9, 2009].
Inventor: Jain M
2. 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
3. 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
Media news/views articles
1. A glimpse of sequencing technologies. July 2017, Medical Buyer. Guest column (ADI Media Pvt. Ltd.).
2. Natural saffron molecules inhibit cancer cell growth. May 16, 2017, IndiaBioscience. Jeenisha Dabreo.
3. Scientists uncover remarkable protein diversity in corn. July 30, 2016, The Munich Eye. Ankita Shastri.
4. UN urged to demand free access to crop data. April 22, 2015, . Andrea Rinaldi.
5. Genotypic, NIPGR launch chickpea microarray. November 29, 2012, Biospectrum Asia. . Jain M, Mugasimangalam R.
Scientific leadership/membership
1. Member (VC Nominee), Special Committee (Board of Studies), Special Centre for Molecular Medicine, JNU (September 2019 onwards).
2. Concurrent Faculty, School of Sanskrit and Indic Studies, JNU (August 2019 onwards).
3. Nodal Presenter, for the area ‘Agricultural Data Mining and Informatics’ in “DBT-National Bioinformatics Network Meeting” August 29, 2018 organized by the Department of Biotechnology.
4. Conceived and coordinated “Challenge Programme on Chickpea Functional Genomics” for funding from the Department of Biotechnology, Government of India (2015-2020); secured funding for INR ~8.0 crores as Coordinator.
5. Member, Expert Committee of Innovative Young Biotechnologists Award, Department of Biotechnology, Government of India (2016-2019).
6. Member, Special Committee (Board of Studies), School of Computational & Integrative Sciences, JNU, New Delhi (October 2015 onwards).
7. External Expert, Selection Committee for PhD Program on Bioinformatics/Biostatistics 2018, Regional Centre for Biotechnology. Faridabad.
8. Member, Screening Committee, Faculty (Assistant/Associate Professor) positions at SCIS, JNU 2017 & 2019.
9. Member, Selection Committee, for MSc, PGD and PhD programs in Computational & Integrative Sciences at SCIS, JNU (2015 onwards).
10. External expert, qualifying viva-voce examination at IASRI, New Delhi (November, 2017).
11. Member, Selection Committee for ‘AcSIR-Dr. APJ Abdul Kalam Summer Training Program 2018’.
12. External Expert Member, Board of Studies, Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur (2017 onwards).
13. External Expert Member, Board of Studies, Bioinformatics, Mahila Maha Vidyalaya, Banaras Hindu University (2016-2018).
14. Member, Board of Studies, School of Computational & Integrative Sciences, JNU (2015 onwards).
15. Chair/Co-chair, Session on different topics in International/National conferences/workshops.
16. Jury member, oral/poster presentations, at national and international conferences.
17. Member, Academic Review Committee, Indian Institute of Technology (IIT), Jodhpur (2016).
18. Group Leader, independent group of more than 10 researchers, including Ph.D. students, Research Fellows and Post-Doctoral Fellows at NIPGR/JNU (April 2008 onwards).
19. Group Leader, Chickpea Genome Annotation and Transcriptome Sequencing Group, at NIPGR, New Delhi (September 2009 – September 2014).
20. Working in collaboration with several National and International research groups.
21. Invited Speaker, National and International workshops/symposia/conferences.
22. Jury member, INSPIRE National Level Exhibition & Project Competition 2013-2016, New Delhi.
23. Jury member, INSPIRE award, GNCT, Directorate of Education 2013, New Delhi.
24. External expert, Ph.D. thesis evaluation/viva-voce at IIT-Roorkee, IISER-Bhopal, UDSC, IISER-Kolkata, CSIR-NBRI, GGS Indraprastha University- Delhi, Kerala University.
25. External expert, B. Tech/M. Tech (practical/project) exams; selection committee JRF/SRF at GGS Indraprastha University, Delhi.
Administrative and organizing role/activities
1. Member Secretary, Institutional Biosafety Committee (IBSC), JNU, New Delhi (January 2020-January 2023).
2. Vice-President & Convener, Institution’s Innovation Council (IIC), JNU, New Delhi (September 2019-Present).
3. Officiating Director, Research & Development Cell, JNU (December 30-31, 2018; December 27, 2019-January 3, 2020; other occasions in the absence of Director R & D).
4. Co-organizer, Regional Young Investigator’s Meeting (R-YIM), Delhi-NCR 2019 (August 6-7, 2019).
5. Member, Organizing Committee, 5th International Conference on Plant Genetics and Genomics on “Germplasm to Genome Engineering” (October 17-18, 2019), NASC Complex, Pusa, New Delhi.
6. Member, Committee for establishment for Transdisciplinary Research Clusters at JNU (2019).
7. Acting Dean, School of Computational & Integrative Sciences, JNU (June 3-12, 2019).
8. Programme Coordinator, Innovative PhD Thesis Award (IPTA), JNU (established IPTA, JNU with format and guidelines).
9. VC Nominee, Purchase Committee, School of Life Sciences, JNU (August 1, 2019-July 31, 2021).
10. Coordinator, 113th Orientation Programme at UGC-HRDC, JNU (March 5-29, 2019).
11. Member, Graduate Advisory Committee (GAC), SCIS, JNU, New Delhi (December 2015 – January 2017 and September 2019 - Present).
12. Member, Project Implementation Group, DST-FIST programme at SCIS, JNU (2019 onwards).
13. Member, CoE Expenditure Committee, SCIS, JNU (2019 onwards).
14. Single Point of Contact (SPOC), JNU for the Smart India Hackathon 2019 organized by MHRD.
15. Organized Workshop on Intellectual Property Rights, SLS, JNU (January 10, 2019).
16. Organized Webinar episodes of India First Leadership Talk Series by MHRD by IIC-JNU (2019).
17. Convener, Institution’s Innovation Council (IIC), JNU, New Delhi (October 2018 -August 2019).
18. Observer, National Testing Agency, MHRD for the NEET examination 2019.
19. Member, Organizing Committee, Science Day, JNU, New Delhi (2017 - 2019).
20. Member, Admission Committee-SCIS, JNU (2018-19).
21. Special Invitee/Member, Golden Jubilee Celebrations Committee 2018, JNU, New Delhi.
22. Member, Steering Committee for Convocation (2018-19), JNU, New Delhi.
23. Member, School Level Grievance Redressal Committee (GRC), SCIS, JNU, New Delhi (April 2018 onwards).
24. Treasurer, Asia Pacific Bioinformatics Interaction and Networking Society (APBIAN), New Delhi.
25. Member, Core Organizing Committee, International Conference on Bioinformatics 2018 (InCoB 2018), JNU, New Delhi (September 24-26, 2018).
26. Chairman, Student Faculty Committee (SFC), SCIS, JNU, New Delhi (January 2017 – October 2018).
27. Faculty In-charge, Annual Student’s Symposium “Scientegration” at SCIS, JNU (2016-Present).
28. Member/Chairman, purchase/technical committees for various equipments at SCIS, JNU and NIPGR.
29. Member, Scientific Program Committee, International Symposium on Rice Functional Genomics (ISRFG - 2013)” held during November 20 – 23, 2013 at INSA, New Delhi.
30. Member, Facilitation Committee, Indo-German Symposium on “Plant Biology” held during October 18 – 20, 2011 at INSA, New Delhi.
31. Convener, workshop on “Advances & Challenges in Next Generation Sequencing & Bioinformatics of Genome Analysis” held at NIPGR, New Delhi (March 28-30, 2011).
32. Member, Organization Committee, Annual Symposium at DPMB, University of Delhi South Campus (February, 2005).
33. Facilitated and organized weekly departmental meetings, DPMB, University of Delhi South Campus.
Invited talks/lectures
1. Jain M (2019). Integrating Multi-omics Approaches for Divulging Regulation of Seed Development for Crop Improvement. In: “International Conference on Plant Genetics & Genomics-Germplasm to Genome Engineering”. (October 17-18), NASC Complex, Pusa, New Delhi.
2. Jain M (2019). Unveiling gene/genome regulation for translational research in plants. In: “Indo-German Matchmaking Workshop”. (October 10-11), IIT, Madras.
3. Jain M (2019). Long non-coding RNAs: A novel prediction tool and regulatory aspects in plants. In: “NGBT 2019'”. (September 30-October 1), Hotel Taj Lands End, Mumbai.
4. Jain M (2019). RNA-seq for transcriptome construction and identification of differentially expressed genes. (September 7), ICAR-CAFT Training Programme on “Next generation sequencing and its applications in crop science”, (September 3-23) NIPB, New Delhi.
5. Jain M (2019). Methods for next generation sequencing and data analysis: Applications in agriculture. (August 20), 24th Refresher Course in Life Sciences & Biotechnology, (August 19-August 30, 2019) UGC-HRDC, JNU, New Delhi.
6. Jain M (2019). Exploring gene regulatory network and discovery of candidate genes associated with seed development/size determination in chickpea via deep sequencing. (July 29-30, 2019), In: 6th Plant Genomics & Gene Editing Congress Asia". (July 30), Hotel Grand Millennium, Malaysia. Hosted by, University of Nottingham Malaysia (UNM) and the Crops for the Future Research Centre (CFF).
7. Jain M (2019). Integrated Genomics Approaches for Crop Improvement. (April 23), In: Vigyan Manthan Series, JNU". (April 23), Convention Centre, JNU.
8. Jain M (2019). RNA Sequencing for Generation of a Blueprint for Crop Improvement. (March 16), In: National Workshop on "Foldscope and Symposium on Applied Biotechnology". (March 15-16), Department of Biotechnology, IIS University, Jaipur.
9. Jain M (2019). Next generation sequencing and its applications. (January 24-25), In: National Workshop on "Whole Genome Data Analysis using Computational Framework and Tools". (January 24-25), MBBT, Tezpur University, Tezpur.
10. Jain M (2018). Computational tools and high-throughput data analyses for crop genomics. (December 15), In: “1st National Genetics Congress on Genetics for Sustainable Food, Health and Nutrition Security”. (December 14-16), NASC Complex, New Delhi.
11. Jain M (2018). Discovery of candidate molecular signatures associated with abiotic stress response/adaptation via integrated genomics approaches. (December 7), In: “4th WUN Workshop on Climate Resilient Open Partnership for Food Security (CROP-FS)”. (December 7-8), ICGEB & JNU, New Delhi.
12. Jain M (2018). Integrated genomics approaches for discovery of molecular signatures associated with seed traits in chickpea. (December 2), In: “4th International Plant Physiology Congress”. (December 2-5), Indira Gandhi Prathisthan-Lucknow.
13. Jain M (2018). Genomics approaches for understanding the biology of agronomic traits and translational research for crop improvement. (October 28), In: “International Conference on Bioinformatics and Systems Biology”. (October 26-28), IIIT-Allahabad.
14. Jain M (2018). Connecting genes and (epi)genomic variations to abiotic stress response/adaptation in rice via integrated genomics approaches. (October 17), 5th International Rice Congress 2018 (IRC2018), (October 15-17, 2018) Marina Bay Sands, Singapore.
15. Jain M (2018). Next generation sequencing and data analysis: Applications in agriculture. (October 10), 23rd Refresher Course in Life Sciences & Biotechnology on “Basic Research to Translational Research”, (October 8-November 2, 2018) UGC-HRDC, JNU, New Delhi.
16. Jain M (2018). Next generation sequencing and data analysis: Applications in health and agriculture. (October 10), Continuous Education Programme (CEP) on “Recent Trends in Data Analysis”, (October 9-11, 2018) Defence Institute of Physiology and Allied Sciences, DRDO, New Delhi.
17. Jain M (2018). Exploring gene regulatory network and molecular signatures associated with seed development/size determination in chickpea via deep sequencing. In: “NGBT 2018'”. (September 30-October 1), Hotel Fairmont, Jaipur.
18. Jain M (2018). RNA-seq for transcriptome construction and identification of differentially expressed genes. (September 1), ICAR-CAFT Training Programme on “Next generation sequencing and its applications in crop science”, (August 28-September 17) NRCPB, New Delhi.
19. Jain M (2018). Agricultural informatics and data mining: Status, challenges and future prospects. In: “National Bioinformatics Network Meet”. (August 29), ICGEB, New Delhi.
20. Jain M (2018). Genomics approaches for divulging gene/genome regulation and translational research for crop improvement. In: “International Conference on Plant Genetics and Genomics-Next Gen Crops for Sustainable Agriculture”. (July 19-20), Hotel Hometel, Chandigarh.
21. Jain M (2018). Next generation sequencing: methods and applications. In: “Summer School 2018”. (July 10), SCIS-JNU, New Delhi.
22. Jain M (2018). RNA-seq for transcriptome construction and discovery of candidate genes for crop improvement. (March 12-14), Workshop on “Computational Biology”, NABI, Chandigarh.
23. Jain M (2017). A blueprint for crop improvement via next generation genomics. (December 15), DRDO, DIBER, Haldwani, Uttarakhand.
24. Jain M (2017). RNA-seq for transcriptome construction and identification of differentially expressed genes. (December 1-21), ICAR-CAFT Training Programme on “Next generation sequencing and its applications in crop science”, NRCPB, New Delhi.
25. Jain M (2017). Genomics and beyond: Unveiling gene/genome regulation for translational research in crop plants. (April 19), SCIS, JNU, New Delhi.
26. Jain M (2017). Next Generation Genomics: A Blueprint to Divulge Genome Regulation and Genetic Enhancement of Crop Plants. (April 11), (Rajib Goyal Prize lecture) Kurukshetra University, Kurukshetra.
27. Jain M (2017). Next generation genomics approaches for discovery of candidate genes and divulging gene/genome regulation for crop improvement. In: World Biotechnology Congress 2017” (February 20-22), JNU, New Delhi.
28. Jain M (2017). Exploring gene regulatory network determining seed development/size in chickpea via deep sequencing. In: International symposium on “Insights to Plant Biology in the Modern Era” (February 8-10), Bose Institute, Kolkata.
29. Jain M (2016). Genome Science: A Gateway to Decipher Molecular Mechanisms and Identify Targets for Crop Improvement. (October 25), (B.K. Bachhawat Memorial Young Scientist Lecture Award) University of Delhi South Campus, New Delhi.
30. Jain M (2016). Genomics approaches for divulging gene/genome regulation and translational research for crop improvement. In: “SBC(I): Innovations in Biological Research in Health and Disease'”. (October 21-24), CFTRI, Mysore.
31. Jain M (2016). Exploring transcriptional regulatory network determining seed size in crop plants. In: “NGBT 2016'”. (October 3-5), Hotel Le Meridien, Kochi.
32. Jain M (2016). Genome Editing in Plant Science/Agriculture: Potential Applications and Challenges in India. In: “Practical Considerations of Applications of Genome Editing”. (September 23), Hotel Mercure, Hyderabad.
33. Jain M (2016). Integrated next generation genomics approaches for discovery of molecular signatures associated with agronomic traits in crop plants. In: “AgriGenomics 2016'”. (August 19-20), Radisson Blu Plaza, New Delhi.
34. Jain M (2016). Next generation genomics tools for rapid discovery of genes associated with agronomic traits in crop plants. In: “Application of Genomic Tools in Plant Science'”. (August 9-12), Central University of Kerala, Kerala.
35. Jain M (2016). Translational genomics for improvement of grain legume chickpea. In: “Foundation Day and Annual General Body Meeting, NAAS'”. (June 4-5), NASC Complex, New Delhi.
36. Jain M (2016). Integrated genomics approaches for translational plant biology. In: “Symposium on Genome Biology and Big Data Bioinformatics'”. (March 29), UDSC, New Delhi.
37. Jain M (2016). Genome-wide discovery of non-coding RNAs and their differential regulation: A case study in chickpea. In: “National Workshop on NGS Data: Assembly and Exploration'”. (March 10-11), NIPGR, New Delhi.
38. Jain M (2016). Genomics approaches for discovery of candidate genes and (epi)genomic variations involved in abiotic stress response/adaptation. In: “Science Day 2016”. (February 26), JNU, New Delhi.
39. Khemka N, Singh VK, Garg R, Jain M (2016). Genome-wide discovery and differential regulation of long intergenic non-coding RNAs during flower development in chickpea. In: “Science day”. (February 26), JNU, New Delhi.
40. Jain M (2016). Next generation genomics for rapid discovery of genes associated with agronomic traits in chickpea. In: “37th Annual Meeting of PTCA (India) & National Symposium on 'Plant Biotechnology for Crop Improvement'”. (February 25-27), NBRI, Lucknow, India.
41. Jain M (2016). Genomics approaches for connecting genes and (epi)genomic variations to abiotic stress response/adaptation. In: “2nd International South Asian Biotechnology Conference 2016 on Biotechnology for Sustainable Development”. (February 5-6), University of Dhaka, Dhaka, Bangladesh.
42. Jain M (2015). Next generation genomics: Connecting genes and (epi)genomic variations to abiotic stress response/adaptation. In: “3rd International Plant Physiology Congress-Challenges and Strategies in Plant Biology Research”. (December 11-14), Jawaharlal Nehru University, New Delhi.
43. Jain M (2015). DNA microarrays and its applications in gene expression profiling. In: “DBT sponsored short term training course on Methodologies used in gene expression analysis”. (September 29 – October 20), SP Pune University, Pune.
44. Jain M (2015). Next generation sequencing in transcriptome analysis and gene expression profiling. In: “DBT sponsored short term training course on Methodologies used in gene expression analysis”. (September 29 – October 20), SP Pune University, Pune.
45. Jain M (2015). Next generation genomics for mining genes/alleles associated with agronomic traits. In: “National Bioinformatics Training Program on High-throughput Omics Data for mining of important genes/traits linked to Agricultural Productivity”. (September 9-12), GBPAU, Pantnagar.
46. Jain M (2015). Genome-wide discovery and differential regulation of conserved and novel microRNAs in crop plants via deep sequencing. In: Summer School on RNA interference as a tool for plant functional genomics and crop improvement. (May 6-26), NRCPB, New Delhi.
47. Jain M (2015). Next generation genomics: Connecting genes and (epi)genomic variations to agronomic traits. In: Indo-US Bilateral Conference cum Workshop on Big Data Analysis and Translation in Disease Biology. (January 18-22), JNU, New Delhi.
48. Jain M (2015). Genome-wide discovery and differential regulation analysis of miRNAs: A case study in chickpea. In: Workshop on Computational identification of microRNA for biotic and abiotic stress tolerance in cereals. (January 12-14), Meerut University, Meerut, UP.
49. Jain M (2014). Transcriptome analysis for discovery of candidate genes involved in agronomic traits. In: DBT-sponsored Short term Training Course on Plant Transgenic Technologies. (October 1-16, 2014), M. D. University, Rohtak, Haryana.
50. Jain M (2014). Discovery of trait determining transcriptomic, genomic and epigenomic variations in crop plants via next generation sequencing. In: Conference on Applying NGS: Basic Research, Agriculture & Healthcare. (September 11, 2014), Hotel Capitol, Bangalore.
51. Jain M (2014). Genomics and bioinformatics: Introduction, challenges and opportunities. In: Workshop on Genomics and Bioinformatics. (July 19), Sadhu Vaswani International School for Girls, Shantiniketan, New Delhi.
52. Jain M (2014). Genome and transcriptome landscape: A blueprint for functional and translational genomics for crop improvement. In: National Workshop on Genomics in Crop Improvement. (February 27-28), M. D. University, Rohtak, Haryana.
53. Jain M (2014). Next generation sequencing – Applications and implications in plants and clinic. In: National-level ‘Training Program on Bioinformatics for Medical Research’. (February 13), IIT, New Delhi.
54. Jain M (2014). Next generation sequencing data analysis for identification of important genes and functional markers in crop plants. In: Workshop on Use of Bioinformatics in Crop Biotechnology. (January 6-8), Meerut University, Meerut, UP.
55. Jain M (2013). Next generation sequencing: A turbo for functional and applied genomics in crop plants. In: 2013 NextGen Genomics & Bioinformatics Technologies (NGBT) Conference (November 14-16), CSIR-IGIB, Delhi, India.
56. Jain M (2013). NGS: A revolutionary tool for functional and applied genomics in plants. In: NGS-IGIB 2013 (November 9-13), CSIR-IGIB, Mathura Road Campus, New Delhi, India.
57. Jain M (2013). Genome and transcriptome landscape in chickpea: A rich resource for functional and applied genomics. (September 7), NABI, Mohali, India.
58. Jain M (2013). Next generation genomics approaches for prioritization of Indian bioresources. In: Brain Storming session on "Prioritizing Research Areas on Bioinformatics for Documentation of Himalayan Bioresources and Discovery of Novel Molecules" (July 12-13), GBPUAT, Pantnagar, India. (Co-chaired the session "Bioinformatics for Documentation of Himalayan Bioresources and Discovery of Novel Molecules")
59. Jain M (2013). Harnessing the potential of next generation sequencing technologies for generation of genomic resources for orphan crops. In: Biosparks-2013 (February 15-16), JNU Campus, New Delhi, India.
60. Jain M (2012). Next generation genomics: Applications, challenges and use in crop improvement. In: Workshop on Role of Bioinformatics in Genomics (December 27-28), Gargi College, New Delhi, India.
61. Jain M (2012). Next generation genomics for crop improvement. In: International Conference on Statistics and Informatics in Agricultural Research (December 18-20), IASRI, New Delhi, India.
62. Jain M (2012). Next Generation Sequencing Technologies-Applications in Transcriptome Analysis. In: Workshop on “Computational Genome Analysis Techniques in Discovery of Agronomically Important Crop Genes”, (September 24-29, 2012) NBPGR, New Delhi.
63. Jain M (2012). RNA-seq: A revolutionary tool for transcriptome analysis in non-model plants. In: Symposium-cum-Workshop on “High-throughput Data-Driven Biology”, (September 12-14, 2012) IBAB, Bangalore. Abstract pp 22.
64. Jain M (2011). Next generation sequencing technologies-introduction and applications in transcriptome characterization. In: National Workshop on “Genome Annotation” (September 29-30), ICGEB, New Delhi.
65. Jain M (2011). A next generation approach to the characterization of chickpea transcriptome. In: 22nd Mid-year Meeting of Indian Academy of Sciences (July 8-9), Indian Institute of Science, Bangalore. Abstract pp 14.
66. Jain M (2011). Optimization of de novo transcriptome assembly using NGS data. In: National workshop on “Advances & challenges in next generation sequencing and bioinformatics of genome analysis” (March 28-30), National Institute of Plant Genome Research, New Delhi.
67. Jain M (2011). De novo transcriptome assembly from next generation sequencing data. In: 1st regional workshop on “Next generation sequencing experimental design and quantitative genomics” (February 25-26), Biotech Centre, University of Delhi South Campus, New Delhi.
68. Jain M (2009). DNA Microarray and its applications in plant biology. In: National Workshop on “Use of Bioinformatics in Plant Biology” (March 12-13), NIPGR, New Delhi.
69. Jain M (2008). DNA Microarray and its applications. In: Winter School on “Recent Techniques on Structural and Functional Genomics” (December 3-12), CIMAP, Lucknow.
70. Jain M, Tyagi AK, Khurana JP (2008). Novel role of putative topoisomerase 6 genes from rice in stress tolerance. In: 95th Indian Science Congress Association (January 3-7), Visakhapatnam, India. (Young scientist award lecture)
71. Jain M, Tyagi AK, Khurana JP (2007). Novel role of putative topoisomerase 6 genes from rice in stress tolerance. In: 95th Indian Science Congress Association: Young Scientists’ Award Programme (October 13), Visakhapatnam, India. Abstract pp 55.
Poster/paper presentation
1. Rajkumar MS, Khemka N, Singh VK, Garg R and Jain M (2019). Integrated genomics approaches to identify regulatory pathways involved in seed development and seed size/weight determination. In: “National Science Day” (February 28), Jawaharlal Nehru University (JNU), New Delhi.
2. Khemka N, Rajkumar MS, Garg R and Jain M (2019). Discovery of miRNAs during seed development and their functional relevance in seed size/weight determination in chickpea. In: “National Science Day” (February 28), Jawaharlal Nehru University (JNU), New Delhi.
3. Dwivedi AK and Jain M (2018). Cracking the Genetic Code for Smart Crops. In JNU Open day “Jan-Jan JNU” (November 30) Jawaharlal Nehru University (JNU), New Delhi.
4. Singh U, Khemka N, Rajkumar MS, Garg R, Jain M (2018). PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice. 5th International Rice Congress 2018 (IRC2018), (October 15-17, 2018) Marina Bay Sands, Singapore.
5. Gupta K, Jain M, Garg R (2018). Decoding the DNA methylation dynamics during abiotic stress response in Chickpea. In: International Conference on “17th annual International Conference on Bioinformatics (InCoB 2018)” (September 26-28), Jawaharlal Nehru University (JNU), New Delhi.
6. Khemka N, Singh U, Rajkumar MS, Garg R, Jain M (2018). PLncPRO: A novel tool for prediction of long non-coding RNAs. In: National Science day-2018 (February 28), Jawaharlal Nehru University (JNU), New Delhi.
7. Gupta K, Rajkumar MS, Garg R, Jain M (2018). Deep sequencing revealed stage-specific expression patterns of apocarotenoid biosynthesis pathways genes during stigma development in Crocus sativus. In: “National Science Day” (February 28), Jawaharlal Nehru University (JNU), New Delhi.
8. Gupta K, Rajkumar MS, Garg R, Jain M (2017). Deep sequencing revealed stage-specific expression patterns of apocarotenoid biosynthesis pathways genes during stigma development in Crocus sativus. In: National conference on “Recent Trends in Cell & Molecular Biology Research” (October 27-28), SNU, Greater Noida.
9. Khemka N, Rajkumar MS, Garg R, Jain M (2017). Genomics and beyond: Cracking the Plant DNA Code towards Super Crops. In JNU Open day “Jan-Jan JNU” (October 27) Jawaharlal Nehru University (JNU), New Delhi.
10. Shankar R and Jain M (2017). Allele-Specific Methylations in Different Rice Cultivars with Contrasting Drought and Salinity Stress Responses. In: “National Science day” (February 28) Jawaharlal Nehru University (JNU), New Delhi.
11. Khemka N, Singh VK, Garg R, Jain M (2016). Genome-wide discovery and differential regulation of long intergenic non-coding RNAs during flower development in chickpea. In: “National Science day”. (February 26), JNU, New Delhi.
12. Khemka N, Singh VK, Garg R, Jain M (2016). Discovery of long intergenic non-coding RNAs and their potential roles in flower development in chickpea. In: “EMBO workshop on Systems biology of non-coding RNAs”. (February 8-11), Rehovot, Israel.
13. Shankar R, Bhattacharjee A, Chevala N, Garg R and Jain M (2015). Understanding Transcriptional and Epigenomic Regulation of Abiotic Stress Responses in Rice. In: International conference “3rd International Plant Physiology Congress” (December 11-14) Jawaharlal Nehru University (JNU), New Delhi.
14. Jain M (2015). Resources for functional and applied genomics in chickpea for crop improvement. In: 5th International Conference on Next Generation Genomics and Integrated Breeding for Crop Improvement. (February 18-20), ICRISAT, Hyderabad.
15. Singh VK, Garg R, Jain M (2015). Transcriptome dynamics during flower development and genome-wide analysis of GH3 gene family in chickpea. In: 5th International Conference on Next Generation Genomics and Integrated Breeding for Crop Improvement. (February 18-20), ICRISAT, Hyderabad.
16. Jain M, Moharana KC, Shankar R, Kumari R, Garg R (2013). Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. In: 11th International Symposium on Rice Functional Genomics (ISRFG) (November 20-23), New Delhi, India.
17. Bhattacharjee A, Jain M (2013). Exploring the role of rice homeobox transcription factors in abiotic stress responses. In: 11th International Symposium on Rice Functional Genomics (ISRFG) (November 20-23), New Delhi, India.
18. Garg R, Verma M, Agrawal S, Shankar R, Majee M, Jain M (2013). Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. In: 11th International Symposium on Rice Functional Genomics (ISRFG) (November 20-23), New Delhi, India.
19. Shankar R, Bhattacharjee A, Jain M (2013). Exploring transcriptional complexity under abiotic stresses in rice via deep sequencing. In: 11th International Symposium on Rice Functional Genomics (ISRFG) (November 20-23), Hotel Grand, New Delhi, India.
20. Chevala VVSN, Garg R, Jain M (2013). Genome-wide identification and analysis of microRNAs in chickpea. In: Indraprastha International Conference on Biotechnology (IICB 2013) (October 22-25), GGS Indraprastha University, New Delhi, India.
21. Jain M (2012). Transcriptome sequencing of chickpea for discovery of novel genes and genetic variations. In: VIth International Conference on Legume Genetics and Genomics (October 2-7), ICRISAT, Hyderabad, India.
22. Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2012). Deep sequencing of chickpea transcriptome for gene discovery, marker development and gene expression studies. In: VIth International Conference on Legume Genetics and Genomics (October 2-7), ICRISAT, Hyderabad, India.
23. Kim KD, Jain M, Jackson SA (2012). DNA methylation landscape of the soybean genome. In: Molecular & Cellular Biology of the Soybean Conference (August 12-15, 2012), Des Moines, Iowa, USA. PP 63.
24. Jain M, Garg R, Jhanwar S, Patel RK, Priya P, Tyagi AK (2012). Unraveling the chickpea transcriptome for gene discovery and marker development using next generation sequencing technologies. In: “Plant & Animal Genome XX” (January 14-18), San Diego, California, USA.
25. Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011). Unraveling the chickpea transcriptome using next generation sequencing technologies. In: Indo-German Symposium on “Plant Biology” (October 18-20), INSA, New Delhi. Abstract pp 26.
26. Jain M, Yadav B, Jhanwar S, Garg R, Tyagi AK (2010). Comparative transcriptome analyses of six legume species reveal multiple conserved, legume-specific and species-specific genes. In: Vth International Congress on Legume Genetics and Genomics (July 2-8), Asilomar Conference Grounds, Pacific Groove, CA, USA. Abstract pp 105.
27. Bhatia S, Gaur R, Choudhary S, Gupta S, Jain M, Yadav G, Chattopadhyay D, Tyagi AK (2010). Whole genome sequencing and molecular mapping in chickpea (Cicer arietinum L.). In: Vth International Congress on Legume Genetics and Genomics (July 2-8), Asilomar Conference Grounds, Pacific Groove, CA, USA. Abstract pp 81.
28. Bhaskar A, Jain M, Paul LK, Jha SN, Khurana JP (2008) Rice type-A response regulator, OsRRa, mediates cross-talk between cytokinin and abiotic stress signaling. In: 2nd International Conference on Trends in Cellular and Molecular Biology (January 5-7), New Delhi, India. Abstract pp 63.
29. Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008) Basic leucine zipper transcription factor family in rice: genomic survey, classification and gene expression analysis. In: 2nd International Conference on Trends in Cellular and Molecular Biology (January 5-7), New Delhi, India. Abstract pp 64. (Best poster award)
30. Jain M, Tyagi AK, Khurana JP (2006). Genome-wide analysis of auxin- and cytokinin-responsive transcriptome in rice (Oryza sativa). In: International Conference on Bioinformatics (December 18-20), New Delhi, India. Abstract pp 255.
31. 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). In: 8th International Congress of Plant Molecular Biology (August 20-25), Adelaide, Australia. Abstract pp 83.
32. Jain M, Tyagi AK, Khurana JP (2005). Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa). In: International conference on “Plant Genomics and Biotechnology: Challenges & Opportunities”. (October 26-28), Indira Gandhi Agricultural University, Raipur, Chhattisgarh, India. Abstract pp 72.
33. Khurana JP, Tyagi AK, Jain M (2004). Differential expression and hormonal regulation of archaebacterial topoisomerase 6 subunits A and B homologues from rice (Oryza sativa indica). In: 2nd International Symposium of Rice Functional Genomics. (November 15-17), Tucson, Arizona. Abstract pp 113.
34. Jain M, Tyagi AK, Khurana JP (2004). Differential expression and hormonal regulation of archaebacterial topoisomerase 6 subunits A and B homologues from rice (Oryza sativa indica). In: 9th National Rice Biotechnology Network Meeting (April 15-17), NASC Complex, New Delhi, India. Abstract pp 204.
35. Kumar D, Jain M, Tyagi SB, Tyagi AK, Khurana JP (2003). Molecular characterization of blue light receptors, Cryptochrome2 and Phototropin1, from rice (Oryza sativa L. subsp. indica). In: XVI National Symposium on “Photobiology in the Genomics and Post-Genomics Era.” (March 27-29), University of Delhi South Campus, India. Abstract pp 57.
36. Khurana JP, Tyagi AK, Kumar D, Jain M, Tyagi SB (2002). Molecular characterization of blue light receptors, Cryptochrome2 and Phototropin1, from rice (Oryza sativa L. subsp. indica). In: The Blue Light Syndrome IV; International Meeting on UV/blue light: Perception and Responses in Plants and Microorganisms. (December 16-18), Okazaki, Japan. Abstract pp 20.
Database submissions
1. Genome sequences (assembly) submitted to at NCBI.
Crocus sativus genome sequence (in process)
Oryza coarctata genome sequence JAAAWL000000000 (version JAAAWL010000000)
Chickpea (desi) genome sequence AHII00000000 (version AHII00000000.1)
2. Next generation sequencing data submitted to Short Read Archive (SRA) database at NCBI.
Roche 454 sequencing data
➢ Transcriptome sequencing of chickpea (genotype ICCV2) (~1.8 million reads) (SRA052099).
➢ Transcriptome sequencing of chickpea (Cicer reticulatum genotype PI489777) (~1.2 million reads) (SRA037766).
➢ Transcriptome sequencing of chickpea (genotype ICC4958) (~2.5 million reads) (SRA030696). Bioproject accession no. PRJNA80011.
Illumina sequencing data
➢ Genome sequencing of Crocus sativus (>500 million reads) (PRJNA613151).
➢ Genome sequencing of Oryza coarctata (>250 million reads) (PRJNA598408).
➢ Transcriptome sequencing of chickpea (genotype ICCV2) (~108 million reads) (SRA052099).
➢ Transcriptome sequencing of chickpea (genotype ICC4958) (~130 million reads) (SRA023503).
➢ Transcriptome sequencing of chickpea (WR315, K850 and JG62) (~130 million reads) (PRJNA293928).
PacBio sequencing data
➢ Full-length transcriptome sequencing of Crocus sativus (8 SMRTs) (PRJNA613348).
➢ Full-length transcriptome sequencing of Chickpea (6 SMRTs) (PRJNA613159).
3. Next generation sequencing data submitted to Gene Expression Omnibus (GEO) database at NCBI.
ChIP-Sequencing for OsHOX24 binding sites in rice (GSE144419; 16 samples)
DNA methylation during seed development in large-seeded chickpea (GSE131665; 11 samples)
DNA methylation during seed development in small-seeded chickpea (GSE131669; 5 samples)
Small RNAs during seed development in large-seeded chickpea (GSE131424; 15 samples)
Small RNAs during seed development in small-seeded chickpea (GSE131431; 15 samples)
Single-base resolution DNA methylome maps of different organs in chickpea (GSE103575; 5 samples)
Small RNA sequencing in wild chickpea (GSE103571; 1 sample)
Gene expression profiling in different organs of chickpea (GSE103561; 5 samples)
Transcriptome dynamics during seed development in chickpea (JGK3) (GSE79719; 24 samples)
Transcriptome dynamics during seed development in chickpea (Himchana) (GSE79720; 24 samples)
Chickpea Transcriptome Atlas – I: Flower development (GSE42679; 11 samples)
Chickpea Transcriptome Atlas – II: Abiotic Stress (GSE53711; 8 samples)
Transcriptional response to drought stress in chickpea: (GSE70274; 8 samples)
Transcriptional response to salinity stress in chickpea: (GSE70377; 8 samples)
Chickpea Small RNA Atlas - Development (GSE51300; 7 samples)
Porteresia transcriptome sequencing (GSE44913; 5 samples)
Catharanthus Transcriptome and Gene Expression (GSE57326; 3 samples)
Saffron Transcriptome and Gene Expression (GSE65103, 5 samples)
Rice stress-responsive gene expression (GSE60287; 7 samples)
Rice methylome (whole genome bisulphite sequencing) (GSE60288; 7 samples)
Rice Small RNAs (stress-related cultivars) (GSE64651; 3 samples)
4. Microarray data series submitted to GEO database at NCBI.
➢ Design and validation of microarray for chickpea (Cicer arietinum) (GSE78985, GSE78986, GSE78987)
➢ Platform for Custom Agilent Chickpea Whole Genome 8x60K (AMADID: 037094) (GPL21437)
➢ Design and validation of 8X60k gene-expression microarray for chickpea (Cicer arietinum) based on the transcriptome data (GSE76972)
➢ Gene expression analysis in wild-type and OsHOX24 rice overexpression line under control and drought stress conditions (GSE79212; 12 samples)
➢ Gene expression analysis in wild-type and OsHOX24 Arabidopsis overexpression line (GSE79188; 4 samples)
➢ Gene expression analysis in wild-type and OsGRX8 overexpression
line in response to various treatments (GSE41963; 16 samples)
➢ Gene expression analysis in wild-type and OsGSTU4 overexpression
line in response to various treatments (GSE53152; 4 samples)
➢ Gene expression analysis in response to various hormone treatments (GSE37557; 16 samples)
➢ ChIP-Chip and gene expression data for gbf1, gbf1 hy5, and gbf1 hyh mutants (GSE36964; 8 samples and GSE36965; 12 samples)
➢ Rice reproductive development (GSE6893; 45 samples)
➢ Seedling hormone treatment (GSE5167; 6 samples)
➢ Light and ABA treatment to atmyc2, cop1, and atmyc2 cop1 Arabidopsis mutants (GSE8955; 24 samples)
➢ Transgenic plants overexpressing OsTOP6A1 (GSE6812; 6 samples) and OsTOP6A3 and OsTOP6B (GSE5465; 6 samples) cDNAs
5. 9,679 expressed sequence tags (ESTs) of Polypleurum stylosum submitted to dbEST database (accession no. EH624491- EH628365, EW701866-EW702541 and FK260237-FK265364).
6. Contributed annotations of early auxin-responsive GH3, Aux/IAA and SAUR, cytokinin-responsive type-A response regulator, topoisomerase 6, and F-box protein-encoding gene families to the Community Annotation of Gene Families at Rice Genome Annotation Project website ().
7. Several cDNA sequences encoding type-A response regulators, topoisomerase 6 subunits, REC14, Aux/IAA, glutathione S-transferases, and F-box proteins in rice submitted to EMBL database.
(MUKESH JAIN)[pic]
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