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PUBLICATIONS

(A). Refereed and Peer-reviewed Research and Review Articles.

  1. Naithani S. P. Gupta, J. Preece, P. D'Eustachio, J. Elser, J. Kiff, P. Garg, D.A. Dikeman$, A.J. Olson, S. Wei, M.K. Tello-Ruiz, J. Cook, A. Fabregat, T. Cheng, E. Bolton, A.F. Muñoz-Pomer, S. Mohammed, I. Papatheodorou, L. Stein, D. Ware, and P. Jaiswal (2020). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 48(D1): D1093-D1103. https://doi.org/10.1093/nar/gkz996
  2. Howe K.L., B. Contreras-Moreira, N. De Silva, G. Maslen, W. Akanni, J. Allen, J. Alvarez-Jarreta, M. Barba, D.M. Bolser, L. Cambell, M. Carbajo, M. Chakiachvili, M. Christensen, C. Cummins, A. Cuzick, P. Davis, S. Fexova, A. Gall, N. George, L. Gil, P. Gupta, K. E. Hammond-Kosack, E. Haskell, S. E. Hunt, P. Jaiswal, S. H. Janacek, P. J. Kersey, N. Langridge, U. Maheswari, T. Maurel, M. D. McDowall, B. Moore, M. Muffato, G. Naamati, S. Naithani, A. Olson, I. Papatheodorou, M. Patricio, M. Paulini, H. Pedro, E. Perry, J. Preece, M. Rosello, M. Russell, V. Sitnik, D. M. Staines, J. Stein, M. K. Tello-Ruiz, S. J. Trevanion, M. Urban, S. Wei, D. Ware, G. Williams, A. D. Yates, P. Flicek (2020). Ensembl Genomes 2020—enabling non-vertebrate genomic research. Nucleic Acids Res. 48(D1): D689-D695. https://doi.org/10.1093/nar/gkz890 
  3. Naithani S., P. Gupta, J. Preece, P. Garg, V. Fraser, L.K. Padgitt-Cobb, M. Martin, K. Vining and P. Jaiswal (2019). Involving community in genes and pathway curation. Database, 2019:1-8, https://doi.org/10.1093/database/bay146.
  4. Harper L., J. Campbell, E. K.S. Cannon, S. Jung, M. Poelchau, R. Walls, C. Andorf, E. Arnaud, T. Berardini, C. Birkett, S. Cannon, J. Carson, B. Condon, L. Cooper, N. Dunn, C. G. Elsik, A. Farmer, S. P. Ficklin, D. Grant, E. Grau, N. Herndon, Z.-L. Hu, J. Humann, P. Jaiswal, C. Jonquet, M.-A. Laporte, P. Larmande, G. Lazo, F. McCarthy, N. Menda, C. Mungall, M. Munoz-Torres, S. Naithani, et al. (2018). AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, 2018:1-32, https://doi.org/10.1093/database/bay088.
  5. Tello-Ruiz M.K., S. Naithani, J. C. Stein, P. Gupta, M. Campbell, A. Olson, S. Wei, J. Preece, M.J. Geniza, Y. Jiao, Y.K. Lee, B. Wang, J. Mulvaney, K. Chougule, J. Elser, N. Al-Bader, S. Kumari, J. Thomason, V. Kumar, D.M. Bolser, G. Naamati, E. Tapanari, N. Fonseca, L. Huerta, H. Iqbal, M. Keays, A. Munoz-Pomer Fuentes, A. Tang, A. Fabregat, P. D'Eustachio, J. Weiser, L.D. Stein, R. Petryszak, I. Papatheodorou, P.J. Kersey, P. Lockhart, C. Taylor, P. Jaiswal and D. Ware (2018). Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46(D1): D1181-D1189, https://doi.org/10.1093/nar/gkx1111.
  6. Naithani S., J. Preece, P. D'Eustachio, P. Gupta, V. Amarasinghe, P. D. Dharmawardhana, G. Wu, A. Fabregat, J. L. Elser, J. Weiser, M. Keays, A. M.-P. Fuentes, R. Petryszak, L. D. Stein, D. Ware and P. Jaiswal (2017). Plant Reactome: A resource for plant pathways and comparative analysis.  Nucleic Acids Res., 4: 45(D1): D1029-D1039. https://doi.org/10.1093/nar/gkw932.
  7. Naithani S., M. Geniza, and P. Jaiswal (2017): Variant Effect Prediction analysis using resources available at Gramene database. Methods in Molecular Biology (in "Plant Genomics Databases" series), 1533:279-2297, Aalt-Jan van Dijk ed., Springer, New York, ISBN- 978-1-4939-6656-1. https://doi.org/10.1007/978-1-4939-6658-5_17.
  8. Naithani S., and P. Jaiswal (2017). Pathway Analysis and Omics Data Visualization using Pathway Genome Databases: FragariaCyc, a Case Study. Methods in Molecular Biology (in "Plant Genomics Databases" series), 1533: 241-256, Aalt- Jan van Dijk ed., Springer, New York, ISBN- 978-1-4939-6656-1. https://doi.org/10.1007/978-1-4939-6658-5_14 .
  9. Naithani S., H. Nonogaki and P. Jaiswal (2017). Exploring crossroads between seed development and stress-response. In “Mechanism of Plant Hormone Signaling under Stress”, 1st edition, Girdhar K. Pandey ed., Wiley-Blackwell. https://doi.org/10.1002/9781118889022.ch32.Year 2016
  10. Gupta P., S. Naithani, M. K. Tello-Ruiz, K. Chougule, P. D’Eustachio, A. Fabregat, Y. Jiao, M. Keays, Y-K Lee, S. Kumari, J. Mulvaney, A. Olson, J. Preece, J. Stein, S. Wei, J. Weiser, R. Petryszak, P. Kersey, L. D. Stein, D. Ware, and P. Jaiswal (2016): Gramene database: Navigating plant comparative genomics resources. Curr. Plant Biol., 7-8: 10-15. https://doi.org/10.1016/j.cpb.2016.12.005
  11. Adam-Blondon A.-F., M. Alaux, C. Pommier, D. Cantu, Z.-M. Cheng, G. Cramer, C. Davies, S. Delrot, L. Deluc, G. D. Gaspero, J. Grimplet, A. Fennell, J. Londo, P. Kersey, F. Mattivi, S. Naithani, P. Neveu, M. Nikolski, M. Pezzotti, B. I. Reisch, R. Toepfer, M. Vivier, D. Ware, and H. Quesneville (2016). Towards an open grapevine information system. Horticulture Research, 3, 16056; https://doi.org/10.1038/hortres.2016.56.
  12. Naithani S., C.M. Partipilo, R. Raja, J. Elser and Pankaj Jaiswal (2016). FragariaCyc: a metabolic pathways database for woodland strawberry Fragaria vesca. Frontiers in Plant Science. 7: 242-. https://doi.org/10.3389/fpls.2016.00242.
  13. Tello-Ruiz M.K., J. Stein, X-H Wei, J. Preece, A. Olson, S. Naithani, V. Amarasinghe, P. Dharmawardhana, Y-P Jiao, J. Mulvaney, S. Kumari, K. Chougule, J. Elser, B. Wang, J. Thomason, D. Bolser, A. Kerhornou, B. Walts, N. Fonseca, L H. Martinez, M. Keays, A. Tang, H. Parkinson, P. D'Eustachio, G. Wu, L. Stein, R. Petryszak, P. Kersey, and P. Jaiswal (2016). ‘Gramene 2016: Comparative Plant Genomics and Pathway Resources’. Nucleic Acids Res., 4;44(D1): D1133-40. https://doi.org/10.1093/nar/gkv1179.
  14. Naithani S., R. Raja, E.N. Waddell, J. Elser, S. Gouthu, L.G. Deluc and P. Jaiswal (2014). VitisCyc, a metabolic pathways knowledgebase for grapevine (Vitis vinifera). Frontiers in Plant Science, 5: 1, https://doi.org/10.3389/fpls.2014.00644.
  15. Vining K.J., E. Romanel, R.C. Jones, A. Klocko, M. Alves-Ferreira, C.A. Hefer, V. Amarasinghe, P. Dharmawardhana, S. Naithani, M. Ranik, J. Wesley-Smith, L. Solomon, P. Jaiswal, A.A. Myburg and S. Strauss (2014). The floral Transcriptome of Eucalyptus grandis. New Phytology, 206:1406-1422, https://doi.org/10.1111/nph.13077.
  16. Myburg A.A., D. Grattapaglia, G.A. Tuskan, U. Hellsten, R.D. Hayes, G.J.J. Jenkins, E. Lindquist, H. Tice, D. Bauer, D.M. Goodstein, I. Dubchak, A. Poliakov, E. Mizrachi, A.R.K. Kullan, I.V. Jaarsveld, S.G. Hussey, D. Pinard, K.V.D. Merwe, P. Singh, O.B. Silva-Junior, R.C. Togawa, M.R. Pappas, D.A. Faria, C.P. Sansaloni, C.D. Petroli, X. Yang, P. Ranjan, T.J. Tschaplinski, C.-Y. Ye, T. Li, L. Sterck, K. Vanneste, F. Murat, M. Soler, H.S. Clemente, N. Saidi, H. Cassan-Wang, C. Dunand, C.A. Hefer, E. Bornberg-Bauer, A.R. Kersting, K. Vining, V. Amarasinghe, M. Ranik, S. Naithani, et al. (2014). The genome of Eucalyptus grandis - a global tree for fiber and energy. Nature, 19; 510(7505): 356-362. https://doi.org/10.1038/nature13308.
  17. Fox S.E., M. Geniza, M. Hanumappa, S. Naithani, C. Sullivan, J. Preece, V.K. Tiwari, J. Elser, J.M. Leonard, A. Sage, C. Gresham, A. Kerhornou, D. Bolser, F. McCarthy, P. Kersey, G.R. Lazo and P. Jaiswal (2014). De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS ONE, 12;9(5): e96855. https://doi.org/10.1371/journal.pone.0096855.
  18. Monaco M.K., J. Stein, S. Naithani, S. Wei, P. Dharmawardhana, S. Kumari, V. Amarasinghe, K. Youens-Clark, J. Thomason, J. Preece, S. Pasternak, A. Olson, Y. Jiao, Z. Lu, D. Bolser, A. Kerhornou, D. Staines, B. Walts, G. Wu, P. D'Eustachio, R. Haw, D. Croft, P.J. Kersey, L. Stein, P. Jaiswal, and D. Ware (2014). Gramene 2013: comparative plant genomics resources. Nucleic Acids Res., 42(Database issue): D1193-9. https://doi.org/10.1093/nar/gkt1110.
  19. Monaco M.K., Z.T. Sen, P. Dharmawardhana, L. Ren, M. Schaeffer, S. Naithani, V. Amarasinghe, J. Thomason, L. Harper, J. Gardiner, E.K.S. Cannon, C.J. Lawrence, D. Ware, and P. Jaiswal (2013). Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6: 1-12. https://doi.org/10.3835/plantgenome2012.09.0025.
  20. Naithani S., P. Dharmawardhana and J.B. Nasrallah (2013). SCR, in “Handbook of Biologically Active Peptides”, 2nd edition, Abba J. Kastin ed., Elsevier Publication, pp. 58-66. ISBN-13: 978-0123850959.
  21. Shulaev V., D.J. Sargent, R.N. Crowhurst, T. Mockler, R.E. Veilleux, O. Folkerts, A.L. Delcher, P. Jaiswal, A. Liston, S.P. Mane, P. Burns, K. Mockaitis, T.M. Davis, J.P. Slovin, N. Bassil, R.P. Hellens, C. Evans, R.V. Jensen, A.C. Allan, T.P. Michael, J.C. Setubal, J-M Celton, D.J.G. Rees, K.P. Williams, S.H. Holt, A. Dickerman, J.J.R. Rojas, M. Chatterjee, B. Liu, H. Silva, L. Meisel, A. Adavo, S. Filichkin, R. Velasco, M. Troggio, R. Viola, M. Borodovsky, T-L Ashman, A. Aharoni, J. Bennetzen, P. Dharmawardhana, J. Elser, R. Raja, H.D. Priest, D.W. Bryant Jr., S.E. Fox, A. Scott, S.A. Givan, S. Naithani, et al. (2011). The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43:109-116. https://doi.org/10.1038/ng.740.
  22. Jaiswal P., P. Dharmawardhana and S. Naithani (2010). A model plant genome database and comparative genomics. Acta Horticulturae, 859:31-41.
  23. Naithani S., T. Chookajorn, D.R. Ripoll and J.B. Nasrallah (2007). Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain. Proc. Natl. Acad. Sci., U S A, 104:12211-12216. https://doi.org/10.1073/pnas.0705186104 [Selected by faculty of 1000 Prime Biology; https://f1000.com/prime/1088221]
  24. Naithani S. D.R. Ripoll and J.B. Nasrallah (2006). The S-locus cysteine-rich peptide SCR/SP11. In “Handbook of Biologically Active Peptides”, Abba J. Kastin ed., Elsevier Publication, pp. 41-48. ISBN-13: 978-0123694423.
  25. Naithani S., S.A. Saracco, C. Butler and T.D. Fox (2003). Interactions among COX1, COX2 and COX3 mRNA-specific translational activator proteins on inner surface of mitochondrial inner membrane in S. cerevisiae. Molecular Biology of the Cell, 14:324-333. https://doi.org/10.1091/mbc.E02-08-0490.
  26. Johnson T.W., S. Naithani, C. Stewart, B. Zybailov, A.D. Jones, J.H. Golbeck and P.R. Chitnis (2003). The menD and menE homologues code for 2-succinyl-6-hydroxyl-2, 4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA ligase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803. Biochim. Biophys. Acta (Bioenergetics), 1557: 67-76. https://doi.org/10.1016/S0005-2728(02)00396-1.
  27. Naithani S., H.J. Mein and P.R. Chitnis (2000). Targeted inactivation of psaK1, psaK2 and psaM genes encoding subunits of photosystem I in the cyanobacterium Synechocystis sp. PCC 6803. Photosyn. Res., 63: 225-236. https://doi.org/10.1023/A:1006463932538
  28. Reddy M.S.S., S. Naithani, R. Tuli and P.V. Sane (2000). Diurnal regulation of plastid gene expression in Populus deltoides. India J. Biochem. Biophys., 37:453-445.
  29. Naithani S., P.K. Trivedi, R. Tuli and P.V. Sane (1997). The psbE-F-L-J operon from chloroplast genome of Populus deltoides: cloning, nucleotide sequence and transcript analysis. J. Genet, 76:61-72.
  30. Naithani S., P.K. Trivedi and P.V. Sane (1997). Characterization of orf31 (ycf7)-petG gene cluster from chloroplast genome of Populus deltoides. Biochem. Mol. Biol. Int., 43:433-442. https://doi.org/10.1080/15216549700204221.
  31. Tuli R., S. Naithani and H.S. Misra (1996). Cyanobacterial photosynthesis and the problem of oxygen in nitrogen fixation. J. Sci. Indus. Res., 55:638-657.

(B). Tributes:

  1. Naithani S., D. Arp, L. Ciuffetti, S. Coakley, D. Mills, D. Simpson, J. Spatafora, T. Wolpert, and D. Zobel (2019). Remembering Donald J. Armstrong (1937–2019). Curr. Plant Biol., 20: 2-5. https://doi.org/10.1016/j.cpb.2019.100130.
  2. Naithani S. and Govindjee (2018). Remembering Professor Prasanna K. Mohanty (April 1, 1934 – March 9, 2013), Curr. Plant Biol. 13: 2-5, https://doi.org/10.1016/j.cpb.2018.05.002.

(C). Editorial Articles:

  1. Naithani S. and D. Kumar (2020). Editorial for the Special Issue on Plant interactions with microbes and environment. Curr. Plant Biol., 23:1. https://doi.org/10.1016/j.cpb.2020.100168 .
  2. D. Edwards and S. Naithani (2020). Editorial for the Special Issue on AGRI2019. Curr. Plant Biol., 22:1. https://doi.org/10.1016/j.cpb.2020.100155.
  3. Naithani S. (2020). Editorial for the Special Issue on Plant Genomics and Bioinformatics. Curr. Plant Biol., 21: 1. https://doi.org/10.1016/j.cpb.2020.100142.
  4. Naithani S. (2019). A role of high-throughput data and predictive modeling in crop management. Curr. Plant Biol., 19:1, https://doi.org/10.1016/j.cpb.2019.100120.
  5. Naithani S. (2019) Editorial for the Special Issue on ‘Plant genomics and bioinformatics’. Curr. Plant Biol., 18:1, https://doi.org/10.1016/j.cpb.2019.100114.
  6. Naithani S. and D. Kumar (2018). Editorial for regular issue of Curr. Plant Biol., 16:1, https://doi.org/10.1016/j.cpb.2018.12.001.
  7. Naithani S. (2018) Exploring genomics and transcriptomics: the way forward in improving crops and other economically important plant species. Current Plant Biology, 14: 1, https://doi.org/10.1016/j.cpb.2018.10.002
  8. Naithani S. and D. Kumar (2018). Editorial for regular issue of Curr. Plant Biol., 13: 1. https://doi.org/10.1016/j.cpb.2018.06.001.
  9. Naithani S. and Albrecht A. (2017). Publisher’s note, Curr. Plant Biol., 9-10: 1. https://doi.org/10.1016/j.cpb.2017.08.001.
  10. Naithani S. (2017). Editorial for the special issue on Plant Development. Curr. Plant Biol., 9-10: 2. https://doi.org/10.1016/j.cpb.2017.08.002 .
  11. Naithani S. and Y. V. de Peer (2016). Genomic resources and databases for plant research community. Curr. Plant Biol., 7-8: 1. https://doi.org/10.1016/j.cpb.2016.12.007.
  12. Naithani S. (2016). Plants and global climate change: a need for sustainable agriculture. Current Plant Biology, 6: 1-1. https://doi.org/10.1016/j.cpb.2016.09.002.

(D). Presentations at Professional Meetings:

PRESENTATIONS: (Serving as presenting author)

  1. Naithani S., J. Preece, P. Gupta, P. D’Eustachio2, J. L. Elser, and P. Jaiswal (2019) Plant Reactome Knowledgebase: A Resource for Plant Synthetic Biology. 3rd International Plant Synthetic Biology, Bioengineering and Biotechnology, Cambridge, UK
  2. Naithani S., J. Preece, P. Gupta, P. D’Eustachio2, J. L. Elser, and P. Jaiswal (2019) Plant Reactome Knowledgebase: A Resource for Plant Synthetic Biology. Plant Genome Evolution 2019, Sitges, Spain
  3. Naithani S., J. Preece, P. Gupta and P. Jaiswal (2019) Involving the Research Community in Biocuration of Genes and Pathways. XXVII International Plant and Animal Genome Conference, San Diego, CA, USA.
  4. Naithani S., J. Preece, P. Gupta, J.L. Elser, P. D'Eustachio, A. Fabregat, J. Weiser, L. Stein, D. Ware, and P. Jaiswal (2017) Gramene's Plant Reactome portal: A resource for comparative plant pathway analysis. 10th International Biocuration Conference, Stanford University
  5. Naithani S., J. Preece, P. Gupta, P. D'Eustachio, J.L. Elser, S. Wei, R. Petryszak, P.J. Kersey, L. Stein, D. Ware, and P. Jaiswal (2017) Resources for Comparative Pathway Analysis for Grapevine. XXV International Plant and Animal Genome Conference, San Diego, CA, USA.
  6. Naithani S., C.M. Partipilo, R. Raja, J. Elser, and P. Jaiswal (2016) FragariaCyc: A Metabolic Pathway Network for Diploid Strawberry F. vesca. The XXIV International Plant and Animal Genome Conference, San Diego, CA, USA.
  7. Naithani S., C.M. Partipilo, B. Mohanty, L. Dong-Yup, and P. Jaiswal (2016) Rice Stress-Response Gene-Network: An Example of Community Curation in WikiPathways for Plants. The XXIV International Plant and Animal Genome Conference, San Diego, CA, USA.
  8. Naithani S., J. Elser, E.N. Waddell and Pankaj Jaiswal (2014) VitisCyc: A Metabolic Pathway Knowledgebase for Grape (Vitis vinifera). The XXIII International Plant and Animal Genome Conference, San Diego, California, USA.
  9. Naithani S., J. Elser, R. Rajani, P. Dharmawardhana, J. Preece, V. Amarasinghe, G. Wu, P. D'Eustachio, M.K. Monaco, D. Beorchia, K. Amoss, D. Croft, R. Haw, L. Stein, D. Ware, and P. Jaiswal (2013) Resources for plant metabolic network analyses: Gramene, VitisCyc, and FragariaCyc. Metabolic Pathway Analysis meeting, 16th-20th Sept. 2013, Corpus Christi College, Oxford, UK.
  10. Naithani, S., Dharmawardhana, P., Preece, J., Amarasinghe, V., Wu, G., Beorchia, D., Amoss, K., D'Eustachio, P., Nahal, H., Monaco, M., Croft, D., Haw, R., Provart, N., Hermjakob, H., Stein, L., Ware, D., Jaiswal, P. (2013) Plant Reactome: A Metabolic and Regulatory Networks Resource for Plants. System Biology: Networks meeting, March 13-16, 2013, Cold Spring Harbor Laboratory, New York.
  11. Naithani S., R. Raja, J. L. Elser, P. Dharmawardhana, D. Petty, L. G. Deluc and P. Jaiswal (2013). VitisCyc: A Species-Specific Metabolic Pathway Database for Grape (Vitis vinifera). The 2013 International Plant and Animal Genome Conference, San Diego, California, USA.
  12. Naithani S., R. Raja, J. Else, P. Dharmawardhana and P. Jaiswal (2011). Functional annotation of metabolic networks involved in strawberry fruit development. Plant Biology 2011 annual meeting, organized by ASPB, Minneapolis, MN, USA.
  13. Naithani S., T. Chookajorn, D.R. Ripoll and J.B. Nasrallah (2008). Structural modules for receptor- dimerization in the S-locus receptor kinase extracellular domain. Frontiers of Sexual Plant Reproduction III meeting, organized by University of Arizona, Tucson, AZ, USA.
  14. Naithani S., M. E. Nasrallah and J. B. Nasrallah. Specificity determinants of the Brassica self-incompatibility S-locus receptor kinase. Plant Biology 2005, annual meeting organized by ASPB.
  15. Naithani S., S.A. Saracco and T.D. Fox (2001). Interactions among COX1, COX2 and COX3 mRNA-specific translational activator proteins in S. cerevisiae. North East Regional Yeast meeting organized by University of Toronto, Toronto, ON, Canada.
  16. Naithani S., R. F. Reategui, T. W. Johnson, J.H. Golbeck and P. R. Chitnis: Cyanobacterial mutants in phylloquinone biosynthesis. 1999. 1st Annual Plant Biochemistry and Molecular biology. Iowa State University.
  17. Naithani S., R. F. Reategui, T.W. Johnson, J. H. Golback and P. R. Chitnis: Mutational analyses of men gene(s) in Synechocystis Sp. 6803. 1998. 24th Midwest Photosynthesis Meeting, Indiana.
  18. Naithani S., P.K. Trivedi, R. Tuli and P.V. Sane (1997). Characterization of the psbE-F-L-J operon from plastid genome of poplar. International Symposium on Crop Improvement and Biotechnology, organized by National Botanical Research Institute, Lucknow, Lucknow, India.
  19. Naithani S., R. Tuli, P. K. Trivedi and P.V. Sane: Characterization of 5’-region of the psbE gene from plastid genome of Populus deltoides, National Symposia organized by the Society of Biological Chemists 1996, organized by Indian Institute of Science, Bangalore, India.
  20. Naithani S., P. K. Trivedi, R. Tuli and P. V. Sane: Transcript analysis and promoter/terminator fusion studies of psbE operon from plastid genome of Populus deltoids. 1996. National Symposium organized by Society for Plant Biochemistry and Biotechnology, Haryana Agri. Univ., India.
  21. Naithani S., U. Pathre, R. Tuli and Sane P. V.: Nonsynonymous substitutions are under functional constraints in chloroplast genome during evolution, presented in XVIIIth All India Cell Biology Conference 1995, held at NBRI, Lucknow, India.

CONTRIBUTED PRESENTATIONS: (presented by a colleague or a collaborator)

  1. Tello-Ruiz M.K., A. Olson, S. Wei, J. Preece, P. Gupta, S. Naithani, B. Wang, K. Chougule, S. Kumari, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2020). Exploring the fluid gene space of plants using the Gramene comparative genomic and pathway resource. Biology of Genomes 2020 meeting (Virtual poster at CSHL, NY).
  2. Dikeman D.A., P. Garg and S. Naithani (2020): Evolutionary expansion, gene structure and expression of the rice (Oryza sativa) S-domain kinase (SD-RLK) gene family. XXVIII International Plant and Animal Genome Conference, San Diego, CA, USA.
  3. Gupta P., J. Preece, S. Naithani, P. D’Eustachio, J.L. Elser, A. Fabregat, L. Stein, D. Ware and P. Jaiswal (2019). Plant Reactome: Plant Pathway Network and Analysis Resource. Plant Biology 2019 meeting, San Jose, CA, USA.
  4. Tello-Ruiz M.K., S. Wei, A. Olson, J. Preece, J. Stein, P. Gupta, S. Naithani, Y. Jiao, B. Wang, K. Chougule, V. Kumar, S. Kumari, L. Zhang, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2019). Gramene: Unifying Comparative Genomics and Pathway Resources for Plant Communities” was presented at ASPB’s Plant Biology 2019 meeting, San Jose, CA, USA.
  5. Tello-Ruiz M.K., J. Stein, S. Wei, A. Olson, J. Preece, P. Gupta, S. Naithani, Y. Jiao, B. Wang, K. Chogule, V. Kumar, S. Kumari, L. Zhang, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2019). Arabidopsis Functional Comparative Analyses with Gramene. International Conference on Arabidopsis Research (ICAR 2019), Wuhan, China.
  6. Tello-Ruiz M.K., S. Wei, A. Olson, J. Preece, S. Naithani, P. Gupta, Y. Jiao, B. Wang, K. Chougule, V. Kumar, S. Kumari, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2019). Gramene: Unifying comparative genomics and pathway analysis. Plant Genomes, Systems & Engineering, Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
  7. Tello-Ruiz M.K., S. Wei, A. Olson, J. Preece, J. Stein, P. Gupta, S. Naithani, Y. Jiao, B. Wang, K. Chougule, V. Kumar, S. Kumari, L. Wang, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2019). Gramene: Unifying comparative genomics & pathway resources for plant communities. Genome Informatics 2019 meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
  8. Dikeman D.A., P. Garg, and S. Naithani (2019): Evolutionary expansion, gene structure and expression of the rice (Oryza sativa) S-domain kinase (SD-RLK) gene family. Genome Research and Biocomputing (CGRB) Fall Conference, Oregon State University, Corvallis, OR, USA.
  9. Tello-Ruiz M.K., S. Wei, A. Olson, J. Preece, J. Stein, P. Gupta, S. Naithani, Y. Jiao, B. Wang, K. Chougule, V. Kumar, S. Kumari, L. Zhang, P. D’Eustachio, B. Contreras, I. Papatheodorou, P. Jaiswal, and D. Ware (2019). Mining maize with Gramene. Maize Genetics Conference 2019, St. Louis, Missouri, USA
  10. Jaiswal P., S. Naithani, M.K. Tello-Ruiz, J. Preece, S. Wei, A. Olson, D. Bolser, P. Gupta, P., J. Stein, Y. Jiao, B. Wang, S. Kumari, L. Zhang, N. Al-Bader, D. Muna, P. D'Eustachio, I. Papatheodorou, and D. Ware. Gramene (2019): A comparative genomics resource leveraging genome to nucleotide to pathway-level views, searches and analysis across the plant tree of life. XXVII International Plant and Animal Genome Conference, San Diego, CA, USA.
  11. Preece J., S. Naithani, P. Gupta, J.L. Elser, P. D'Eustachio, A. Fabregat, J. Weiser, L. Stein, D. Ware and P. Jaiswal (2017) Plant Reactome: A resource for comparative plant pathway analysis. Systems Biology Networks conference, Cold Spring Harbor Laboratory, New York, NY, USA.
  12. Jaiswal P., J. Preece, P. Gupta, S. Naithani, P. D'Eustachio, J. Elser, L. Stein and D. Ware (2017) Plant Reactome: A Resource for Comparative analysis of Plant Pathways. The XXV International Plant and Animal Genome Conference, San Diego, CA, USA.
  13. Naithani S., J. Preece, P. D'Eustachio, J. Elser, P. Gupta, A. F. Mundo, J. Weiser, M.K. Tello-Ruiz, L. Stein, D. Ware, P. Jaiswal (2016) Plant Reactome: A Resource for Comparative Pathway Analysis. Biological Data Science Meeting, Cold Spring Harbor Laboratory, New York, NY, USA.
  14. Naithani S., J. Preece, P. D'Eustachio, J. L. Elser, P. Gupta, A. Fabregat, J. Weiser, S. McKay, L. Stein, D. Ware and P. Jaiswal (2016) Pathway Resources for Solanaceae crops. SolGenomics: From Advances to Applications, UC Davis, CA, USA.
  15. Gupta P., S. Naithani, J. Preece, P. D'Eustachio, J. L. Elser, A. Fabregat, J. Weiser, S. McKay, L. Stein, D. Ware and P. Jaiswal (2016) Plant Reactome: A resource for comparative plant pathway analysis. ICBO-BioCreative, Corvallis, OR, USA
  16. Preece P., S. Naithani, P. D'Eustachio, J. L. Elser, P. Gupta, A. Fabregat, J. Weiser, S. McKay, L. Stein, D. Ware and P. Jaiswal (2016) Plant Reactome: A resource for comparative plant pathway analysis. Plant Biology 2016 Meeting, Austin, Texas, USA
  17. Tello-Ruiz M.K., J. Stein, S. Wei, J. Preece, S. Naithani, A. Olson, Y. Jiao, J. Mulvaney, P. Gupta, S. Kumari, K. Chougule, J. Elser, B. Wang, J. Thomason, P. D’Eustachio, R. Petryszak, P. Kersey, P. Jaiswal, and D. Ware (2016) Gramene: a resource for comparative plant genomics and pathway analysis. Plant Biology 2016 meeting, Austin, Texas, USA
  18. Lee Y.K., M.K. Tello-Ruiz, J. Stein, S. Wei, J. Preece, S. Naithani, A. Olson, Y. Jiao, J. Mulvaney, P. Gupta, S. Kumari, L. Wang, K. Chougule, J. Elser, B. Wang, J. Thomason, P. D’Eustachio, R. Petryszak, P. Kersey, P. Jaiswal, and D. Ware (2016) Gramene: Comparative Plant Genomics and Pathway Resources at ICAR 2016 meeting, South Korea
  19. Tello-Ruiz M.K., J. Stein, S. Wei, J. Preece, S. Naithani, A. Olson, Y. Jiao, J. Mulvaney, P. Gupta, S. Kumari, K. Chougule, J. Elser, B. Wang, J. Thomason, P. D’Eustachio, R. Petryszak, P. Kersey, P. Jaiswal, and D. Ware (2016) Gramene: Comparative Plant Genomics and Pathway Resources at Biology of Genomes meeting, Cold Spring Harbor Laboratory, New York, NY, USA.
  20. Jaiswal P., J. Preece, P. D'Eustachio, S. Naithani, J. Elser, A.F. Mundo, J. Weiser, S. McKay, P. Gupta, L. Stein and D. Ware (2016) Plant Reactome: A Resource for Comparative Plant Pathway Analysis. The XXIV International Plant and Animal Genome Conference, San Diego, CA, USA.
  21. Preece J., S. Naithani, P. Gupta, A.F. Mundo, R. Haw, S. McKay, J. Weiser, P. D’Eustachio, L. Stein, P. Jaiswal and D. Ware (2015) Plant Reactome: A reference resource for analyzing plant metabolic and regulatory pathways. Plant Genomes and Biotechnology 2015 meeting at CSHL, NY, USA
  22. Jaiswal P., J. Preece, V. Amarasinghe, P. Dharmawardhana, P. D’Eustachio, S. Naithani, G. Wu, A.F. Mundo, R. Haw, S. McKay, J. Weiser, L. Stein and D. Ware (2015) Plant Reactome: A reference resource for analyzing plant metabolic and regulatory pathways, Genome Informatics 2015 meeting at CSHL, NY, USA
  23. Joshua S., S. Wei, J. Preece, S. Naithani, A. Olson, Y. Jiao, J. Mulvaney, M. Geniza, S. Kumari, K. Chougule, J. Elser, B. Wang, J. Thomason, P. D’Eustachio, R. Petryszak, P. Kersey, P. Jaiswal, D. Ware (2015) Gramene: Comparative Plant Genomics and Pathway Resources, Genome Informatics 2015 meeting at CSHL, NY, USA.
  24. Partipilo C.M., R. Raja, J. Elser, P. Jaiswal and S. Naithani (2015). FragariaCyc: a metabolic pathway knowledgebase for Fragaria vesca. The 2015 Center for Genome Research and Biocomputing (CGRB) Fall Conference, Oregon State University, Corvallis, OR, USA.
  25. Dharmawardhana, P., J. Preece, V. Amarasinghe, G. Wu, D. Beorchia, K. Amoss, S. Naithani, P. D'Eustachio, H. Nahal, M.K. Monaco, D. Croft, R. Haw, N. Provart, H. Hermjakob, L. Stein, D. Ware, and P. Jaiswal (2014). Plant Reactome: Metabolic and regulatory networks for plants. Molecular Life Sciences Poster Session, Oregon State University, Corvallis, OR, USA.
  26. Waddell E.N., S. Naithani, R. Raja, J. Elser, S. Gouthu, L.G. Deluc and P. Jaiswal (2014) VitisCyc, a metabolic pathways knowledgebase for grapevine (Vitis vinifera). Plant Biology 2014 annual meeting held at Portland, Oregon.
  27. Monaco M.K., V. Amarasinghe, P. Dharmawardhana, Y. Jiao, S. Kumari, S. Naithani, Pasternak S, Stein J, Thomason J, Wei S, Youens-Clark K, Stein L, Kersey P, Jaiswal P, Ware D (2014) 56th Annual Maize Genetics Conference.
  28. Wei S., V. Amarasinghe, P. Dharmawardhana, Y. Jiao, S. Kumari, M. K. Monaco, S. Naithani, A. Olson, S. Pasternak, J. Preece, J. Stein, J. Thomason, B. Wang, K. Youens-Clark, H. Parkinson, P.J. Kersey, P. Jaiswal, and D. Ware (2013) Gramene: A Resource for Comparative Plant Genomics. Plant Genomics & Biotechnology, Cold Spring Harbor Laboratory, New York.
  29. Stein J.C., V. Amarasinghe, P. Dharmawardhana, S. Kumari, M.K. Monaco, S. Naithani, A. Olson, J. Preece, J. Thomason, S. Wei, K. Youens-Clark, P. Kersey, L. Stein, P. Jaiswal, and D. Ware (2013) Gramene: A resource for comparative plant genomics. Biology of Genomes, Cold Spring Harbor Laboratory, New York
  30. Monaco M.K., V. Amarasinghe, P. Dharmawardhana, Y. Jiao, S. Kumari, S. Naithani. S., Pasternak, J. Stein, J. Thomason, S. Wei, K. Youens-Clark, L. Stein, P. Kersey, P. Jaiswal, and D. Ware (2013): Gramene Build 38: A Resource for Comparative Plant Genomics. Plant Biology 2013 annual meeting, organized by ASPB, Providence, RI, USA.
  31. Stein J.C., V. Amarasinghe, P. Dharmawardhana, Y. Jiao S. Kumari, M.K. Monaco, S. Naithani, A. Olson, S. Pasternak, J. Preece, J. Thomason, B. Wang, S. Wei, K. Youens-Clark, H. Parkinson, P. J. Kersey, P. Jaiswal, and D. Ware (2013). Gramene: An Integrated Phylogenomics Resource for the Oryza Genus. Plant Biology 2013 annual meeting, organized by ASPB, Providence, RI, USA.
  32. Monaco M.K., V. Amarasinghe, P. Dharmawardhana, Y. Jiao, S. Kumari, S. Naithani, S. Pasternak, J. Stein, J. Thomason, S. Wei, K. Youens-Clark, L. Stein, P.J. Kersey, P. Jaiswal and D. Ware (2013) Gramene: A Resource for Comparative Plant Genomics. Genome Informatics, Cold Spring Harbor Laboratory, New York, USA.
  33. Klocko A.L., K. Vining, V. Amarasinghe, E. Romanel, M. Alves-Ferreira, P. Dharmawardhana, S. Naithani, C. Sullivan, R. Jones, P. Jaiswal, M. Ranik, M. Hanumappa, J. Wesley-Smith, C.A. Hefer, A. Myburg, L. Solomon, S. Strauss (2013) Floral Transcriptome of Eucalyptus grandis. The 2013 International Plant and Animal Genome Conference, San Diego, California, USA.
  34. Dharmawardhana P., J. Preece, V. Amarasinghe, G. Wu, D. Beorchia, K. Amoss, S. Naithani, P. D'Eustachio, H. Nahal, M. K. Monaco, D. Croft, R. Haw, N. Provart, H. Hermjakob, L. Stein, D. Ware, and P. Jaiswal (2013) Plant Reactome: Metabolic and Regulatory Network for Plants. The 2013 International Plant and Animal Genome Conference, San Diego, California, USA.
  35. Jaiswal, P., V. Amarasinghe, E. Buckler, T. Casstevens, C. Chen, P. Dharmawardhana, S. Fox, M. Hanumappa, S. Kumari, S. McCouch, M.K. Monaco, S. Naithani, S. Pasternak, J. Stein, C. Sullivan, J. Thomason, D. Ware, S. Wei, K. Youens-Clark, and J. Zhang (2012) Gramene: A Community Resource for Comparative Rice and Plant Genomics. 10th Rice Functional Genomics, Chiang Mai, Thailand.
  36. Jaiswal, P. and S. Naithani. Using Gramene as a tool to explore and analyze user data on grape genomics (2012). 4th Grape Research Coordination Network Meeting, Oregon State University, Corvallis, OR, USA
  37. Monaco M., T. Sen, L. Ren, P. Dharmawardhana, M. Schaeffer, V. Amarasinghe, J. Thomason, L. C. Harper, S. Naithani, J. Gardiner, C.J. Lawrence, D. Ware and P. Jaiswal (2012) MaizeCyc: Metabolic Networks in Maize. The 2012 International Plant and Animal Genome Conference, San Diego, California, USA.
  38. Amarasinghe V., S. Naithani, R. Raja, P. Dharmawardhana and P. Jaiswal (2012) A Metabolic Network for Vitis vinifera. The 2012 International Plant and Animal Genome Conference, San Diego, California, USA.
  39. Rutschow H.L., S. Naithani , C. Cheong and K. J. van Wijk (2006). Implications of Arabidopsis thaliana Trigger Factor in chloroplast protein targeting and chaperone function, Plant Biology 2006 annual meeting, organized by ASPB.
  40. Trivedi P. K., R. Dixit, S. Naithani, R. Tuli and P. V. Sane. Organization and expression of the PSII genes from chloroplasts of Populus deltoides (1997). 5th International Congress of Plant Molecular Biology, Singapore.
  41. Dixit R., S. Naithani, P. K. Trivedi, R. Tuli and P. V. Sane: Expression studies of photosystem II genes from Populus deltoides, in International Symposium on Crop, Improvement, and Biotechnology 1997, organized by NBRI, Lucknow, India
  42. Tuli R., P.K. Trivedi, MSS Reddy , S. Naithani, Dixit R, Singh MP, and Sane PV: Studies on chloroplast genome and their application to plant transformation, In National Symposia on advances in plant Science held at Banaras Hindu University, India, Nov 1995.
  43. Dixit R., S. Naithani, M. S S. Reddy, P. K. Trivedi and P. V. Sane: Photosystem II genes from chloroplasts of Populus deltoides: cloning and nucleotide sequence analysis, presented in Annual symposia organized by Society for Plant Biochemistry and Biotechnology 1995 at Jaipur, India,
  44. Reddy M.S.S., S. Naithani, R Tuli and P. V. Sane: Organization and expression of petA gene in chloroplast genome of Populus deltoides, presented in XVIIIth All India Cell Biology Conference 1995, held at NBRI, Lucknow, India