Chougule, Kapeel Publications

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Chougule, Kapeel

Number of items at this level: 17.

Paper

Gladman, Nicholas, Hufnagel, Barbara, Regulski, Michael, Liu, Zhigang, Wang, Xiaofei, Chougule, Kapeel, Kochian, Leon, Magalhães, Jurandir, Ware, Doreen (May 2022) Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct, 6 (5). e393. ISSN 2475-4455

Gladman, Nicholas, Olson, Andrew, Wei, Sharon, Chougule, Kapeel, Lu, Zhenyuan, Tello-Ruiz, Marcela, Meijs, Ivar, Van Buren, Peter, Jiao, Yinping, Wang, Bo, Kumar, Vivek, Kumari, Sunita, Zhang, Lifang, Burke, John, Chen, Junping, Burow, Gloria, Hayes, Chad, Emendack, Yves, Xin, Zhanguo, Ware, Doreen (January 2022) SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta: an international journal of plant biology, 255 (2). p. 35. ISSN 0032-0935

Yates, Andrew D, Allen, James, Amode, Ridwan M, Azov, Andrey G, Barba, Matthieu, Becerra, Andrés, Bhai, Jyothish, Campbell, Lahcen I, Carbajo Martinez, Manuel, Chakiachvili, Marc, Chougule, Kapeel, Christensen, Mikkel, Contreras-Moreira, Bruno, Cuzick, Alayne, Da Rin Fioretto, Luca, Davis, Paul, De Silva, Nishadi H, Diamantakis, Stavros, Dyer, Sarah, Elser, Justin, Filippi, Carla V, Gall, Astrid, Grigoriadis, Dionysios, Guijarro-Clarke, Cristina, Gupta, Parul, Hammond-Kosack, Kim E, Howe, Kevin L, Jaiswal, Pankaj, Kaikala, Vinay, Kumar, Vivek, Kumari, Sunita, Langridge, Nick, Le, Tuan, Luypaert, Manuel, Maslen, Gareth L, Maurel, Thomas, Moore, Benjamin, Muffato, Matthieu, Mushtaq, Aleena, Naamati, Guy, Naithani, Sushma, Olson, Andrew, Parker, Anne, Paulini, Michael, Pedro, Helder, Perry, Emily, Preece, Justin, Quinton-Tulloch, Mark, Rodgers, Faye, Rosello, Marc, Ruffier, Magali, Seager, James, Sitnik, Vasily, Szpak, Michal, Tate, John, Tello-Ruiz, Marcela K, Trevanion, Stephen J, Urban, Martin, Ware, Doreen, Wei, Sharon, Williams, Gary, Winterbottom, Andrea, Zarowiecki, Magdalena, Finn, Robert D, Flicek, Paul (November 2021) Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. ISSN 0305-1048

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

Vaughn, Justin N, Korani, Walid, Stein, Joshua C, Edwards, Jeremy D, Peterson, Daniel G, Simpson, Sheron A, Youngblood, Ramey C, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen H, McClung, Anna M, Scheffler, Brian E (March 2021) Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics, 17 (3). e1009389. ISSN 1553-7404

Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D'Eustachio, P., Stein, L. D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P. J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. (January 2021) Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49 (D1). D1452-d1463. ISSN 0305-1048 (Print)0305-1048

Liu, J., Seetharam, A.S., Chougule, K., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.R., Manchanda, N., Presting, G.G., Kudrna, D., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M. B., Dawe, R.K. (May 2020) Gapless Assembly of Maize Chromosomes Using Long-Read Technologies. Genome Biology, 21 (1). p. 121. ISSN 1474-7596

Ou, S. J., Liu, J. N., Chougule, K. M., Fungtammasan, A., Seetharam, A.S., Stein, J. C., Llaca, V., Manchanda, N., Gilbert, A. M., Wei, S. R., Chin, C. S., Hufnagel, D. E., Pedersen, S., Snodgrass, S. J., Fengler, K., Woodhouse, M., Walenz, B. P., Koren, S., Phillippy, A. M., Hannigan, B. T., Dawe, R. K., Hirsch, C. N., Hufford, M. B., Ware, D. (May 2020) Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications, 11 (1). p. 2288. ISSN 2041-1723

Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Buren, P. V., Ware, D. (February 2020) Variant phasing and haplotypic expression from long-read sequencing in maize. Commun Biol, 3 (1). p. 78. ISSN 2399-3642 (Public Dataset)

Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N., Hufford, M. B. (December 2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol, 20 (1). p. 275. ISSN 1474-7596 (Public Dataset)

Tello-Ruiz, M. K., Marco, C. F., Hsu, F. M., Khangura, R. S., Qiao, P., Sapkota, S., Stitzer, M. C., Wasikowski, R., Wu, H., Zhan, J., Chougule, K., Barone, L. C., Ghiban, C., Muna, D., Olson, A. C., Wang, L., Ware, D., Micklos, D. A. (October 2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS ONE, 14 (10). Article number e0224086. ISSN 19326203 (ISSN)

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., Ware, D. (August 2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics. e53. ISSN 1934-3396

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., Song, X., Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J. S. S., Talag, J., Danowitz, A., Rivera, L. F., Gschwend, A. R., Noutsos, C., Wu, C. C., Kao, S. M., Zeng, J. W., Wei, F. J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M. C., Lasserre, E., Cooke, R., Rosa Farias, D. D., da Maia, L. C., Dos Santos, R. S., Nyberg, K. G., McNally, K. L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K. K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y. C., Kurata, N., de Oliveira, A. C., Panaud, O., Jackson, S. A., Machado, C. A., Sanderson, M. J., Long, M., Ware, D., Wing, R. A. (January 2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet, 50 (2). pp. 285-296. ISSN 1061-4036

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048

Gupta, Parul, Naithani, Sushma, Tello-Ruiz, Marcela Karey, Chougule, Kapeel, D’Eustachio, Peter, Fabregat, Antonio, Jiao, Yinping, Keays, Maria, Lee, Young Koung, Kumari, Sunita, Mulvaney, Joseph, Olson, Andrew, Preece, Justin, Stein, Joshua, Wei, Sharon, Weiser, Joel, Huerta, Laura, Petryszak, Robert, Kersey, Paul, Stein, Lincoln D., Ware, Doreen, Jaiswal, Pankaj (November 2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8. pp. 10-15. ISSN 2214-6628

Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (January 2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Conference or Workshop Item

Tello-Ruiz, Marcela Karey, Wei, Sharon, Olson, Andrew, Gupta, Parul, Naithani, Sushma, Chougule, Kapeel, Kumari, Sunita, Kumar, Vivek, D'Eustachio, Peter, Papatheodorou, Irene, Contreras-Moreira, Bruno, Jaiswal, Pankaj, Ware, Doreen (September 2021) Gramene's Reference Genomes and Comparative Resources for Horticultural Species. In: Abstracts of Presentations from American Society of Horticultural Science 2021 Annual Conference.

This list was generated on Mon Oct 3 08:16:56 2022 EDT.
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