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8 results on '"Quezada-Rodríguez, Elsa H"'

1. Vision, challenges and opportunities for a Plant Cell Atlas.

Author

Plant Cell Atlas Consortium, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-Shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer An, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, and Rhee, Seung Y

Subjects
Plant Cell Atlas Consortium, 4D imaging, A. thaliana, Plant Cell Atlas, cell biology, chlamydomonas reinhardtii, location-to-function, maize, science forum, single-cell omics, translational research, Biochemistry and Cell Biology
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

2. Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions

Author

Hafner, Alenka, primary, DeLeo, Victoria, additional, Deng, Cecilia, additional, Elsik, Christine G., additional, Fleming, Damarius, additional, Harrison, Peter W., additional, Kalbfleisch, Theodore S., additional, Petry, Bruna, additional, Pucker, Boas, additional, Quezada-Rodríguez, Elsa H., additional, Tuggle, Christopher K., additional, and Koltes, James, additional

Published
2024
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3. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Author

National Science Foundation (US), National Institute of Food and Agriculture (US), Deng, Cecilia H. [0000-0002-2954-762X], Naithani, Sushma [0000-0001-7819-4552], Kumari, Sunita [0000-0001-9166-1450], Cobo-Simón, Irene [0000-0002-7648-7471], Quezada-Rodríguez, Elsa H. [0000-0001-7789-4987], Skrabisova, Maria [0000-0003-2879-1062], Gladman, Nick [0000-0002-9000-8377], Correll, Melanie J. [0000-0002-2432-6107], Sikiru, Akeem Babatunde [0000-0003-4956-7094], Marrano, Annarita [0000-0001-9560-2706], Rebollo, Ines [0000-0002-9899-0801], Jung, Sook [0000-0003-3968-2769], Deng, Cecilia H., Naithani, Sushma, Kumari, Sunita, Cobo-Simón, Irene, Quezada-Rodríguez, Elsa H., Skrabisova, Maria, Gladman, Nick, Correll, Melanie J., Sikiru, Akeem Babatunde, Afuwape, Olusola, Marrano, Annarita, Rebollo, Ines, Zhang, Wentao, Jung, Sook, National Science Foundation (US), National Institute of Food and Agriculture (US), Deng, Cecilia H. [0000-0002-2954-762X], Naithani, Sushma [0000-0001-7819-4552], Kumari, Sunita [0000-0001-9166-1450], Cobo-Simón, Irene [0000-0002-7648-7471], Quezada-Rodríguez, Elsa H. [0000-0001-7789-4987], Skrabisova, Maria [0000-0003-2879-1062], Gladman, Nick [0000-0002-9000-8377], Correll, Melanie J. [0000-0002-2432-6107], Sikiru, Akeem Babatunde [0000-0003-4956-7094], Marrano, Annarita [0000-0001-9560-2706], Rebollo, Ines [0000-0002-9899-0801], Jung, Sook [0000-0003-3968-2769], Deng, Cecilia H., Naithani, Sushma, Kumari, Sunita, Cobo-Simón, Irene, Quezada-Rodríguez, Elsa H., Skrabisova, Maria, Gladman, Nick, Correll, Melanie J., Sikiru, Akeem Babatunde, Afuwape, Olusola, Marrano, Annarita, Rebollo, Ines, Zhang, Wentao, and Jung, Sook

Abstract

Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

Published
2023

4. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Author

Deng, Cecilia H, primary, Naithani, Sushma, additional, Kumari, Sunita, additional, Cobo-Simón, Irene, additional, Quezada-Rodríguez, Elsa H, additional, Skrabisova, Maria, additional, Gladman, Nick, additional, Correll, Melanie J, additional, Sikiru, Akeem Babatunde, additional, Afuwape, Olusola O, additional, Marrano, Annarita, additional, Rebollo, Ines, additional, Zhang, Wentao, additional, and Jung, Sook, additional

Published
2023
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5. Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length

Author

López-Ruiz, Brenda Anabel, primary, Quezada-Rodríguez, Elsa H., additional, Piñeyro-Nelson, Alma, additional, Tovar, Hugo, additional, García-Ponce, Berenice, additional, Sánchez, María de la Paz, additional, Álvarez-Buylla, Elena R., additional, and Garay-Arroyo, Adriana, additional

Published
2022
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6. Vision, challenges and opportunities for a Plant Cell Atlas

Author

Ahmed, Jahed, Alaba, Oluwafemi, Ameen, Gazala, Arora, Vaishali, Arteaga-Vazquez, Mario A, Arun, Alok, Bailey-Serres, Julia, Bartley, Laura E, Bassel, George W, Bergmann, Dominique C, Bertolini, Edoardo, Bhati, Kaushal Kumar, Blanco-Touriñán, Noel, Briggs, Steven P, Brumos, Javier, Buer, Benjamin, Burlaocot, Adrien, Cervantes-Pérez, Sergio Alan, Chen, Sixue, Contreras-Moreira, Bruno, CORPAS, Francisco J, Cruz-Ramirez, Alfredo, Cuevas-Velazquez, Cesar L, Cuperus, Josh T, David, Lisa I, de Folter, Stefan, Denolf, Peter H, Ding, Pingtao, Dwyer, William P, Evans, Matthew MS, George, Nancy, Handakumbura, Pubudu P, Harrison, Maria J, Haswell, Elizabeth S, Herath, Venura, Jiao, Yuling, Jinkerson, Robert E, John, Uwe, Joshi, Sanjay, Joshi, Abhishek, Joubert, Lydia-Marie, Katam, Ramesh, Kaur, Harmanpreet, Kazachkova, Yana, Raju, Sunil K Kenchanmane, Khan, Mather A, Khangura, Rajdeep, Kumar, Ajay, Kumar, Arun, Kumar, Pankaj, Kumar, Pradeep, Lavania, Dhruv, Lew, Tedrick Thomas Salim, Lewsey, Mathew, Lin, Chien-Yuan, Liu, Dianyi, Liu, Le, Liu, Tie, Lokdarshi, Ansul, Luong, Ai My, Macaulay, Iain C, Mahmud, Sakil, Mähönen, Ari Pekka, Malukani, Kamal Kumar, Marand, Alexandre P, Martin, Carly A, McWhite, Claire D, Mehta, Devang, Martín, Miguel Miñambres, Mortimer, Jenny C, Nikolov, Lachezar A, Nobori, Tatsuya, Nolan, Trevor M, Ogden, Aaron J, Otegui, Marisa S, Ott, Mark-Christoph, Palma, José M, Paul, Puneet, Rehman, Atique U, Romera-Branchat, Maida, Romero, Luis C, Roth, Ronelle, Sah, Saroj K, Shahan, Rachel, Solanki, Shyam, Song, Bao-Hua, Sozzani, Rosangela, Stacey, Gary, Stepanova, Anna N, Taylor, Nicolas L, Tello-Ruiz, Marcela K, Tran, Tuan M, Tripathi, Rajiv Kumar, Vadde, Batthula Vijaya Lakshmi Vadde, Varga, Tamas, Vidovic, Marija, Walley, Justin W, Wang, Zhiyong, Weizbauer, Renate A, Whelan, James, Wijeratne, Asela J, Xiang, Tingting, Xu, Shouling, Yadegari, Ramin, Yu, Houlin, Yuan, Hai Ying, Zanini, Fabio, Zhao, Feng, Zhu, Jie, Zhuang, Xiaohong, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Brophy, Jennifer AN, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, and Rhee, Seung Y

Subjects
Uncategorized
Abstract

Note: for full list of Plant Cell Atlas Consortium, see publication (p17). With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021
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7. Vision, challenges and opportunities for a Plant Cell Atlas

Author

Plant Cell Atlas Consortium (ukupan broj autora: 110), Plant Cell Atlas Consortium, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer AN, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, Rhee, Seung Y, Rodgers, Peter, Loissel, Elsa, Vidović, Marija, Plant Cell Atlas Consortium (ukupan broj autora: 110), Plant Cell Atlas Consortium, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer AN, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, Rhee, Seung Y, Rodgers, Peter, Loissel, Elsa, and Vidović, Marija

Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

8. Vision, challenges and opportunities for a Plant Cell Atlas.

Author

Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JA, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, and Rhee SY

Subjects
Agriculture, Chlamydomonas reinhardtii, Chloroplasts, Computational Biology, Image Processing, Computer-Assisted, Plant Development, Plants classification, Plants genetics, Zea mays, Plant Cells physiology
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., Competing Interests: SJ, AB, BC, NF, AF, SH, PK, ML, NP, SR, MS, PA, AA, CA, SB, JB, PD, LD, ME, SG, FG, KK, DK, SK, AM, NN, TO, MO, GP, EQ, RS, RU, JW, KV, RW, DE, KB, SR No competing interests declared, (© 2021, Plant Cell Atlas Consortium et al.)

Published
2021
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