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Doreen Ware

Doreen Ware

Adjunct Professor

Ph.D., Ohio State University, 2000

ware@cshl.edu | 516-367-6979

Ware Lab Website   Faculty Profile

When we think of evolution, we often think about physical changes, like a plant developing broader leaves to collect more solar energy. Such evolution actually occurs within the plant’s DNA. I am using computational analysis and modeling to visualize how plant genomes have evolved over time, particularly those of staple crops. We are learning from this work to improve the range and yield of modern plants.

Using multidisciplinary approaches that combine computational analysis, modeling, and prediction with experimental verification, Doreen Ware’s lab seeks a deeper understanding of the evolution of genome sequences in plants and their implications for agricultural improvement. By looking comparatively across the genomes of plants in the same lineage, they seek answers to the following questions: How are genes conserved and lost over time? What are the fates of duplicated genes? What is the impact of structural variation on phenotypic variation? Ware’s team also studies gene regulation in plants, focusing on gene regulatory networks, targeting transcription factors and microRNA genes with the objective of understanding how these parts of the plant genome work together in determining spatial and temporal expression of genes. The lab had an important role in the project to produce a haplotype map reference genome of maize, spearheading the most comprehensive analysis of the crop yet. This has provided important information on the variation of the reference genome, as well as comparative data showing changes in the genome acquired through domestication and breeding. They have devoted special attention to examining diversity within maize, grape, and tomato, aiming to accelerate the development of strategies to introduce new germplasm that is needed to meet demands of increasing population and a changing environment. The lab also has brought fully sequenced genomes into an integrated data framework, to enhance the power of their comparative studies. This past year, Ware was named as its principal investigator for the National Science Foundation-funded Gramene project, a comparative genomics resource for agriculturally important crops and models to support sustainable food and fuel production. Ware, as principal investigator for plants, has also helped lead an effort funded by the Department of Energy to create—out of many separate streams of biological information—a single, integrated cyber-“knowledgebase” for plants and microbial life.

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All Publications

Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.

8 Mar 2022 | Genome Biology | 23(1):76
Ou, Shujun, Su, Weijia, Liao, Yi, Chougule, Kapeel, Agda, Jireh, Hellinga, Adam, Lugo, Carlos, Elliott, Tyler, Ware, Doreen, Peterson, Thomas, Jiang, Ning, Hirsch, Candice, Hufford, Matthew

SorghumBase: a web-based portal for sorghum genetic information and community advancement.

11 Jan 2022 | Planta: an international journal of plant biology | 255(2):35
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

SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data

2022 | Methods in Molecular Biology | 2443:197-209
Wang, Liya, Lu, Zhenyuan, Van Buren, Peter, Ware, Doreen

Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

1 Jan 2022 | Methods in Molecular Biology | 2443:101-131
Tello-Ruiz, Marcela, Jaiswal, Pankaj, Ware, Doreen

Expression Atlas update: gene and protein expression in multiple species

24 Nov 2021 | Nucleic Acids Research
Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark, Nawijn, Martijn, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan, Brazma, Alvis, Papatheodorou, Irene

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

13 Nov 2021 | Nucleic Acids Research
Yates, Andrew, Allen, James, Amode, Ridwan, Azov, Andrey, Barba, Matthieu, Becerra, Andrés, Bhai, Jyothish, Campbell, Lahcen, Carbajo Martinez, Manuel, Chakiachvili, Marc, Chougule, Kapeel, Christensen, Mikkel, Contreras-Moreira, Bruno, Cuzick, Alayne, Da Rin Fioretto, Luca, Davis, Paul, De Silva, Nishadi, Diamantakis, Stavros, Dyer, Sarah, Elser, Justin, Filippi, Carla, Gall, Astrid, Grigoriadis, Dionysios, Guijarro-Clarke, Cristina, Gupta, Parul, Hammond-Kosack, Kim, Howe, Kevin, Jaiswal, Pankaj, Kaikala, Vinay, Kumar, Vivek, Kumari, Sunita, Langridge, Nick, Le, Tuan, Luypaert, Manuel, Maslen, Gareth, 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, Trevanion, Stephen, Urban, Martin, Ware, Doreen, Wei, Sharon, Williams, Gary, Winterbottom, Andrea, Zarowiecki, Magdalena, Finn, Robert, Flicek, Paul

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum.

11 Nov 2021 | Current Plant Biology | :100229
Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel, Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher, Arkin, Adam, Ware, Doreen

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.

6 Aug 2021 | Science | 373(6555):655-662
Hufford, Matthew, Seetharam, Arun, Woodhouse, Margaret, Chougule, Kapeel, Ou, Shujun, Liu, Jianing, Ricci, William, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher, Marand, Alexandre, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela, Piri, Rebecca, Wang, Na, Kim, Dong, Zeng, Yibing, O'Connor, Christine, Li, Xianran, Gilbert, Amanda, Baggs, Erin, Krasileva, Ksenia, Portwood, John, Cannon, Ethalinda, Andorf, Carson, Manchanda, Nancy, Snodgrass, Samantha, Hufnagel, David, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael, Kudrna, David, Llaca, Victor, Fengler, Kevin, Schmitz, Robert, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan, Hirsch, Candice, Ware, Doreen, Dawe, R

Ranked Choice Voting for Representative Transcripts with TRaCE

23 Jul 2021 | Bioinformatics
Olson, Andrew, Ware, Doreen

Gene disruption by structural mutations drives selection in US rice breeding over the last century.

Mar 2021 | PLoS Genetics | 17(3):e1009389
Vaughn, Justin, Korani, Walid, Stein, Joshua, Edwards, Jeremy, Peterson, Daniel, Simpson, Sheron, Youngblood, Ramey, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen, McClung, Anna, Scheffler, Brian

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