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.

See all Ware news

All Publications

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype

2 May 2023 | G3: Genes, Genomes, Genetics | 13(5):jkad067
Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela, Vitulo, Nicola, Ware, Doreen, Rustenholz, Camille, Whiteman, N

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.

21 Mar 2023 | Nature Communications | 14(1):1567
Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod

Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

12 Jan 2023 | Current Opinion in Biotechnology | 79:102886
Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William, Ware, Doreen

Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes

2022 | Frontiers in Plant Science | 13:1040909
Voelker, William, Krishnan, Krittika, Chougule, Kapeel, Alexander, Louie, Lu, Zhenyuan, Olson, Andrew, Ware, Doreen, Songsomboon, Kittikun, Ponce, Cristian, Brenton, Zachary, Boatwright, J, Cooper, Elizabeth

Toward a Data Infrastructure for the Plant Cell Atlas

6 Oct 2022 | Plant Physiology
Fahlgren, Noah, Kapoor, Muskan, Yordanova, Galabina, Papatheodorou, Irene, Waese, Jamie, Cole, Benjamin, Harrison, Peter, Ware, Doreen, Tickle, Timothy, Paten, Benedict, Burdett, Tony, Elsik, Christine, Tuggle, Christopher, Provart, Nicholas

Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis

4 Aug 2022 | International Journal of Molecular Sciences | 23(15):8665
Lee, Young, Kumari, Sunita, Olson, Andrew, Hauser, Felix, Ware, Doreen

Sorghum root epigenetic landscape during limiting phosphorus conditions

14 May 2022 | Plant Direct | 6(5):e393
Gladman, Nicholas, Hufnagel, Barbara, Regulski, Michael, Liu, Zhigang, Wang, Xiaofei, Chougule, Kapeel, Kochian, Leon, Magalhães, Jurandir, Ware, Doreen

Transcriptional regulation of primary and specialized metabolism

13 May 2022 | The FASEB Journal | 36(S1)
Brady, Siobhan

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

19 Apr 2022 | Genome Biology | 23(1):101
Ferrero-Serrano, Ángel, Sylvia, Megan, Forstmeier, Peter, Olson, Andrew, Ware, Doreen, Bevilacqua, Philip, Assmann, Sarah

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

See more publications