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鈥檚 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鈥檚 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鈥檚 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鈥攐ut of many separate streams of biological information鈥攁 single, integrated cyber-鈥渒nowledgebase鈥 for plants and microbial life.
Uplands Farm: Grounds for discovery
November 12, 2025
How a 12-acre research station is inspiring innovations needed to feed and fuel the world far into the future.
CSHL goes to the White House for Easter EGGucation
April 8, 2024
CSHL plant scientists taught kids the basics of plant biology and its role in the environment at an event hosted by First Lady Jill Biden.
New CSHL website brings together sorghum researchers
May 9, 2022
Plant researchers and breeders are now using a website created by CSHL to get the latest intel on sorghum crop research.
The race to protect sweet corn
April 22, 2022
Breeding a variety that can withstand disease and taste better too
Do you have the dirt on plant research?
March 31, 2022
New research is constantly sprouting. Take this quiz and test your plant knowledge.
The secret history of corn is revealed in its genome
August 5, 2021
For the first time, scientists have assembled in-depth maps of dozens of corn genomes, filling in gaps related to key agricultural traits.
Teachers make genomes more useful鈥 from home
May 21, 2020
Researchers and educators participated in an online annotation jamboree to help researchers understand the corn genome.
CSHL investigators rank among world鈥檚 most highly cited
December 11, 2019
Seven researchers affiliated with CSHL are among the scientists producing the top 1 percent of the most highly-cited research in the world.
Researchers double sorghum grain number to improve food supply
October 30, 2019
A set of hormone-controlling genes may be the key to doubling grain number in sorghum plants.
Leading discovery
May 20, 2019
Current discoveries about DNA and human genome position CSHL scientists to make life-changing breakthroughs that will improve the human condition.
All Publications
23 Jul 2025 | Nature Communications | 16(1):6790
Cahn, Jonathan; Regulski, Michael; Lynn, Jason; Ernst, Evan; de Santis Alves, Cristiane; Ramakrishnan, Srividya; Chougule, Kapeel; Wei, Sharon; Lu, Zhenyuan; Xu, Xiaosa; Ramu, Umamaheswari; Drenkow, Jorg; Danyko, Cassidy; Kramer, Melissa; Seetharam, Arun; Hufford, Matthew; McCombie, W; Ware, Doreen; Jackson, David; Schatz, Michael; Gingeras, Thomas; Martienssen, Robert;
22 May 2025 | Plant Biology
Mishra, A; Bhat, A; Kumari, S; Sharma, R; Braynen, J; Tadesse, D; El Alaoui, S; Seaver, S; Grosjean, N; Ware, D; Xie, M; Paape, T;
4 Apr 2025 | Database : the journal of biological databases and curation | 2025
Wei, Sharon; Chougule, Kapeel; Olson, Andrew; Lu, Zhenyuan; Tello-Ruiz, Marcela; Kumar, Vivek; Kumari, Sunita; Zhang, Lifang; Olson, Audra; Kim, Catherine; Gladman, Nick; Ware, Doreen;
25 Mar 2025 | bioRxiv
Zali, Narges; El Damerash, Osama; Chougule, Kapeel; Lu, Zhenyuan; Ware, Doreen; Stillman, Bruce;
20 Feb 2025 | bioRxiv
Contreras-Moreira, Bruno; Sharma, Eshan; Saraf, Shradha; Naamati, Guy; Gupta, Parul; Elser, Justin; Chebotarov, Dmytro; Chougule, Kapeel; Lu, Zhenyuan; Wei, Sharon; Olson, Andrew; Tsang, Ian; Lodha, Disha; Zhou, Yong; Yu, Zhichao; Zhao, Wen; Zhang, Jianwei; Amberkar, Sandeep; Sue-Ob, Kawinnat; Martin, Maria; McNally, Kenneth; Ware, Doreen; Sun, Zhi; Deutsch, Eric; Copetti, Dario; Wing, Rod; Jaiswal, Pankaj; Dyer, Sarah; Jones, Andrew;
30 Dec 2024 | Nature Communications | 15(1):10854
Cahn, Jonathan; Regulski, Michael; Lynn, Jason; Ernst, Evan; de Santis Alves, Cristiane; Ramakrishnan, Srividya; Chougule, Kapeel; Wei, Sharon; Lu, Zhenyuan; Xu, Xiaosa; Ramu, Umamaheswari; Drenkow, Jorg; Kramer, Melissa; Seetharam, Arun; Hufford, Matthew; McCombie, W; Ware, Doreen; Jackson, David; Schatz, Michael; Gingeras, Thomas; Martienssen, Robert;
28 Nov 2024 | Frontiers in Genetics | 15:1460351
Kapoor, Muskan; Ventura, Enrique; Walsh, Amy; Sokolov, Alexey; George, Nancy; Kumari, Sunita; Provart, Nicholas; Cole, Benjamin; Libault, Marc; Tickle, Timothy; Warren, Wesley; Koltes, James; Papatheodorou, Irene; Ware, Doreen; Harrison, Peter; Elsik, Christine; Yordanova, Galabina; Burdett, Tony; Tuggle, Christopher;
6 Nov 2024 | Genome Research
Koren, Sergey; Bao, Zhigui; Guarracino, Andrea; Ou, Shujun; Goodwin, Sara; Jenike, Katharine; Lucas, Julian; McNulty, Brandy; Park, Jimin; Rautiainen, Mikko; Rhie, Arang; Roelofs, Dick; Schneiders, Harrie; Vrijenhoek, Ilse; Nijbroek, Koen; Nordesjo, Olle; Nurk, Sergey; Vella, Mike; Lawrence, Katherine; Ware, Doreen; Schatz, Michael; Garrison, Erik; Huang, Sanwen; McCombie, William; Miga, Karen; Wittenberg, Alexander; Phillippy, Adam;
10 Oct 2024 | Journal of Biological Chemistry | :107888
Grosjean, Nicolas; Zhang, Lifang; Kumaran, Desigan; Xie, Meng; Fahey, Audrey; Santiago, Kassandra; Hu, Fangle; Regulski, Michael; Blaby, Ian; Ware, Doreen; Blaby-Haas, Crysten;
25 Sep 2024 | bioRxiv
Gladman, Nicholas; Kumari, Sunita; Fahey, Audrey; Regulski, Michael; Ware, Doreen;