Colleen Doherty

Laosuntisuk, K., Vennapusa, A., Somayanda, I. M., Leman, A. R., Jagadish, S. V. K., & Doherty, C. J. (2024, January 30). A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses. PLANT JOURNAL, Vol. 1. https://doi.org/10.1111/tpj.16654

Land, E. S., Sheppard, J., Doherty, C. J., & Perera, I. Y. (2024). Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments. FRONTIERS IN PLANT SCIENCE, 14. https://doi.org/10.3389/fpls.2023.1308713

Schrickx, H. M., Gyurek, S., Moore, C., Hernandez-Pagan, E., Doherty, C. J., Kudenov, M. W., & Brendan T. O'Connor. (2024, February 8). Flexible Self-Powered Organic Photodetector with High Detectivity for Continuous On-Plant Sensing. ADVANCED OPTICAL MATERIALS, Vol. 2. https://doi.org/10.1002/adom.202400005

Krafft, D., Scarboro, C. G., Hsieh, W., Doherty, C., Balint-Kurti, P., & Kudenov, M. (2024). Mitigating Illumination-, Leaf-, and View-Angle Dependencies in Hyperspectral Imaging Using Polarimetry. Plant Phenomics. https://doi.org/10.34133/plantphenomics.0157

Laosuntisuk, K., Vennapusa, A., Somayanda, I. M., Leman, A. R., Jagadish, S. V. K., & Doherty, C. J. (2023, October 29). A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses. https://doi.org/10.1101/2023.10.28.564442

Tiwari, M., Kumar, R., Subramanian, S., Doherty, C. J., & Jagadish, S. V. K. (2023). [Review of Auxin-cytokinin interplay shapes root functionality under low-temperature stress]. TRENDS IN PLANT SCIENCE, 28(4), 447–459. https://doi.org/10.1016/j.tplants.2022.12.004

Yow, A. G., Laosuntisuk, K., Young, R. A., Doherty, C. J., Gillitt, N., Perkins-Veazie, P., … Iorizzo, M. (2023). Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple. SCIENTIFIC REPORTS, 13(1). https://doi.org/10.1038/s41598-023-45722-y

Kudenov, M. W., Krafft, D., Scarboro, C. G., Doherty, C. J., & Balint-Kurti, P. (2023). Hybrid spatial-temporal Mueller matrix imaging spectropolarimeter for high throughput plant phenotyping. APPLIED OPTICS, 62(8), 2078–2091. https://doi.org/10.1364/AO.483870

Laosuntisuk, K., Elorriaga, E., & Doherty, C. J. (2023). [Review of The Game of Timing: Circadian Rhythms Intersect with Changing Environments]. ANNUAL REVIEW OF PLANT BIOLOGY, 74, 511–538. https://doi.org/10.1146/annurev-arplant-070522-065329

Horvath, D. P., Doherty, C. J., Desai, J., Clark, N., Anderson, J. V., & Chao, W. S. (2023). Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions. AOB PLANTS, 15(3). https://doi.org/10.1093/aobpla/plad013

Laosuntisuk, K., Desai, J. S., & Doherty, C. J. (2022, May 13). Arabidopsis cell suspension culture that lacks circadian rhythms can be recovered by constitutive ELF3 expression (Vol. 5). Vol. 5. https://doi.org/10.1101/2022.05.12.491735

Knight, M. S., Doherty, C. J., & Nielsen, D. M. (2022, December 2). Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data. https://doi.org/10.1101/2022.12.01.518235

Tolsma, J. S., Torres, J. J., Richards, J. T., Perera, I. Y., & Doherty, C. J. (2022). Evaluating the Effects of the Circadian Clock and Time of Day on Plant Gravitropic Responses. PLANT GRAVITROPISM, Vol. 2368, pp. 301–319. https://doi.org/10.1007/978-1-0716-1677-2_19

Scarboro, C. G., Doherty, C. J., Balint-Kurti, P. J., & Kudenov, M. W. (2022). Multistatic fiber-based system for measuring the Mueller matrix bidirectional reflectance distribution function. APPLIED OPTICS, 61(33), 9832–9842. https://doi.org/10.1364/AO.470608

Laosuntisuk, K., & Doherty, C. J. (2022). [Review of The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures]. BIOCHEMICAL SOCIETY TRANSACTIONS, 50(3), 1151–1165. https://doi.org/10.1042/BST20190572

Kudenov, M. W., Krafft, D., Scarboro, C. G., Doherty, C. J., & Balint-Kurti, P. (2021). Fieldable Mueller matrix imaging spectropolarimeter using a hybrid spatial and temporal modulation scheme. POLARIZATION SCIENCE AND REMOTE SENSING X, Vol. 11833. https://doi.org/10.1117/12.2593970

Bheemanahalli, R., Knight, M., Quinones, C., Doherty, C. J., & Jagadish, S. V. K. (2021). Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice. SCIENTIFIC REPORTS, 11(1). https://doi.org/10.1038/s41598-021-85921-z

Scarboro, C. G., Ruzsa, S. M., Doherty, C. J., & Kudenov, M. W. (2021). Quantification of gray mold infection in lettuce using a bispectral imaging system under laboratory conditions. PLANT DIRECT, 5(3). https://doi.org/10.1002/pld3.317

Tolsma, J. S., Ryan, K. T., Torres, J. J., Richards, J. T., Richardson, Z., Land, E. S., … Doherty, C. J. (2021). The Circadian-clock Regulates the Arabidopsis Gravitropic Response. Gravitational and Space Research. https://doi.org/10.2478/gsr-2021-0014

Sheppard, J., Land, E. S., Toennisson, T. A., Doherty, C. J., & Perera, I. Y. (2021). Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots. LIFE-BASEL, 11(10). https://doi.org/10.3390/life11101010

Desai, J. S., Lawas, L. M. F., Valente, A. M., Leman, A. R., Grinevich, D. O., Jagadish, S. V. K., & Doherty, C. J. (2021). Warm nights disrupt transcriptome rhythms in field-grown rice panicles. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(25). https://doi.org/10.1073/pnas.2025899118

Vennapusa, A. R., Somayanda, I. M., Doherty, C. J., & Jagadish, S. V. K. (2020). A universal method for high-quality RNA extraction from plant tissues rich in starch, proteins and fiber. SCIENTIFIC REPORTS, 10(1). https://doi.org/10.1038/s41598-020-73958-5

Current status of the multinational Arabidopsis community. (2020). Plant Direct, 4(7). https://doi.org/10.1002/pld3.248

Scarboro, C. G., Ruzsa, S. M., Doherty, C. J., & Kudenov, M. W. (2020, April 25). Detection of Gray Mold Infection in Plants Using a Multispectral Imaging System (Vol. 4). Vol. 4. https://doi.org/10.1101/2020.04.23.051300

Slabaugh, E., Desai, J. S., Sartor, R. C., Lawas, L. M. F., Krishna Jagadish, S. V., & Doherty, C. J. (2019). Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. RNA, 25(6), 669–684. https://doi.org/10.1261/rna.070227.118

Doherty, C., Friesner, J., Gregory, B., Loraine, A., Megraw, M., Meyers, B. C., … Wurtele, E. (2019). Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. PLANT DIRECT, 3(1). https://doi.org/10.1002/pld3.109

Argueso, C. T., Assmann, S. M., Birnbaum, K. D., Chen, S., Dinneny, J. R., Doherty, C. J., … Williams, C. M. (2019). Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct, 3(4), e00133. https://doi.org/10.1002/pld3.133

Moghimi, N., Desai, J. S., Bheemanahalli, R., Impa, S. M., Vennapusa, A. R., Sebela, D., … Jagadish, S. V. K. (2019). New candidate loci and marker genes on chromosome 7 for improved chilling tolerance in sorghum. J. Exp. Bot, 4. https://doi.org/10.1093/jxb/erz143

Grinevich, D. O., Desai, J. S., Stroup, K. P., Duan, J., Slabaugh, E., & Doherty, C. J. (2019). Novel transcriptional responses to heat revealed by turning up the heat at night. Plant Molecular Biology, 101(1-2), 1–19. https://doi.org/10.1007/s11103-019-00873-3

Liebelt, D. J., Jordan, J. T., & Doherty, C. J. (2019). Only a matter of time: the impact of daily and seasonal rhythms on phytochemicals. Phytochemistry Reviews, 18(6), 1409–1433. https://doi.org/10.1007/s11101-019-09617-z

Desai, J. S., Lawas, L. M. F., Valente, A. M., Leman, A. R., Grinevich, D. O., Jagadish, S. V. K., & Doherty, C. J. (2019, July 16). Warm nights disrupt global transcriptional rhythms in field-grown rice panicles (Vol. 7). Vol. 7. https://doi.org/10.1101/702183

Desai, J. S., Slabaugh, E., Liebelt, D. J., Fredenberg, J. D., Gray, B. N., Jagadish, S. V. K., … Doherty, C. J. (2018). Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance. FRONTIERS IN PLANT SCIENCE, 9. https://doi.org/10.3389/fpls.2018.01585

Desai, J. S., Sartor, R. C., Lawas, L. M., Jagadish, S. V. K., & Doherty, C. J. (2017). Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. Scientific Reports. https://doi.org/10.1038/s41598-017-17143-1

Shani, E., Salehin, M., Zhang, Y., Sanchez, S. E., Doherty, C., Wang, R., … Estelle, M. (2017). Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. CURRENT BIOLOGY, 27(3), 437–444. https://doi.org/10.1016/j.cub.2016.12.016

Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., … Brady, S. M. (2017, December). The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. PLANT PHYSIOLOGY, Vol. 175, pp. 1499–1509. https://doi.org/10.1104/pp.17.01490

Desai, J. S., Sartor, R. C., Lawas, L. M., Jagadish, S. V. K., & Doherty, C. J. (2016, December 24). Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes (Vol. 12). Vol. 12. https://doi.org/10.1101/093807

Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. (2015). Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1513609112

Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network. (2015). The Plant Journal : for Cell and Molecular Biology. https://doi.org/10.1111/tpj.12796

A genome-scale resource for the functional characterization of Arabidopsis transcription factors. (2014). Cell Reports. https://doi.org/10.1016/j.celrep.2014.06.033

Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. (2012). Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1200355109

CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. (2012). Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1209148109

Circadian surprise--it's not all about transcription. (2012). Science (New York, N.Y.). https://doi.org/10.1126/science.1230008

A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. (2011). Journal of Experimental Botany. https://doi.org/10.1093/jxb/err066

Circadian control of global gene expression patterns. (2010). Annual Review of Genetics. https://doi.org/10.1146/annurev-genet-102209-163432

Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. (2009). The Plant Cell. https://doi.org/10.1105/tpc.108.063958