CT
Christopher N. Topp
plant biologyphenotypingrootsPlant RootsRoot system architectureGenome, PlantImaging, Three-DimensionalInflorescencemesocosmmorphology
On Valency
published · living versionsW_d56k6yy8·v1 · currentpublished
Segmenting root systems in X-ray computed tomography images using level sets
with Amy Tabb, Keith E. Duncan
1 version
Preprints & journals
54 papers in the corpus · 2002–2026The carbon-nitrogen metabolism gene E1OGDH1 influences maize root system architecture and nitrogen plasticity10.64898/2026.07.21.739812v1 · Cho, M., Liu, Z., Luebbert, C. et al.2026 · 0 citationsbioRxiv
Diversity of root system architecture and root-shoot biomass allocation in industrial hemp (Cannabis sativa L.).41650193 · Morales, Elisa Y, Griffiths, Marcus, Mankar, Sumeet P et al.2026 · 5 citationsPloS one. 2026;21(2):e0339929
Phenome-to-genome insights for evaluating root system architecture in field studies of maize.40851219 · Hein, Kirsten M, Liu, Alexander E, Mullen, Jack L et al.2025 · 5 citationsThe plant genome. 2025;18(3):e70100
Seeing the unseen: A novel approach to extract latent plant root traits from digital images.41416208 · Shoaib, Mirza, Dimech, Adam M, Rochfort, Simone J et al.2025 · 2 citationsPlant phenomics (Washington, D.C.). 2025;7(3):100088
TopoRoot+: computing whorl and soil line traits of field-excavated maize roots from CT imaging.39187896 · Ju, Yiwen, Liu, Alexander E, Oestreich, Kenan et al.2024 · 5 citationsPlant methods. 2024;20(1):132
Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture.38288407 · Li, Mao, Liu, Zhengbin, Jiang, Ni et al.2024 · 6 citationsFrontiers in plant science. 2023;14:1260005
A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions.37426970 · Griffiths, Marcus, Liu, Alexander E, Gunn, Shayla L et al.2023 · 7 citationsFrontiers in plant science. 2023;14:1145389
A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize.36896653 · Murphy, Katherine M, Dowd, Tyler, Khalil, Ahmed et al.2023 · 12 citationsPlant physiology. 2023;192(2):1338-1358
A temporal atlas and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions10.1101/2023.01.14.524046v1 · Griffiths, M., Liu, A. E., Gunn, S. L. et al.2023 · 0 citationsbioRxiv
Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms.36589101 · Dowd, Tyler G, Li, Mao, Bagnall, G Cody et al.2023 · 14 citationsFrontiers in plant science. 2022;13:1041404
Root biology never sleeps: 11th Symposium of the International Society of Root Research (ISRR11) and the 9th International Symposium on Root Development (Rooting2021), 24-28 May 2021.35979688 · Carley, Clayton N, Chen, Guanying, Das, Krishna K et al.2022 · 4 citationsThe New phytologist. 2022;235(6):2149-2154
Accumulation of the gaseous hormone ethylene helps roots sense compact soil.35979143 · Kramer, Eric M, Masle, Josette, Robinson, Sarah et al.2023 · 0 citationsFaculty reviews. 2022;11:20
A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays).10.1101/2022.07.21.500061v1 · Murphy, K. M., Dowd, T., Khalil, A. et al.2022 · 0 citationsbioRxiv
X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs.34618094 · Duncan, Keith E, Czymmek, Kirk J, Jiang, Ni et al.2022 · 87 citationsPlant physiology. 2022;188(2):831-845
Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants.34726737 · Cox, Kevin L, Gurazada, Sai Guna Ranjan, Duncan, Keith E et al.2022 · 25 citationsPlant physiology. 2022;188(2):703-712
Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops.34914117 · Griffiths, Marcus, Delory, Benjamin M, Jawahir, Vanessica et al.2022 · 99 citationsPlant, cell & environment. 2022;45(3):751-770
Phenotyping Complex Plant Structures with a Large Format Industrial Scale High-Resolution X-Ray Tomography Instrument.35895201 · Duncan, Keith E, Topp, Christopher N2022 · 3 citationsMethods in molecular biology (Clifton, N.J.). 2022;2539:119-132
TopoRoot: a method for computing hierarchy and fine-grained traits of maize roots from 3D imaging.34903248 · Zeng, Dan, Li, Mao, Jiang, Ni et al.2021 · 33 citationsPlant methods. 2021;17(1):127
Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.).34876178 · Bucciarelli, Bruna, Xu, Zhanyou, Ao, Samadangla et al.2021 · 37 citationsPlant methods. 2021;17(1):125
Complementary Phenotyping of Maize Root System Architecture by Root Pulling Force and X-Ray Imaging.34870229 · Shao, M R, Jiang, N, Li, M et al.2026 · 37 citationsPlant phenomics (Washington, D.C.). 2021;2021:9859254
Rated-M for mesocosm: allowing the multimodal analysis of mature root systems in 3D.33555320 · Dowd, Tyler, McInturf, Samuel, Li, Mao et al.2021 · 19 citationsEmerging topics in life sciences. 2021;5(2):249-260
Complementary Phenotyping of Maize Root Architecture by Root Pulling Force and X-Ray Computed Tomography10.1101/2021.03.03.433776v2 · Shao, M.-R., Jiang, N., Li, M. et al.2021 · 5 citationsbioRxiv
A Statistical Growth Property of Plant Root Architectures.33313546 · Sultan, Sam, Snider, Joseph, Conn, Adam et al.2026 · 5 citationsPlant phenomics (Washington, D.C.). 2020;2020:2073723
Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences.32162345 · Li, Mao, Shao, Mon-Ray, Zeng, Dan et al.2021 · 43 citationsThe New phytologist. 2020;226(6):1873-1885
Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density.31504758 · Li, Mao, Klein, Laura L, Duncan, Keith E et al.2020 · 33 citationsJournal of experimental botany. 2019;70(21):6261-6276
Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures.31123089 · Jiang, Ni, Floro, Eric, Bray, Adam L et al.2020 · 49 citationsThe Plant cell. 2019;31(8):1708-1722
Convergent evolution of root system architecture in two independently evolved lineages of weedy rice.30883803 · Wedger, Marshall J, Topp, Christopher N, Olsen, Kenneth M2020 · 22 citationsThe New phytologist. 2019;223(2):1031-1042
The Quantitative Genetic Control of Root Architecture in Maize.30020530 · Bray, Adam L, Topp, Christopher N2018 · 68 citationsPlant & cell physiology. 2018;59(10):1919-1930
Segmenting root systems in X-ray computed tomography images using level sets1809.06398v1 · Amy Tabb, Keith E. Duncan, Christopher N. Topp2018 · 12 citations2018 IEEE Winter Conference on Applications of Computer Vision (WACV), Lake Tahoe, NV/CA. pp. 586-595on Valency
The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology.29871979 · Li, Mao, Frank, Margaret H, Coneva, Viktoriya et al.2019 · 61 citationsPlant physiology. 2018;177(4):1382-1395
Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences.28659934 · Bucksch, Alexander, Atta-Boateng, Acheampong, Azihou, Akomian F et al.2023 · 89 citationsFrontiers in plant science. 2017;8:900
Persistent homology and the branching topologies of plants.28341629 · Li, Mao, Duncan, Keith, Topp, Christopher N et al.2018 · 47 citationsAmerican journal of botany. 2017;104(3):349-353
Whole-Plant Manual and Image-Based Phenotyping in Controlled Environments.31725975 · Agnew, Erica, Bray, Adam, Floro, Eric et al.2020 · 8 citationsCurrent protocols in plant biology. 2017;2(1):1-21
Persistent homology: a tool to universally measure plant morphologies across organs and scales10.1101/104141v1 · Li, M., Frank, M. H., Coneva, V. et al.2017 · 9 citationsbioRxiv
Hope in Change: The Role of Root Plasticity in Crop Yield Stability.27578845 · Topp, Christopher N2018 · 23 citationsPlant physiology. 2016;172(1):5-6
The Quest for Understanding Phenotypic Variation via Integrated Approaches in the Field Environment.27482076 · Pauli, Duke, Chapman, Scott C, Bart, Rebecca et al.2018 · 142 citationsPlant physiology. 2016;172(2):622-634
How can we harness quantitative genetic variation in crop root systems for agricultural improvement?26911925 · Topp, Christopher N, Bray, Adam L, Ellis, Nathanael A et al.2016 · 68 citationsJournal of integrative plant biology. 2016;58(3):213-25
Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics.26535051 · Das, Abhiram, Schneider, Hannah, Burridge, James et al.2015 · 197 citationsPlant methods. 2015;11:51
DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.26030757 · Symonova, Olga, Topp, Christopher N, Edelsbrunner, Herbert2016 · 52 citationsPloS one. 2015;10(6):e0127657
Applying high-throughput phenotyping to plant-insect interactions: picturing more resistant crops.32846711 · Goggin, Fiona L, Lorence, Argelia, Topp, Christopher N2020 · 105 citationsCurrent opinion in insect science. 2015;9:69-76
Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture.25673779 · Zurek, Paul R, Topp, Christopher N, Benfey, Philip N2016 · 65 citationsPlant physiology. 2015;167(4):1487-96
Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits.25658908 · Chitwood, Daniel H, Topp, Christopher N2015 · 57 citationsCurrent opinion in plant biology. 2015;24:54-60
Combined 3D PET and Optical Projection Tomography Techniques for Plant Root Phenotyping1501.00242v1 · Qiang Wang, Sergey Komarov, Aswin J. Mathews et al.2015 · 4 citationsarXiv
3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.23580618 · Topp, Christopher N, Iyer-Pascuzzi, Anjali S, Anderson, Jill T et al.2013 · 292 citationsProceedings of the National Academy of Sciences of the United States of America. 2013;110(18):E1695-704
GiA Roots: software for the high throughput analysis of plant root system architecture.22834569 · Galkovskyi, Taras, Mileyko, Yuriy, Bucksch, Alexander et al.2014 · 389 citationsBMC plant biology. 2012;12:116
Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning.21352520 · Gent, Jonathan I, Schneider, Kevin L, Topp, Christopher N et al.2011 · 32 citationsEpigenetics & chromatin. 2011;4:3
DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA.20140237 · Du, Yaqing, Topp, Christopher N, Dawe, R Kelly2010 · 140 citationsPLoS genetics. 2010;6(2):e1000835
Identification of a maize neocentromere in an oat-maize addition line.19556776 · Topp, C N, Okagaki, R J, Melo, J R et al.2009 · 74 citationsCytogenetic and genome research. 2009;124(3-4):228-38
Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z.17220196 · Deal, Roger B, Topp, Christopher N, McKinney, Elizabeth C et al.2007 · 316 citationsThe Plant cell. 2007;19(1):74-83
Transformation of rice with long DNA-segments consisting of random genomic DNA or centromere-specific DNA.17103243 · Phan, Bao H, Jin, Weiwei, Topp, Christopher N et al.2007 · 54 citationsTransgenic research. 2007;16(3):341-51
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