Publications

Bull, T., Van Blair, J., Sutton, S., Colwell, H. and Khakhar, A., 2025. Molecular Bonsai: Elucidating the design principles for engineering plant organ size. bioRxiv, pp.2025-06. https://doi.org/10.1101/2025.06.22.660808

Desai, S.A. and Stroock, A.D., 2025. Abscisic acid-mediated water stress regulation can mechanistically explain oscillations and water stress memory in stomatal conductance. bioRxiv, pp.2025-12. https://doi.org/10.64898/2025.12.26.696581

Hernández-Sánchez, I.E., Tarbiyyah, I., Kearly, A., Martinez-Seidel, F., Maruri-Lopez, I., Chen, Y., Rissland, O.S., Wang, W., Sioud, S., Schwarzenberg, A., Nelson Dittrich, A.C., Nelson, A.D.L., Chodasiewicz, M. 2025. RBP47 family members are negative regulators of heat stress tolerance in Arabidopsis thaliana. bioRxiv, pp.2025-05. https://doi.org/10.1101/2025.05.18.654719

Twohey III, R.J., Christenson, C.G., Li, C., Bacher, H., Calleja, S., Pastor, B., Hanneman, M., Wickes-Do, L., Gore, M.A., Pauli, D., Moose, S.P. & Studer, A.J. Investigating the role of stomatal dynamics on agronomic traits using a slac1-2 Zea mays mutant. bioRxiv 634166 (2025). https://www.biorxiv.org/content/10.1101/2025.01.21.634166v1

Yu, L.A., Melandri, G., Nelson Dittrich, A.C., Calleja, S., Rozzi, B., Palos, K., Srinivasan, A., Brewer, E.K., Fischer, H., Obata, T., Abd Elgawad, H., Beemster, G.T.S., Henderson, R., Garcia, C.D., Zhang, X., Strern, D., Eveland, A., Schroeder, A.F., Skirycz, A., Lyons, E., Arnold, A.E., Gregory, B.D., Nelson, A.D.L. & Pauli, D. A field-focused systems approach reveals mRNA covalent modifications linked to sorghum growth and development under drought stress. bioRxiv, 2025-2001 (2025). https://doi.org/10.1101/2025.01.17.633510

Peer Reviewed Publications

Yan, Y., Baldwin, M., Lee, J., Wang, Z., Li, G., Han, I., He, P., Srinivasan, V., Wickes-Do, L., Gore, M.A. and Gu, A.Z., 2025. Discovering Polyphosphate and Polyhydroxyalkanoate-Accumulating Organisms Across Ecosystems: Phenotype-targeted Genotyping via FACS-sequencing. Environmental Science & Technology. https://doi.org/10.1021/acs.est.5c07205

Wang, Z., Yan, Y., He, P., Baldwin, M.T., Fitzgerald, K., Wells, G., Tyo, K. and Gu, A.Z., 2025. Single-Cell Raman Spectroscopy Enables High-Resolution Detection and Semiquantification of Intracellular Cyanophycin across Biological and Environmental Samples. Environmental Science & Technology Letters. https://doi.org/10.1021/acs.estlett.5c00890

Jain, P., Sen, S., Rockwell, F.E., Twohey III, R.J., Huber, A.E., Desai, S.A., Wu, I.F., De Swaef, T., Ilman, M.M., Studer, A.J. and Holbrook, N.M., 2025. Loss of conductance between mesophyll symplasm and intercellular air spaces explains nonstomatal control of transpiration. Proceedings of the National Academy of Sciences, 122(47), p.e2504862122. https://doi.org/10.1073/pnas.2504862122

Koe, K., Shah, P.K., Walt, B., Westphal, J., Marri, S., Kamtikar, S., Nam, J.S., Uppalapati, N.K., Chowdhary, G. and Krishnan, G., 2025, May. Precision harvesting in cluttered environments: Integrating end effector design with dual camera perception. In 2025 IEEE International Conference on Robotics and Automation (ICRA) (pp. 13153-13159). IEEE. https://doi.org/10.1109/ICRA55743.2025.11127557

Wu, Y., Chen, C. and Li, S., 2026. Development of a suite of activatable plant synthetic promoter systems using a bacterial LysR-type transcriptional regulator FdeR. Synthetic and Systems Biotechnology, 12, pp.312-319. https://doi.org/10.1016/j.synbio.2025.12.005

Hoyos‐Villegas, V., Jackson, M., Vargas‐Cedeño, M., Farmer, E.E., Hanneman, M., Mazis, A., Singh, K.D., Sangjan, W., McNair, M., Sankaran, S., Tirado Tolosa, S., Gore, M.A. and Rife, T.W. 2025. Affordable phenomics: Expanding access to enhancing genetic gain in plant breeding. The Plant Phenome Journal, 8(1), p.e70034. https://doi.org/10.1002/ppj2.70034

Wang, Z., Han, I.L., Lee, J., Li, G., He, P., Baldwin, M.T., Kao-Kniffin, J., Wu, L., Zhou, J. and Gu, A.Z. Climate Warming Enhances Biodiversity and Stability of Grassland Soil Phosphorus-Cycling Microbial Communities. The ISME Journal, p.wraf118 (2025). https://doi.org/10.1093/ismejo/wraf118

Koe, K., Marri, S., Walt, B., Kamtikar, S., Uppalapati, N.K., Krishnan, G. and Chowdhary, G.. Learning-based position and orientation control of a hybrid rigid-soft arm manipulator. Journal of Mechanisms and Robotics, 17(7), p.071010 (2025). https://doi.org/10.1115/1.4067872

Aktas Eken, G., Chalmpes, N., Huang, Y., Giannelis, E.P. & Ober, C.K. Nanoengineering Carbon Dot‐Polymer Brush Interfaces for Adaptive Optical Materials. Angewandte Chemie International Edition, e202506448 (2025). https://doi.org/10.1002/anie.202506448

Bacheva, V., Madison, I., Baldwin, M., Beilstein, M., Call, D.F., Deaver, J.A., Efimenko, K., Genzer, J., Grieger, K., Gu, A.Z., Ilman, M.M., Liu, J., Li, S., Mayer, B.K., Mishra, A.K., Nino, J.C., Rubambiza, G., Sengers, S., Shepherd, R., Woodson, J., Weatherspoon, H., Frank, M.H., Jones, J., Sozzani, R. & Stroock, A.D. Transdisciplinary collaborations for advancing sustainable and resilient agricultural systems. Global Change Biology 31, 4, e70142 (2025). https://doi.org/10.1111/gcb.70142

Bacheva, V., Rockwell, F., Salmon, J.B., Woodson, J., Frank, M. & Stroock, A. A unified framework for hydromechanical signaling: Do plant signals go with the flow? Proceedings of the National Academy of Sciences 122, 17, e2422692122 (2025). https://www.pnas.org/doi/abs/10.1073/pnas.2422692122

DeBruin, J., Aref, T., Tirado Tolosa, S., Hensley, R., Underwood, H., McGuire, M., Soman, C., Nystrom, G., Parkinson, E., Li, C., Moose, S.P. & Chowdhary, G. Breaking the field phenotyping bottleneck in maize with autonomous robots. Communications Biology 8, 1, 467 (2025). https://www.nature.com/articles/s42003-025-07890-7

Hafner, B., Pietz, O., King, W., Scharfetter, J., Bauerle, T. Early developmental shifts in root exudation profiles of five Zea mays L. genotypes. Plant Science (2025). https://doi.org/10.1016/j.plantsci.2025.112439

He, P., Son, Y., Berkowitz, J., Li, G., Lee, J., Han, I.L., Craft, E., Piñeros, M., Kao-Kniffin, J., Gu, A.Z. Recycled Phosphorus Bioamendments from Wastewater Impact Rhizomicrobiome and Benefit Crop Growth: Sustainability Implications at Water-Food Nexus. Environmental Science & Technology 59, 4,  (2025). https://doi.org/10.1021/acs.est.4c07901

Kumar, R., Azanu, M.K., Lee, K., Kang, M., Zobrist, J., Bùi, J.T., Wang, N., Gordon-Kamm, W., Van Eck, J. & Wang, K. Comparative analysis of maize leaf whorl-based transformation using ABA-induced Bbm/Wus2 removal in two Agrobacterium ternary vector systems. In Vitro Cellular & Developmental Biology-Plant, 1-14 (2025). https://doi.org/10.1007/s11627-025-10531-7

Li, G., Wang, Z., Wu, C., Wang, D., Han, I., Lee, J., Kaeli, D.R., Dy, J.G., Weinberger, K.Q. & Gu, A.Z. Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data. ISME Communications 5, 1, p.ycaf015 (2025). https://doi.org/10.1093/ismeco/ycaf015

Majed, N., Wang, Z., Baldwin, M.T., Uddin, S.M.F., Dash, P. & Gu, A.Z. Advancements in phosphorus species profiling and bioavailability assessment with implications for phosphorus sustainability. Current Opinion in Biotechnology 93, 103295 (2025). https://doi.org/10.1016/j.copbio.2025.103295

Paajanen, P., Tomkins, M., Hoerbst, F., Veevers, R., Heeney, M., Thomas, H.R., Apelt, F., Saplaoura, E., Gupta, S., Frank, M. and Walther, D. Re-analysis of mobile mRNA datasets highlights challenges in the detection of mobile transcripts from short-read RNA-Seq data. Nature Plants (2025). https://doi.org/10.1038/s41477-025-01979-x

Negin, B., Martin-Lesmes, L.D. & Jander, G. Success and limitations in adaptation of Fast-TrACC tissue culture-independent transformation in coffee, cotton, and tree tobacco. PLOS One 20, 5, e0318324 (2025). https://doi.org/10.1371/journal.pone.0318324

Perkins, C.J., Pryze, K. & Palanivelu, R. Peptide Signaling in Flowering Plants: Insights into Reproductive Thermotolerance. Journal Of Experimental Botany, eraf192 (2025). https://doi.org/10.1093/jxb/eraf192

Bellavita, J., Pasquali, T., Del Rio Martin, L., Vella, F. & Guidi, G. Popcorn: Accelerating Kernel K-means on GPUs through Sparse Linear Algebra. in 30th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming 426-440. https://doi.org/10.1145/3710848.3710887

Peer Reviewed Publications

Amir, D., Saran, N., Wilson, T., Kleinberg, R., Shrivastav, V. & Weatherspoon, H. Shale: A Practical, Scalable Oblivious Reconfigurable Network. in ACM SIGCOMM Conference.  449-464 (2024). https://dl.acm.org/doi/10.1145/3651890.3672248

Chin, S.W., Rubambiza, G., Zhao, Y., Malek, K. & Weatherspoon, H. Realtime optimization and management system (ROAM): A decision support system for digital agriculture systems. Smart Agricultural Technology 8, 100452 (2024). https://doi.org/10.1016/j.atech.2024.100452

Christenson, C.G., Mohammad R. Gohardoust, Sebastian Calleja, Kelly R. Thorp, Markus Tuller, and Duke Pauli. Monitoring cotton water status with microtensiometers. Irrigation Science, 1-17 (2024). https://doi.org/10.1007/s00271-024-00930-w

Eken, G.A., Huang, Y.M., Prucker, O., Rühe, J. & Ober, C. Advancing Glucose Sensing Through Auto-Fluorescent Polymer Brushes: From Surface Design to Nano-Arrays. Small 5, 2, 1613–1623 (2024). https://doi.org/10.1021/acsapm.2c02066

Han, J.N., Miller, E.P. & Li, S.J. Cutting-edge plant natural product pathway elucidation. Current Opinion in Biotechnology 87, 103137 (2024). https://doi.org/10.1016/j.copbio.2024.103137

Jain, P., Huber, A.E., Rockwell, F.E., Sen, S., Holbrook, N.M. & Stroock, A. New approaches to dissect leaf hydraulics reveal large gradients in living tissues of tomato leaves. New Phytologist 242, 2, 453-465 (2024). https://doi.org/10.1111/nph.19585

Jain, P., Huber, A.E., Rockwell, F.E., Sen, S., Holbrook, N.M. & Stroock, A.D. Localized measurements of water potential reveal large loss of conductance in living tissues of maize leaves. Plant Physiology 194, 4, 2288-2300 (2024). https://doi.org/10.1073/pnas.2008276118

King, W.L., Hayward, R.J., Goebel, M., Fleishman, S.M., Bauerle, T.L. & Bell, T.H. Getting to the root of root-microbe interactions. Science Progress 107, 3,  (2024). https://doi.org/10.1177/00368504241278783

Lemke, M.D., Abate, A.N. & Woodson, J.D. Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant. Plant Signaling & Behavior 19, 1, 2347783 (2024). https://doi.org/10.1080/15592324.2024.2347783

Lemke, M.D. & Woodson, J.D. A genetic screen for dominant chloroplast reactive oxygen species signaling mutants reveals life stage-specific singlet oxygen signaling networks. Frontiers in Plant Science 14,  (2024). https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1331346

Li, Y.F., Guidi, G. & Acm. High-Performance Sorting-Based k-mer Counting in Distributed Memory with Flexible Hybrid Parallelism. in 53rd International Conference on Parallel Processing (ICPP).  919-928 (2024). https://doi.org/10.1145/3673038.3673072

Lin, M., Bacher, H., Bourgault, R., Qiao, P., Matschi, S., Vasquez, M.F., Mohammadi, M., van Boerdonk, S., Scanlon, M.J., Smith, L.G., Molina, I. & Gore, M.A. Integrative multiomic analysis identifies genes associated with cuticular wax biogenesis in adult maize leaves. G3 Genes|Genomes|Genetics 14, 12, jkae241 (2024). https://doi.org/10.1093/g3journal/jkae241

Mishra, A.K., Kim, J., Baghdadi, H., Johnson, B.R., Hodge, K.T. & Shepherd, R.F. Sensorimotor control of robots mediated by electrophysiological measurements of fungal mycelia. Science Robotics 9, 93, eadk8019 (2024). https://www.science.org/doi/10.1126/scirobotics.adk8019

Richter, A., Schroeder, A.F., Marcon, C., Hochholdinger, F., Jander, G. & Negin, B. Catechol acetylglucose: a newly identified benzoxazinoid-regulated defensive metabolite in maize. New Phytologist 244, 6, 2474-2488 (2024). https://doi.org/10.1111/nph.20209

Roeven, L., Wolf, S.A., Sengers, P., Liu, J., Rubambiza, G., Persaud, D. & Weatherspoon, H. Analyzing abstraction in critical agri-food studies and computer science: toward interdisciplinary analysis of digital agriculture innovation. Agriculture and Human Values, 1-18 (2024). https://doi.org/10.1007/s10460-024-10655-3

Rubambiza, G., Sengers, P., Weatherspoon, H. & Liu, J. Seam Work and Simulacra of Societal Impact in Networking Research: A Critical Technical Practice Approach. in ACM CHI Conf. Hum. Fact. Comp. Sys.  1-19 (ACM, 2024). https://dl.acm.org/doi/full/10.1145/3613904.3642337

Wilson, T., Amir, D., Saran, N., Kleinberg, R., Shrivastav, V. & Weatherspoon, H. Breaking the VLB Barrier for Oblivious Reconfigurable Networks. in 56th Annual ACM Symposium on Theory of Computing (STOC).  1865-1876 (2024). https://dl.acm.org/doi/abs/10.1145/3618260.3649608

Woodson, J.D., Lemke, M.D., Tano, D. & Rai, S.Chloroplast Signals and Their Effect on Nuclear Stress Gene Regulation, Cell Death, and Cellular Degradation Pathways in Nucleic Acids and Molecular Biology (Springer 2024). https://doi.org/10.1016/j.pbi.2019.06.005

Yu, L.A., Dittrich, A.C.N., Zhang, X., Brock, J.R., Thirumalaikumar, V.P., Melandri, G., Skirycz, A., Edger, P.P., Thorp, K.R., Hinze, L., Pauli, D. & Nelson, A.D.L. Regulation of a single inositol 1‐phosphate synthase homeologue by HSFA6B contributes to fibre yield maintenance under drought conditions in upland cotton. Plant Biotechnology Journal 22, 10, 2756-2772 (2024). https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.14402

Peer Reviewed Publications

Amir, D., Wilson, T., Shrivastav, V., Weatherspoon, H. & Kleinberg, R. Scalability and Congestion Control in Oblivious Reconfigurable Networks. in ACM SIGCOMM Conference (SIGCOMM).  1138-1140 (Assoc Computing Machinery, 2023). https://dl.acm.org/doi/10.1145/3603269.3610862

Eken, G.A., Huang, Y.M., Guo, Y.X. & Ober, C. Visualization of the pH Response through Autofluorescent Poly(styrene-alt-N-maleimide) Polyelectrolyte Brushes. Acs Applied Polymer Materials, 11 (2023). https://doi.org/10.1021/acsapm.2c02066

Eken, G.A., Kafer, F., Yuan, C.Y., Andrade, I. & Ober, C.K. Synthesis of N-Substituted Maleimides and Poly(styrene-co-N-maleimide) Copolymers and Their Potential Application as Photoresists. Macromolecular Chemistry and Physics 224, 1, 2200256 (2023). https://doi.org/10.1002/macp.202200256

Han, J.N. & Li, S.J. De novo biosynthesis of berberine and halogenated benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Communications Chemistry 6, 1, 10 (2023). https://doi.org/10.1038/s42004-023-00821-9

Heeney, M. & Frank, M.H. The mRNA mobileome: Challenges and opportunities for deciphering signals from the noise. The Plant Cell 35, 6, 1817–1833 (2023). https://doi.org/10.1093/plcell/koad063

King, W.L., Yates, C.F., Cao, L.L.Y., O’Rourke-Ibach, S., Fleishman, S.M., Richards, S.C., Centinari, M., Hafner, B.D., Goebel, M., Bauerle, T., Kim, Y.M., Nicora, C.D., Anderton, C.R., Eissenstat, D.M. & Bell, T.H. Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites. Plant Cell and Environment 46, 12, 3919-3932 (2023). https://doi.org/10.1111/pce.14705

Rubambiza, G., Chin, S.W., Rehman, M., Atapattu, S., Martínez, J.F. & Weatherspoon, H. Comosum: An Extensible, Reconfigurable, and Fault-Tolerant IoT Platform for Digital Agriculture. in USENIX Ann.Techn. Confer.  197-214 (USENIX Assoc, 2023). https://www.usenix.org/conference/atc23/presentation/rubambiza

Rubambiza, G., Romero Galvan, F., Pavlick, R., Weatherspoon, H. & Gold, K.M. Towards Cloud-Native, Machine Learning Based Detection of Crop Disease with Imaging Spectroscopy. Journal of Geophysical Research: Biogeosciences 128, 6, e2022JG007342 (2023). https://doi.org/10.1029/2022JG007342

Sanghvi, R., Kuo, J., Ravi, A. & Lal, A. Towards Ultra-High Spatial Resolution Sensing of GHz Ultrasound Using Strain Modulation of Field Effect Transistors. in 2023 IEEE 36th International Conference on Micro Electro Mechanical Systems (MEMS).  9-12 (IEEE). https://doi.org/10.1109/MEMS49605.2023.10052433

Wilson, T., Amir, D., Shrivastav, V., Weatherspoon, H. & Kleinberg, R. Extending Optimal Oblivious Reconfigurable Networks to all N. in Symposium on Algorithmic Principles of Computer Systems (APOCS) 1-16 (Society for Industrial and Applied Mathematics). https://doi.org/10.1137/1.9781611977578.ch1

Wong, S.S., Tamarit, C.C. & Martínez, J.F. PUMICE: Processing-using-Memory Integration with a Scalar Pipeline for Symbiotic Execution. in 60th ACM/IEEE Design Automation Conference (DAC).  1-6 (IEEE, 2023). https://ieeexplore.ieee.org/document/10247792

Wu, Y., Gong, F.L. & Li, S. Leveraging yeast to characterize plant biosynthetic gene clusters. Current Opinion in Plant Biology 71, 102314 (2023). https://doi.org/10.1016/j.pbi.2022.102314

Wu, Y.A., Liu, C., Koganitsky, A., Gong, F.L. & Li, S.J. Discovering Dynamic Plant Enzyme Complexes in Yeast for Kratom Alkaloid Pathway Identification. Angewandte Chemie-International Edition 62, 38, e202307995 (2023). https://doi.org/10.1002/anie.202307995

Peer Reviewed Publications

Amir, D., Wilson, T., Shrivastav, V., Weatherspoon, H., Kleinberg, R. & Agarwal, R. Optimal Oblivious Reconfigurable Networks. in 54th Annual ACM SIGACT Symposium on Theory of Computing (STOC).  1339-1352 (Assoc Computing Machinery, 2022). https://doi.org/10.1145/3519935.3520020

Gong, F.L., Han, J.N. & Li, S.J. MULTI-SCULPT: Multiplex Integration via Selective, CRISPR-Mediated, Ultralong Pathway Transformation in Yeast for Plant Natural Product Synthesis. Acs Synthetic Biology, 12 (2022). https://doi.org/10.1021/acssynbio.2c00135

Lemke, M.D. & Woodson, J.D. Targeted for destruction: degradation of singlet oxygen-damaged chloroplasts. Plant Signaling & Behavior 17, 1, 5 (2022). https://doi.org/10.1080/15592324.2022.2084955

Liu, C. & Li, S.J. Engineered biosynthesis of plant polyketides by type III polyketide synthases in microorganisms. Frontiers in Bioengineering and Biotechnology 10, 19 (2022). https://doi.org/10.3389/fbioe.2022.1017190

Noble, J.A., Bielski, N., Liu, M.C.J., DeFalco, T.A., Stegmann, M., Nelson, A.D.L., McNamara, K., Sullivan, B., Dinh, K.K., Khuu, N., Hancock, S., Shiu, S.H., Zipfel, C., Cheung, A.Y., Beilstein, M.A. & Palanivelu, R. Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization. Plant Physiology 190, 4, 2539-2556 (2022). https://doi.org/10.1093/plphys/kiac444

Rubambiza, G., Sengers, P. & Weatherspoon, H. Seamless Visions, Seamful Realities: Anticipating Rural Infrastructural Fragility in Early Design of Digital Agriculture. in ACM CHI Conf. Hum. Fact. Comp. Sys.  1-15 (ACM, 2022). https://doi.org/10.1145/3491102.3517579

Sanghvi, R., Kuo, J. & Lal, A. Liquid Layer Evolution Characterization using GHz Ultrasonic Pulses: Linear and Nonlinear Effects. in Acoustofluidics 2022.  126–127 (Chemical and Biological Microsystems Society). https://acoustofluidics.net/archive/materials/Acoustofluidics_2022_Materials.pdf

Wu, Y.A., Chen, M.N. & Li, S.J. De novo biosynthesis of diverse plant-derived styrylpyrones in Saccharomyces cerevisiae. Metabolic Engineering Communications 14, 12 (2022). https://doi.org/10.1016/j.mec.2022.e00195

Non-Peer Reviewed Publications

The CROPPS Research Community. Digital Biology to Enable Sustainable and Resilient Agriculture in The Bridge     (National Academy of Engineering, 2022). https://www.nae.edu/276545/Digital-Biology-to-Enable-Sustainable-and-Resilient-Agriculture