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EnBiSys Lab

EnBiSys Publications

Recent Publications

Refereed Journal Publications (Advisees of Dr. Williams indicated by underline)

  1. Gordon M, Akyol TY, Amos B, Andersen SU, Williams C. KeySDL: sparse dictionary learning for keystone microbe identification from steady-state observations using a dynamical-systems model. BioData Mining 19, 18, 2026. https://doi.org/10.1186/s13040-026-00527-3
  2. Carbajal M, Jones D, Williams C, Nelson NG. In-season yield forecasting using multitemporal remote sensing environmental observations and machine learning: Applications for sweetpotato in North Carolina, USA. European Journal of Agronomy, 172, 127818, 2026. https://doi.org/10.1016/j.eja.2025.127818
  3. Bloom ZA, Larsen JC, Pena Martinez E, Williams CM, Jones DS, Kudenov MW. High-throughput classification and quantification of skinning phenotype in sweet potatoes. The Plant Phenome Journal, 8, e70023, 2025. https://doi.org/10.1002/ppj2.70023
  4. Madison I, Buckner ED, de Luis Balaguer MA, Song J, Ding J, Kimbell A, Selote D, Hunt A, Bueso E, Sozzani R, Williams C, Long TA. Iron deficiency changes regulatory mechanisms governing sieve element cell differentiation. Nature Communications, 16, 10196, 2025. https://doi.org/10.1038/s41467-025-65428-1 
  5. Schloop AE, Hiremath SV, Shaikh R, Dima SS, Lizardo L, Bhakta A, Williams CM, Reeves GT. Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in Drosophila blastoderm embryos. iScience, 28:7, 112854, 2025. https://doi.org/10.1016/j.isci.2025.112854 
  6. Roberts DL, Gorny A, Jones DS, Kudenov MW, Pratt L, Malcolm N, Williams C. Knowledge and Opportunities for Managing Plant-Parasitic Nematodes Using Decision Intelligence. PhytoFrontiers, 5:275-282, 2025. https://doi.org/10.1094/PHYTOFR-09-24-0099-P
  7. Nguyen, H. M., Gyurek, S., Mierop, R., Pecota, K. V., LaGamba, K., Boyette, M., Yencho, G. C., Williams, C. M., & Kudenov, M. W. (2025). Deployment and analysis of instance segmentation algorithm for in-field yield estimation of sweet potatoes. The Plant Phenome Journal, 8, e70026. https://doi.org/10.1002/ppj2.70026
  8. B.J. Weihs, Z. Tang, S. Roy, Z. Tian, D.J. Heuschele, Z. Zhang, C.M. Williams, Z. Zhang, G. Heineck, S. Saha, Z. Xu, “No more laborious stem counting: AI-powered computer vision enables identification and quantification of solid and hollow alfalfa stems at the pixel level,” Smart Agricultural Technology, 12, 101278, 2025. https://doi.org/10.1016/j.atech.2025.101278
  9. Hadel Y. Al Asafen, Aydin Beseli, Sharva Hiremath, Cranos M. Williams, and Gregory T Reeves, “Dynamics of BMP signaling and stable gene expression in early Drosophila embryo,” Biology Open, 13(9):bio061646, 2024. https://doi.org/10.1242/bio.061646
  10. H. Liu*, S. Hunt*, G. Craig Yencho, K. Pecota, R. Mierop, C. Williams, D. Jones, “Predicting Sweetpotato Traits Using Machine Learning: Impact of Environmental and Agronomic Factors on Shape and Size,”, Computers and Electronics in Agriculture, vol. 225, 109215, 2024. (*co-first authors) https://doi.org/10.1016/j.compag.2024.109215
  11. E. Pena Martinez, M. Kudenov, H. Nguyen, D. Jones, C. Williams, “Evaluating two high-throughput phenotyping platforms at early stages of the post-harvest pipeline of sweetpotatoes,” Smart Agricultural Technology, vol 8, 2024, https://doi.org/10.1016/j.atech.2024.100469 
  12. MT Ahmed, NK Wijewardane, Y Lu, DS Jones, M Kudenov, C. Williams, A Villordon, M Kamruzzaman. Advancing Sweetpotato Quality Assessment with Hyperspectral Imaging and Explainable Artificial Intelligence. Computers and Electronics in Agriculture. Volume 220, 108855. link (2024)
  13. E. Haverroth, M. Gobble, L. Bradley, K. Harris-Gilliam, A. Fischer, C. Williams, T. Long, R. Sozzani, “The Black American experience: Answering the global challenge of broadening participation in STEM/agriculture,” The Plant Cell, 2024;, koae002, https://doi-org.prox.lib.ncsu.edu/10.1093/plcell/koae002
  14. S. Schmittling, D. Muhammad, S. Haque, T. L. Long, C. Williams, “Cellular Clarity: Identifying Epidermis-specific Regulators of Iron Deficiency Response in Arabidopsis,” BMC Genomics, vol. 24, no. 1, pp 620, 2023.
  15. Daniel Sulis, Xiao Jiang, Chenmin Yang, Megan L. Matthews, Barbara Marques, Zachary Miller, Kai Lan, Carlos Cofre-Vega, Baoguang Liu, Runkun Sun, Henry Sederoff, Ryan Bing, Xiaoyan Sun, Cranos M. Williams, Hasan Jameel, Richard Phillips, Hou-min Chang, Ilona Peszlen, Yung-Yun Huang, Wei Li, Robert M. Kelly, Ronald R. Sederoff, Vincent L. Chiang, Rodolphe Barrangou, Jack P. Wang, “Multiplex CRISPR-Editing of Wood for Sustainable Fiber Production,” Science, vol. 381, no. 6654, pp. 216-221, 2023.
  16. S. Busato, M. Gordon, M. Chaudhari, I. Jensen, T. Akyol, S. Andersen, and C. Williams, “Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies,” Current Opinion in Plant Biology, 71, p.102326, 2023.
  17. Y. Mustamin, T. Yigit Akyol, M. Gordon, A. M. Manggabarani, Y. Isomura, Y. Kawamura, M.Bamba, C. M. Williams, S. U. Andersen, S. Sato (corr-auth), “FER and LecRK show haplotype-dependent cold-responsiveness and mediate freezing tolerance in Lotus japonicus,” Plant Physiology, vol 191, Issue 2, Pages 1138–1152, 2023
  18. D. Muhammad, N. M. Clark, S. Haque, C. Williams, R. Sozzani, T. A. Long, “POPEYE intercellular localization mediates cell-specific iron deficiency responses,” Plant Physiology, 2022, kiac357, https://doi.org/10.1093/plphys/kiac357
  19. H. Tong, H. Chen, C. Williams, “Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs,” Viruses, 14(4), 837, 2022; https://doi.org/10.3390/v14040837
  20. M. Kudenov, A. Altaqui, and C. Williams, “Practical spectral photography II: snapshot spectral imaging using linear retarders and microgrid polarization cameras,” Opt. Express 30, 12337-12352, 2022.
  21. H. Tong, H. Chen, and C. Williams. “Gene Regulatory Network of Secondary Cell Wall Biosynthesis during VND7 Induced de novo Xylem Formation.” International Journal of Biotechnology, Bioinformatics and Biomedical, 11(4), 7, 2021.
  22. E. Buckner, H. Tong, C. Ottley, and C. Williams, “High-throughput image segmentation and machine learning approaches in the plant sciences across multiple scales,” Emerging Topics in Life Sciences, https://doi-org.prox.lib.ncsu.edu/10.1042/ETLS20200273, 2021
  23. M. Kudenov, C. G. Scarboro, M. Boyette, G. Craig Yencho, and C. Williams, “Internal defect scanning of sweetpotatoes using scattering spectroscopy,”, PLoS One, vol 16, no. 2, 2021.
  24. C. Y. Lin, Y. Sun, J. Song, H. C. Chen, R. Shi, C. Yang, J. Liu, S. Tunlaya-Anukit, B. Liu, P. L. Loziuk, C. Williams, D. Muddiman, Y. Lin, R. Sederoff, J. Wang, V. Chiang, “Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa,” Frontiers in Plant Science, vol 12, 2021, DOI: 10.3389/fpls.2021.727932
  25. S. Haque, N. Nelson, E. Lobaton, G. C. Yencho, K. Pecota, R. Mierop, M. Kudenov, M. Boyette, and C. Williams, “Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery,“, Computers and Electronics in Agriculture, vol. 182, 2021, https://doi.org/10.1016/j.compag.2021.106011.
  26. M. Matthews and C. Williams, “Multi-scale modeling of cross-regulatory transcript and protein influences,”  In: MUKHTAR S. (eds) Modeling Transcriptional Regulation. Methods in Molecular Biology, vol 2328. Humana, New York, NY, 2021. https://doi.org/10.1007/978-1-0716-1534-8_7
  27. M. Matthews, J. Wang, R. Sederoff, V. L. Chiang, and C. Williams, “A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa,” Computational and Structural Biotechnology Journal, vol. 19, pp. 168-182, 2020. 
  28. Imani Madison, Charles Melvin, Eli Buckner, Cranos Williams, Rosangela Sozzani, Terri Long, “MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy,” Methods in Cell Biology: Plant Cell Biology, vol. 160, pp 405-418, 2020.
  29. Eli Buckner, Imani Madison, Charles Melvin, Terri Long, Rosangela Sozzani, Cranos Williams, “BioVision Tracker: A Semi-automated Image Analysis Software for Spatiotemporal Gene Expression Tracking in Arabidopsis Thalians,” Methods in Cell Biology: Plant Cell Biology, vol. 160, pp. 419-436, 2020.
  30. H. Tong, I. Madison, T. Long, C. Williams, “Computational solutions for modeling and controlling plant response to abiotic stresses: a review with focus on iron deficiency,” Current Opinion in Plant Biology, vol. 57, pp. 8-15, 2020.
  31. L. Van den Broeck, M. Gordon, D. Inzé, C. Williams, R. Sozzani, “Gene regulatory network inference: connecting plant biology and mathematical modeling,” Frontier in Genetics, Bioinformatics and Computational Biology, vol. 11, 2020, p. 457.
  32. M. Matthews, J. Wang, R. Sederoff, V. Chiang, and C. M. Williams, “Modeling cross-regulatory influences on monolignol transcripts and proteins in Populus trichocarpa under single and combinatorial gene knockdowns,” PLoS Computational Biology, vol 16, no 4, 2020.
  33. E. Buckner, I. Madison, H. Chou, C. E. Melvin, R. Sozzani, C. Williams, Terri A. Long, “High Resolution Spatiotemporal Imaging and Analysis of Dynamic Cell Cycle Progression Patterns Under Iron Deficiency and Heat Stress Conditions,” Frontiers in Plant Science, vol. 10, pp. 1487, 2019. (CW and TL co-corresponding authors)
  34. N. Clark, E. Buckner, A. P. Fisher, E. C. Nelson, T. T. Nguyen, A. R. Simmons, M. A. de Luis Balaguer, T. Butler-Smith, P. J. Sheldon, D. C. Bergmann, C. M. Williams, R. Sozzani, “Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of 2 stem-cell-specific gene networks,” Nature Communications, vol. 10, no. 1, pp. 1-11, 2019.
  35. A. Koryachko, A. Matthiadis, S. Haque, D. Muhammad, J. Ducoste, J. Tuck, T. Long, C. Williams, “Dynamic modeling of the iron deficiency modulated transcriptome response in Arabidopsis thaliana roots,” in silico Plants, Volume 1, Issue 1, 2019, diz005, https://doi.org/10.1093/insilicoplants/diz005. (CW and TL co-corresponding authors)
  36. C. T. Argueso, S. M. Assmann, K. D. Birnbaum, S. Chen, J. R. Dinneny, C. J. Doherty, A. L. Eveland, J. Friesner, V. R. Greenlee, J. A. Law, A. Marshall-Colón, G. A. Mason, R. O’Lexy, S. C. Peck, R. J. Schmitz, L. Song, D. Stern, M. J. Varagona, J. W. Walley, and C. M. Williams, “Directions for research and training in plant omics: Big Questions and Big Data,” Plant Direct, vol. 3, no. 4, pp. e00133–16, Apr. 2019. (SMA corresponding author)
  37. J. P. Wang, M. L. Matthews, P. P. Naik, C. M. Williams, J. J. Ducoste, R. R. Sederoff, and V. L. Chiang, “Flux modeling for monolignol biosynthesis.,” Current opinion in Biotechnology, vol. 56, pp. 187–192, Dec. 2018.
  38. S. Haque, J. S. Ahmad, N. M. Clark, C. M. Williams, and R. Sozzani, “Computational prediction of gene regulatory networks in plant growth and development.,” Current Opinion in Plant Biology, vol. 47, pp. 96–105, Nov. 2018. (CW and RS co-corresponding authors).
  39. J. Wang, M. Matthews, C. Williams, R. Shi, C. Yang, S. Tunlaya-Anukit, H. Chen, Q. Li, Jie L., C. Lin, P. Naik, Y. Sun, P. Loziuk, T. Yeh, H. Kim, E. Gjersing, T. Shollenberger, C. Shuford, J. Song, Z. Miller, Y. Huang, C. Edmunds, B. Liu, Y. Sun, Y. Lin, W. Li, H. Chen, I. Peszlen, J. Ducoste, J. Ralph, H. Chang, D. Muddiman, M. Davis, C. Smith, F. Isik, R. Sederoff, and V. Chiang, “Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis,” Nature communications, 9(1), 1579, 2018.
  40. P. Naik, J. Wang, J. Liu, H. Chen, R. Shi, C. M. Shuford, Q. Li, C.Y. Lin, D. C. Muddiman, R. Sederoff, V. Chiang, C. Williams, and J. Ducoste, “Assessing the Impact of the 4cl Complex on the Robustness of Monolignol Biosynthesis Using Metabolic Pathway Analysis,” PLoS ONE, vol. 13, no. 3, e0193896, 2018.
  41. Joanna Friesner, Sarah Assmann, Ruth Bastow, Julia Bailey-Serres, James Beynon, Volker Brendel, Robin Buell, Alexander Buksch, Jose Dinneny, Colleen Doherty, Andrea Eveland, Malia Gehan, Michael Gonzales, Erich Grotewold, Ute Kramer, Cody Markelz, Molly Megraw, Blake C. Meyers, Jim Murray, Nicholas J. Provart, Sue Rhee, Roger Smith, Edgar Spalding, Crispin Taylor, Tracy Teal, Keiko Torii, Chris Town, Matthew Vaughn, Richard Vierstra, Doreen Ware, Olivia Wilkins, Cranos Williams, Siobhan M. Brady, “The Next Generation of Training for Arabidopsis Researchers: Optimizing Training in Bioinformatics and Quantitative Biology for the Future,” Plant physiology 175, no. 4 (2017): 1499-1509.
  42. M. A. de Luis Balaguer, A. P. Fisher, N. M. Clark, M. G. Fernandez-Espinosa, B. K. Möller, D. Weijers, J. U. Lohmann, C. Williams, O. Lorenzo, and R. Sozzani, “Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells,” Proc Natl Acad Sci USA, vol. 114, no. 36, pp. E7632–E7640, Sep. 2017.
  43. D. Muhammad, S. Schmittling, C. Williams, T. A. Long, “More than Meets the Eye: Emergent Properties of Transcription Factors Networks in Arabidopsis,” BBA – Gene Regulatory Mechanisms, Special Issue: Plant Gene Regulatory Mechanisms, vol. 1860, pp. 64-74, 2016. (DM and SS co-first authors)
  44. Jack P Wang, Sermsawat Tunlaya‐Anukit, Rui Shi, Ting‐Feng Yeh, Ling Chuang, Fikret Isik, Chenmin Yang, Jie Liu, Quanzi Li, Philip L Loziuk, Punith P Naik, David C Muddiman, Joel J Ducoste, Cranos M Williams, Ronald R Sederoff, Vincent L Chiang, “A Proteomic‐Based Quantitative Analysis of the Relationship Between Monolignol Biosynthetic Protein Abundance and Lignin Content Using Transgenic Populus trichocarpa,” Recent Advances in Polyphenol Research, vol. 5, pp. 89, 2016.
  45. A. Koryachko, A. Matthiadis, D. Muhammad, J. Foret, S. M. Brady, J. J. Ducoste, J. Tuck, T. A. Long, and C. Williams, “Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response.,” PLoS ONE, vol. 10, no. 8, pp. e0136591–21, 2015. (TL and CW: co-corresponding authors, AK and AM co-first authors) 
  46. A. Koryachko, A. Matthiadis, J. Ducoste, J. Tuck, T. Long, and C. Williams, “Computational approaches to identify regulators of plant stress response,” Current Plant Biology, pp. 1–10, Jun. 2015, doi:10.1016/j.cpb.2015.04.001. (invited review, TL and CW: co-corresponding authors)
  47. C. Lin, J. Wang, Q. Li, H. Chen, J. Liu, P. Loziuk, J. Song, C. Williams, D. Muddiman, R. Sederoff, and V. Chiang, “4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa,” Molecular Plant, vol. 8, no. 1, pp. 176-187, 2015. 
  48. H. Chen, J. Song, J. Wang, Y. Lin, J. Ducoste, C. Shuford, J. Liu, Q. Li, R. Shi, A. Nepomuceno, F. Isik, D. Muddiman, C. Williams, R. Sederoff, and V. Chiang, “Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling,” The Plant Cell Online, vol. 26, no. 3, pp. 876-893, 2014.  (HC and JS, co-first authors, equal credit; CW, RS, and VC, co-corresponding authors)
  49. J. Wang, P. Naik, H. Chen, R. Shi, C. Lin, J. Jiu, C. Shuford, J. Ducoste, Q. Li, C. Williams, D. Muddiman, R. Sederoff, and V. Chiang, “Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa, ” The Plant Cell Online, vol. 26, no. 3, pp. 894-914, 2014. 
  50. M. A. de Luis Balaguer and C. Williams, “Hierarchical modularization of biochemical pathways using Fuzzy-C Means clustering,” IEEE Transactions on Systems, Man, and Cybernetics, Part B, vol. 44 (8), pp. 1473-1484, 2014. 
  51. H. Chen, J. Song, C. Williams, C. Shuford, J. Liu, J. Wang, Q. Li, R. Shi, E. Gokce, J. Ducoste, D. Muddiman, R. Sederoff, and V. Chiang, “Monolignol pathway 4-coumaric acid: CoA ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of CoA Ligation Fluxes,” Plant Physiology, vol. 161, pp. 1501-1516, 2013. 
  52. S. Marvel and C. Williams, “Set membership experimental design for biological systems,” BMC Systems Biology, vol. 6, no. 1, pp. 21, 2013. 
  53. B. Nabavi and C. Williams, “A novel cost function to estimate parameters of oscillatory biochemical systems,” EURASIP Journal on Bioinformatics and Systems Biology, vol. 2012, no. 1, pp. 1-17, 2012. 
  54. J. Wang, C. Shuford, Q. Li, J. Song, Y. Lin, Y. Sun, H. Chen, C. Williams, D. Muddiman, R. Sederoff, and V. Chiang. “Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC–MS/MS based protein quantification and metabolic flux analysis”. Planta, vol. 236, no. 3, pp. 795-808, 2012.