EnBiSys Publications

Recent Publications

Sulis, D. B., Jiang, X., Yang, C., Marques, B. M., Matthews, M. L., Miller, Z., Lan, K., Cofre-Vega, C., Liu, B., Sun, R., Sederoff, H., Bing, R. G., Sun, X., Williams, C. M., Jameel, H., Phillips, R., Chang, H., Peszlen, I., Huang, Y., Li, W., Kelly, R. M., Sederoff, R. R., Chiang, V. L., Barrangou, R., Wang, J. P. (2023). Multiplex CRISPR editing of wood for sustainable fiber production.SCIENCE, 381, 216-221. https://doi.org/10.1126/science.add4514

Busato, S., Gordon, M., Chaudhari, M., Jensen, I., Akyol, T., Andersen, S., Williams, C. (2023). Review of Compositionally, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies. CURRENT OPINION IN PLANT BIOLOGY, 71. https://doi.org/10.1016/j.pbi.2022.102326

Mustamin, Y., Akyol, T. Y., Gordon, M., Manggabarani, A. M., Isomura, Y., Kawamura, Y., Bamba, M., Williams, C. M., Anderson, S. U., Sato, S. (2023). FER and LecRK show haplotype-dependent cold-responsiveness and mediate freezing tolerance in Lotus japonicus. PLANT PHYSIOLOGY, 191(2), 1138–1152. https://doi.org/10.1093/plphys/kiac533

Asafen, H. Y. A., Beseli, A., Hiremath, S., Williams, C. M., Reeves, G. T. (2022). Dynamics of BMP signaling in the early Drosophila embryo. https://doi.org/10.1101/2022.10.20.513072

Tong, H., Chen, H., Williams, C. M. (2022). Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs. VIRUSES-BASEL, 14(4). https://doi.org/10.3390/v14040837

Muhammad, D. S., Clark, N. M., Haque, S., Williams, C. M., Sozzani, R., Long, T. A. (2022). POPEYE intercellular localization mediates cell-specific iron deficiency responses. PLANT PHYSIOLOGY, Vol. 8. https://doi.org/10.1093/plphys/kiac357

Kudenov, M. W., Altaqui, A., Williams, C. (2022). Practical spectral photography II: snapshot spectral imaging using linear retarders and microgrid polarization cameras. OPTICS EXPRESS, 30(8), 12337–12352. https://doi.org/10.1364/OE.453538

Matthews, M. L., Wang, J. P., Sederoff, R., Chiang, V. L., Williams, C. M. (2021). A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 168–182. https://doi.org/10.1016/j.csbj.2020.11.046

Haque, S., Lobaton, E., Nelson, N., Yencho, G. C., Pecota, K. V., Mierop, R., Kudenov, M., Boyette, M., Williams, C. M. (2021). Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery. Computers and Electronics in Agriculture, 182, 106011. https://doi.org/10.1016/j.compag.2021.106011

Lin, C. Y., Sun, Y., Song, J., Chen, H. C., Shi, R., Yang, C., Liu, J., Tunlaya-Anukit, S., Liu, B., Loziuk, P. L., Williams, C. M., Muddiman, D. C., Lin, Y. J., Sederoff, R. R., Wang, J. P., Chiang, V. L. (2021). Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE, 12. https://doi.org/10.3389/fpls.2021.727932

Buckner, E., Tong, H., Ottley, C., Williams, C. (2021). Review of High-throughput image segmentation and machine learning approaches in the plant sciences across multiple scales. EMERGING TOPICS IN LIFE SCIENCES, 5(2), 239–248. https://doi.org/10.1042/ETLS20200273

Kudenov, M. W., Scarboro, C. G., Altaqui, A., Boyette, M., Yencho, G. C., Williams, C. M. (2021). Internal defect scanning of sweetpotatoes using interactance spectroscopy. PLOS ONE, 16(2). https://doi.org/10.1371/journal.pone.0246872

Matthews, M. L., Williams, C. M. (2021). Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences. MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 115–138. https://doi.org/10.1007/978-1-0716-1534-8_7

Kudenov, M. W., Altaqui, A., Williams, C. (2021). Snapshot spectral imaging using Solc-based multivariate optical filters and pixelated polarization cameras. POLARIZATION SCIENCE AND REMOTE SENSING X, Vol. 11833. https://doi.org/10.1117/12.2596580

Buckner, E., Madison, I., Melvin, C., Long, T., Sozzani, R., Williams, C. (2020). BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana. In Methods in Cell Biology (Vol. 160, pp. 419–436). https://doi.org/10.1016/bs.mcb.2020.04.017

Van den Broeck, L., Gordon, M., Inzé, D., Williams, C., Sozzani, R. (2020). Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.00457

Madison, I., Melvin, C., Buckner, E., Williams, C., Sozzani, R., Long, T. (2020). MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy. In Methods in Cell Biology (Vol. 160, pp. 405–418). https://doi.org/10.1016/bs.mcb.2020.04.004

Matthews, M. L., Wang, J. P., Sederoff, R., Chiang, V. L., Williams, C. M. (2020). Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1007197

Haque, S., Ahmad, J. S., Clark, N. M., Williams, C. M., Sozzani, R. (2019). Computational prediction of gene regulatory networks in plant growth and development. Current Opinion in Plant Biology, 47, 96–105. https://doi.org/10.1016/J.PBI.2018.10.005

Argueso, C. T., Assmann, S. M., Birnbaum, K. D., Chen, S., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Friesner, J., Greenlee, V. R., Law, J. A., Marshall-Colón, A., Mason, G. A., O’Lexy, R., Peck, S. C., Schmitz, R. J., Song, L., Stern, D., Varagona, M. J., Walley, J. W., 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

Wang, J. P., Matthews, M. L., Naik, P. P., Williams, C. M., Ducoste, J. J., Sederoff, R. R., Chiang, V. L. (2019). Flux modeling for monolignol biosynthesis. Current Opinion in Biotechnology, 56, 187–192. https://doi.org/10.1016/J.COPBIO.2018.12.003

Clark, N. M., Buckner, E., Fisher, A. P., Nelson, E. C., Nguyen, T. T., Simmons, A. R., de Luis Balaguer, M. A., Butler-Smith, T., Sheldon, P. J., Bergmann, D. C., Williams, C. M., Sozzani, R. (2019). Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks. NATURE COMMUNICATIONS, 10. https://doi.org/10.1038/s41467-019-13132-2