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He Y, Matthews ML. Seasonal climate conditions impact the effectiveness of improving photosynthesis to increase soybean yield. Field Crops Research 2023;296:108907. https://doi.org/10.1016/j.fcr.2023.108907.
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Matthews ML, Marshall-Colón A, McGrath JM, Lochocki EB, Long SP. Soybean-BioCro: a semi-mechanistic model of soybean growth. In Silico Plants 2022;4:diab032. https://doi.org/10.1093/insilicoplants/diab032.
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Lochocki EB, Rohde S, Jaiswal D, Matthews ML, Miguez F, Long SP, et al. BioCro II: a software package for modular crop growth simulations. In Silico Plants 2022;4:diac003. https://doi.org/10.1093/insilicoplants/diac003.
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Matthews ML, Marshall-Colón A. Multiscale plant modeling: from genome to phenome and beyond. Emerging Topics in Life Sciences 2021;5:231–7. https://doi.org/10.1042/ETLS20200276.
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Matthews ML, Wang JP, Sederoff R, Chiang VL, Williams CM. A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa. Computational and Structural Biotechnology Journal 2021;19:168–82. https://doi.org/10.1016/j.csbj.2020.11.046.
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Matthews ML, Williams CM. Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences. In: MUKHTAR S, editor. Modeling Transcriptional Regulation: Methods and Protocols, New York, NY: Springer US; 2021, p. 115–38. https://doi.org/10.1007/978-1-0716-1534-8_7.
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Matthews ML, Wang JP, Sederoff R, Chiang VL, Williams CM. Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa. PLOS Computational Biology 2020;16:e1007197. https://doi.org/10.1371/journal.pcbi.1007197.
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Wang JP, Matthews ML, Naik PP, Williams CM, Ducoste JJ, Sederoff RR, et al. Flux modeling for monolignol biosynthesis. Current Opinion in Biotechnology 2019;56:187–92. https://doi.org/10.1016/j.copbio.2018.12.003.
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Wang JP, Matthews ML, Williams CM, Shi R, Yang C, Tunlaya-anukit S, et al. Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis. Nature Communications 2018;9:1579. https://doi.org/10.1038/s41467-018-03863-z.
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Matthews ML, Williams CM. Region of attraction estimation of biological continuous Boolean models. 2012 IEEE International Conference on Systems, Man, and Cybernetics (SMC), 2012, p. 1700–5. https://doi.org/10.1109/ICSMC.2012.6377982.