Journal Publications

  1. Kudenov, C. G. Scarboro, M. Boyette, G. Craig Yencho, and C. Williams, “Internal defect scanning of sweetpotatoes using scattering spectroscopy,”, PLoS One, accepted.
  2. 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, accepted.
  3. 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.
  4. Matthews and C. Williams, “Multi-scale modeling of cross-regulatory transcript and protein influences,” Methods in Molecular Biology, accepted.
  5. 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, 160, pp 405-418, 2020.
  6. 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 Thaliana,” Methods in Cell Biology: Plant Cell Biology, vol. 160, pp. 419-436, 2020.
  7. 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.
  8. 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.
  9. 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.
  10. Buckner, I. Madison, H. Chou, C. E. Melvin, R. Sozzani, C. Williams, Terri A. Long, “Automated imaging, tracking, and analytics pipeline for differentiating environmental effects on root meristematic cell division,” Frontiers in Plant Science, vol. 10, pp. 1487, 2019. (CW and TL co-corresponding authors)
  11. 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.
  12. 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)
  13. 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)
  14. 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.
  15. 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).
  16. 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.
  17. 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.
  18. Friesner, S. Assmann, R. Bastow, J. Bailey-Serres, J. Beynon, V. Brendel, R. Buell, A. Buksch, J. Dinneny, C. Doherty, A. Eveland, M. Gehan, M. Gonzales, E. Grotewold, U. Kramer, Cody Markelz, Molly Megraw, Blake C. Meyers, Jim Murray, Nicholas J. Provart, S. Rhee, R. Smith, E. Spalding, C. Taylor, T. Teal, K. Torii, C. Town, M. Vaughn, R. Vierstra, D. Ware, O. Wilkins, C. Williams, S. M. Brady, “The Next Generation of Training for Arabidopsis Researchers: Optimizing Training in Bioinformatics and Quantitative Biology for the Future,” Plant physiology175, no. 4 (2017): 1499-1509.
  19. 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.
  20. 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)
  21. Wang, S. Tunlaya‐Anukit, R. Shi, T. Yeh, L. Chuang, F. Isik, C. Yang, J. Liu, Q. Li, P. Loziuk, P. Naik, D. Muddiman, J. Ducoste, C. Williams, R. Sederoff, V. 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.
  22. 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)
  23. 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)
  24. 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.
  25. 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)
  26. 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.
  27. 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.
  28. 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.
  29. Marvel and C. Williams, “Set membership experimental design for biological systems,” BMC Systems Biology, vol. 6, no. 1, pp. 21, 2013.
  30. 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.
  31. 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.

Books and Book Chapters

  1. W. Alexander and C. Williams, Digital Signal Processing: Principles, Algorithms and System Design, Academic Press, 2016.

Conference Proceedings, Refereed

  1. Gordon and C. Williams, “PVC Detection Using a Convolutional Autoencoder and Random Forest Classifier,” in Proceedings for Pacific Symposium on Biocomputing (PSB) 2019, pp. 42-53, https://doi.org/10.1142/9789813279827_0005.
  2. Buckner, C. Melvin, C. Ottley, A. Balaguer, R. Sozzani, and C. Williams, “Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms,” The 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 818-821, 2018.
  3. Koryachko, S. Haque, and C. Williams, “Scalable approach to data driven transcriptome dynamics modeling,” in Proceedings for the10th International Conference on Bioinformatics and Computational Biology (BICoB 2018), pp. 142-137, 2018.
  4. Qazi and C. Williams, “Controller structure for optimized region of attraction of Polynomial Systems,” in Proceeding of the 49th ASILOMAR Conf. on Signals, Systems, and Computer, pp. 952 – 959, 2015.
  5. de Luis Balaguer and C. Williams, “An HMM approach to identify components that influence phenotypes,” in Proceeding of 2014 IEEE International Conference on Systems, Man, and Cybernetics (SMC), pp. 1300-1305, 2014.
  6. Matthews and C. Williams, “Region of attraction estimation of biological continuous Boolean models,” in Proceeding of 2012 IEEE International Conference on Systems, Man, and Cybernetics (SMC), pp. 1700 – 1705, 2012.
  7. Marvel and C. Williams, “Set membership state and parameter estimation for nonlinear differential equations with sparse discrete measurements,” in Proceedings of 2012 IEEE International Conference on Systems, Man, and Cybernetics (SMC), pp. 72-77, 2012.
  8. Nabavi and C. Williams, “A novel cost function for parameters estimation in oscillatory biochemical systems,” in 2012 Proceeding of IEEE SoutheastCon, pp. 1-8, 2012.
  9. Marvel, M. de Luis Balaguer, and C. Williams, “Parameter estimation in biological systems using interval methods with parallel processing,” in Proceedings of the 2011 International Workshop on Computational Systems Biology, pp. 140-143, 2011.
  10. de Luis Balaguer and C. Williams, “Estimation of component concentrations in biological systems via Interval Analysis,” in 2010 IEEE Conference Proceedings of the 44th ASILOMAR Conf. on Signals, Systems, and Computer, pp. 993 – 997, 2010.
  11. Edmonson, S. Ocloo, C. Williams, and W. Alexander, “The use of interval methods in signal processing and control for systems biology,” in Proceedings of the 1st IEEE Symposium on Foundations of Computational Intelligence, pp. 136–142, 2007.
  12. Williams, W. Alexander, W. Edmonson, “Estimating the unmeasured dynamics of biological systems using a constrained real-coded genetic algorithm,” in 2006 IEEE Conference Proceedings of the 40th ASILOMAR Conf. on Signals, Systems, and Computer, pp. 1855-1859, 2006.
  13. Cahill, C. Williams, S. Chen, L. Ray, and M. Goodgame, “Incorporating spatial information into entropy estimates to improve multimodal image registration,” IEEE International Symposium on Biomedical Imaging, pp. 832-835, 2006.
  14. Williams, W. Alexander, and T. Pompey, “Independent and principal component analyses of the global stress response of Bacillus subtilis,” IEEE International Workshop on Genomic Signal Processing and Statistics, May 2005.
  15. Pompey, C. Williams, J. Kim, and W. Alexander, “Analyzing the reliability of ICA estimates of Bacillus subtilis,” IEEE International Workshop on Genomic Signal Processing and Statistics, May 2005.

Patents

  1. Smith, N. Chinta, R. McCormick, D. Ivers, C. Williams, D. Badheka, H. T. Nagle, S. Dasari, S. Samadi, “Predictive QRS Detection and R-to-R Timing Systems and Methods,” U.S. Patent Application 16401368, Filed May 02, 2019.
  2. Chen, L. Ray, N. Cahill, M. Goodgame, and C. Williams, “Method of image registration using mutual information,” U.S. Patent 7,263,243, Aug. 28, 2007.

Research Presentations

  1. Samiul Haque, Sarah Bell, Edgar Lobaton, Natalie Nelson, Michael Kudenov, Mike Boyette, and Cranos Williams,Sweetpotato Shape Classification using Computer Vision and Supervised Machine Learning, National Sweetpotato Collaborators Annual Meeting, January 2020, Nashville, TN, USA.
  2. Haque, S., Muhammad, D., Chou H., Ducoste, J.J., Tuck, J.M., Long, T.A. and Williams, C.M., “Epidermal Gene Regulatory Network of Arabidopsis Thaliana under Iron Deficiency,”2019 Society for Experimental Biology Annual Meeting, Seville, Spain, 2-5 July 2019.
  3. Matthews, M.L., Wang, J.P., Sederoff, R, Chiang, V.L., Williams, C.M., “Computational model for predicting monolignol transcript and protein abundances in Populus trichocarpaunder single and combinatorial monolignol gene knockdowns,” 2019 Society for Experimental Biology Annual Meeting, Seville, Spain, 2-5 July 2019.
  4. Megan Matthews and Cranos Williams, “Computational Model for Predicting Monolignol Transcript and Protein Abundances in Populus trichocarpaunder Single and Combinatorial Monolignol Gene Knockdowns”, Plant and Animal Genome Conference, 2019, California.
  5. Max Gordon and Cranos Williams, “PVC Detection Using a Convolutional Autoencoder and Random Forest Classifier,” Pacific Symposium on Biocomputing (PSB) January 2019, Hawaii, Hawaii.
  6. Eli Buckner and Cranos Williams, “Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms,” 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), July 2018, Hawaii.
  7. “Multiscale Modeling of Lignin Biosynthesis in Populus trichocarpa,” Williams, Plant and Animal Genome International Conference, San Diego, CA., January 2020.
  8. “Dynamic modeling of the iron deficiency modulated transcriptome response in Arabidopsis thaliana roots,” Williams, Poster Presentation, International Plant Systems Biology Conference, Roscoff, France, 2018.
  9. “Systematically uncovering modes of regulation and control in monolignol biosynthesis,” Williams, Forest Tree Molecular Biology and Biotechnology Symposium, Harbin, China, 2018
  10. “From Lab to Field: Developing agro-textile nanotechnology for accelerating the development of stress tolerant high-yield crops” Williams, CALS Innovation Grant Update Meeting, April 2018.