Publications

Journal Publications

  1. 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.
  2. 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 Arabidopsisroot stem cells,” Proc Natl Acad Sci USA, vol. 114, no. 36, pp. E7632–E7640, Sep. 2017.
  3. D. Muhammad, S. SchmittlingC. 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.
  4. 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.
  5. 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) 
  6. 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)
  7. C. Lin, J. Wang, Q. Li, H. Chen, J. Liu, P. Loziuk, J. SongC. 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.
  8. 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)
  9. 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.
  10. 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.
  11. H. Chen, J. SongC. 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.
  12. S. Marvel and C. Williams, “Set membership experimental design for biological systems,” BMC Systems Biology, vol. 6, no. 1, pp. 21, 2013.
  13. 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.
  14. 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 mono- lignol biosynthesis of Populus trichocarpa: LC–MS/MS based protein quantification and metabolic flux analysis”. Planta, vol. 236, no. 3, pp. 795-808, 2012.
Conference Proceedings, Refereed

  1. M. L. Matthews and C. Williams, “Region of attraction estimation of biological continuous Boolean models,” in Proceeding of IEEE Conference on Systems, Man, and Cybernetics, 2012. Link
  2. S. Marvel and C. Williams, “Set Membership State and Parameter Estimation for Nonlinear Differential Equations with Sparse Discrete Measurements,” in Proceedings of IEEE Conference on Systems, Man, and Cybernetics, 2012. Link
  3. S. Nabavi and C. Williams, “A Novel Cost Function for Parameter Estimation in Oscillatory Biochemical Systems,” in Proceeding of the 2012 IEEE SoutheastCon Conference, Orlando, FL., 2012 Link
  4. S. 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, 2011, pp, 140-143. Link
  5. C. Williams and S. Ocloo, “Design of Experiments using Bounded Approaches,” in Proceedings of the 11th International Conference on Systems Biology, October 2010, (Extended Abstract).
  6. M. de Luis Balaguer and C. Williams, “Estimation of Component Concentrations in Biological Systems via Interval Analysis”, in Proceedings of the 11th International Conference on Systems Biology, October 2010, (Extended Abstract) Link.
  7. M. de Luis Balaguer and C. Williams, “An Interval Method for State Estimation in Biological Systems,” in Proc. IEEE 44th ASILOMAR Conf. on Signals, Systems, and Computer, 2010. Link
  8. C. Williams, W. Alexander, and W. Edmonson, “Optimal Control Formulation of Constrained Least-Squares Estimation for Biochemical Pathway Estimation,” in Proceedings of the 8th International Conference on Systems Biology, October 2007, (Extended Abstract).
  9. W. 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, April 2007, pp. 136–142. Link
  10. C. Williams, W. Alexander, W. Edmonson, “Estimating the Unmeasured Dynamics of Biological Systems using a Constrained Real-Coded Genetic Algorithm,” in Proc. IEEE 40th ASILOMAR Conf. on Signals, Systems, and Computers, 2006, pp. 1855-1859. Link
  11. N. 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, April 2006, pp. 832-835. Link
  12. C. 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.
  13. T. 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.

Conference Presentations

  1. C. Williams and S. Marvel, “Set-based Parameter and State Estimation in Nonlinear Differential Equations Using Sparse Measurements,”  SIAM Conference on Uncertainty Quantification, Raleigh, NC, 2012
  2. C. Williams, H. Chen, J. Song, J. Ducoste, C. M. Shuford, Q. Li, J. Liu, R. Shi, D. Muddiman, R. Sederoff, and V. Chiang, “Predictive models of regulatory and metabolic pathways for monolignol biosynthesis,” Plant and Animal Genome Conference XX, San Diego, CA, 2012.
  3. J. Song, H. Chen, C. M. Shuford, Q. Li, J. Liu, R. Shi, D. Muddiman, C. Williams, J. Ducoste, R. Sederoff, and V. Chiang, “Multi-Enzyme System Modeling for Regulated Metabolic Pathways,” Presented at 1st Korean Student Technical and Leadership Conference, Chicago, IL, 2012.
  4. M. L. Matthews and C. Williams, “Estimating Regions of Attractions for Quadratic Nonlinear Biochemical Systems,” Presented at 10th Annual OPT-ED Alliance Day Conference, NC State University, October 2011.
  5. R. Damptey (UG) and C. Williams, “Parameter Estimation of Continuous Boolean Approximations of Enzyme Kinetics,” Presented at the 2011 Annual Biomedical Research Conference for Minority Students, St. Louis, Missouri, November 2011.
  6. J. Smith (UG), C. Williams, and J. Ducoste, “Steady State Analysis of Biological Systems Using Mathematical Modeling,” Presented at the 2011 Annual Biomedical Research Conference for Minority Students, St. Louis, Missouri, November 2011.
  7. R. Damptey (UG) and C. Williams, “Parameter Estimation of Continuous Boolean Approximations of Enzyme Kinetics,” Presented at the 10th Annual OPT-ED Alliance Day Conference, NC State University, October 2011.
  8. R. Damptey (UG) and C. Williams, “Assessing the Dynamics of Biochemical Pathways Using Continuous Boolean Approximations,” Undergraduate Summer Research Symposium, NC State University, August 2011.