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Publications by Shawn Martin
Please contact me for copies of these articles if you want to read them and they are unavailable to you (contact). Also see Google Scholar.

Book Chapters

  1. H. K. Ho, L. Zhang, K. Ramamohanarao, and S. Martin (2013), "A Survey of Machine Learning Methods for Secondary and Supersecondary Protein Structure Prediction," Protein Supersecondary Structure, A. Kister, Ed., Humana Press (Publisher)

  2. M. Misra, S. Martin, and J.-L. Faulon (2011), "Graphs: Flexible Representations of Molecular Structures and Biological Networks," Computational Approaches in Cheminformatics and Bioinformatics , R. Guha and A. Bender, Eds., Wiley. & Sons. (Publisher)

  3. S. Martin (2010), "Machine Learning based Bioinformatics Algorithms: Application to Chemicals," Handbook of Cheminformatics Algorithms, J.-L. Faulon and A. Bender, Eds., CRC Press (publisher)

  4. S. Martin, W. M. Brown, and J.-L. Faulon (2008), "Predicting Protein Interactions using Product Kernels," Advances in Biochemical Engineering/Biotechnology: Protein-Protein Interactions, M. Werther and H. Seitz, Eds., vol. 110, Springer-Verlag. (publisher, presentation)

  5. G. S. Davidson, S. Martin, K. Boyack, B. N. Wylie, J. Martinez, A. Aragon, M. Werner-Washburne, M. Mosquera-Caro, and C. L. Willman (2007), "Robust Methods in Microarray Analysis," Genomics and Proteomics Engineering in Medicine and Biology,  M. Akay, Ed., Wiley/IEEE. (publisher)

Journal Articles

  1. S. Martin (2012), "Lattice Enumeration for Inverse Molecular Design Using the Signature Descriptor," Journal of Chemical Information and Modeling, 52(7):1787-1797. (journal, software)

  2. S. Martin and J.-P. Watson (2011), "Non-Manifold Surface Reconstruction from High Dimensional Point Cloud Data," Computational Geometry: Theory and Applications, 44(8):427-441. (journal, software)

  3. S. Martin, A. Thompson, E. A. Coutsias, and J.-P. Watson (2010), "Topology of Cyclo-Octane Energy Landscape," Journal of Chemical Physics 132:234115. (journal, software, presentation)

  4. S. Martin, G. Chandler, and M. S. Derzon (2008), "Simulation of High Pressure Micro-Capillary 3He Counters," Journal of Physics G: Nuclear and Particle Physics 35:115103. (journal)

  5. W. M. Brown, S. Martin, S. N. Pollock, E. A. Coutsias, and J.-P. Watson (2008), "Algorithmic Dimensionality Reduction for Molecular Structure Analysis," Journal of Chemical Physics 129(6):064118.  (journal)

  6. W. M. Brown, A. Sasson, D. R. Bellew, L. A. Hunsaker, S. Martin, A. Leitao, L. M. Deck, D. L. Vander Jagt, and T. Oprea (2008), "Efficient Calculation of Molecular Properties from Simulation using Kernel Molecular Dynamics," Journal of Chemical Information and Modeling 48(8):1626-1637. (journal)

  7. J.-L. Faulon, M. Misra, S. Martin, K. Sale, and R. Sapra (2008), "Genome Scale Enzyme-Metabolite and Drug-Target Interaction Predictions using the Signature Molecular Descriptor," Bioinformatics 24(2):225-233. (journal, pdf)

  8. S. Martin, Z. Zhang, A. Martino, and J.-L. Faulon (2007), "Boolean Dynamics of Genetic Regulatory Networks Inferred from Microarray Time Series Data," Bioinformatics 23(7):866-874.  (journal, pdf, supplement)

  9. S. Martin, Z. Mao, L. S. Chan, and S. Rasheed (2007), "Inferring Protein-Protein Interaction Networks using Protein Complex Data," International Journal of Bioinformatics Research and Applications 3(4):480-492.   Expanded version of BIOT 2006 conference paper with same authors. (journal)

  10. S. Martin, R. D. Carr, and J.-L. Faulon (2006), "Random Removal of Edges from Scale Free Graphs," Physica A 371(2):870-876. (journal)

  11. C. Wilson, G. S. Davidson, S. Martin, E. Andries, J. Potter, R. Harvey, K. Ar, Y. Xu, K. J. Kopecky, D. P. Ankerst, H. Gundacker, M. L. Slovak, M. Mosquera-Caro, I-M. Chen, D. L. Stirewalt, M. Murphy, F. A. Shultz, H. Kang, X. Wang, J. P. Radich, F. R. Appelbaum, S. R. Atlas, J. Godwin, and C. L. Willman (2006), “Gene Expression Profiling of Adult Acute Myeloid Leukemia Identifies Novel Biologic Clusters for Risk Classification and Outcome Prediction,” Blood  108(2): 685-696. (journal, pdf)

  12. W. M. Brown, S. Martin, Mark D. Rintoul, and J.-L. Faulon (2006), "Designing Novel Polymers with Targeted Properties using the Signature Molecular Descriptor," Journal of Chemical Information and Modeling 46(2): 826-835. (journal)

  13. W. M. Brown, S. Martin, J. Chabarek, C. Strauss, and J.-L. Faulon (2006), "Prediction of Beta-Strand Packing Interactions using the Signature Product," Journal of Molecular Modeling 12(3):355-361. (journal, poster)

  14. J.-L. Faulon, W. M. Brown, and S. Martin (2005), "Reverse Engineering Chemical Structures from Molecular Descriptors: How Many Solutions?," Journal of Computer Aided Molecular Design 19(9-10):637-650. (journal)

  15. S. Martin, D. Roe, and J.-L. Faulon (2005), "Predicting Protein-Protein Interactions using Signature Products," Bioinformatics 21(2):218-226. (journal, pdf, software)

  16. C. Churchwell, M. D. Rintoul, S. Martin, D. P. Visco Jr., A. Kotu, R. S. Larson, L. O. Sillerud, D. C. Brown, and J.-L. Faulon (2004), "The Signature Molecular Descriptor 3. Inverse-Quantitative Structure-Activity Relationship of ICAM-1 Inhibitory Peptides," Journal of Molecular Graphics and Modeling 43(3):721-734. (journal)

  17. S. Martin, M. Kirby, and R. Miranda (2000), "Symmetric Veronese Classifiers with Application to Materials Design," Engineering Applications of Artificial Intelligence 13(5):513-520. (journal)

Letter to the Editor

  1. S. Martin, M. P. Mosquera-Caro, J. W. Potter, G. S. Davidson, E. Andries, H. Kang, P. Helman, R. L. Veroff, S. R. Atlas, M. Murphy, X. Wang, K. Ar, Y. Xu, I-M. Chen, F. A. Schultz, C. S. Wilson, R. Harvey, E. Bedrick, J. Shuster, A. J. Carroll, B. Camitta, and C. L. Willman (2007), "Gene Expression Overlap affects Karyotype Prediction in Pediatric ALL," Leukemia 21:1341-1344. (journal)

Conference Proceedings

  1. S. Martin, V. Subramanya, and S. Mills (2012), "Using Graph Layout to Generalise Focus+Context Image Magnification and Distortion," Image and Vision Computing New Zealand (IVCNZ): 97-102. (proceedings, presentation)

  2. S. Martin, W. M. Brown, R. Klavans, and K. Boyack (2011), "OpenOrd: An Open-Source Toolbox for Large Graph Layout," Visualization and Data Analysis (VDA): 7868-06. (proceedings, presentation, software)

  3. S. Martin and S. McKenna, (2007), "Predicting Building Contamination using Machine Learning," International Conference on Machine Learning and Applications (ICMLA): 192-197. (proceedings, presentation)

  4. J. Joo, S. Plimpton, S. Martin, L. Swiler, and J.-L. Faulon (2007), "Sensitivity Analysis of a Computational Model of the IKK-NF-kB-IkBa-A20 Signal Transduction Network," Annals of the New York Academy of Sciences 1115:221-239. (proceedings)

  5. S. Martin (2006), "An Approximate Version of Kernel PCA," Proceedings of the 5th International Conference on Machine Learning and Applications (ICMLA):239-244. (proceedings, presentation, poster)

  6. S. Martin, Z. Mao, L. S. Chan, S. Rasheed (2006), "Protein Interactions Extrapolated from Feline Protein Complexes," Proceedings of the 3rd Biotechnology and Bioinformatics Symposium (BIOT):45-52. (pdf, presentation)

  7. S. Martin (2006), "The Numerical Stability of Kernel Methods," Proceedings of the 9th International Symposium on Artificial Intelligence and Mathematics (AIMATH):P01. (pdf, presentation)

  8. S. Martin (2005), "Training Support Vector Machines using Gilbert's Algorithm," Proceedings of the 5th IEEE International Conference on Data Mining (ICDM):306-313.  (proceedings, presentation, software)

  9. S. Martin and A. Backer (2005), "Estimating Manifold Dimension by Inversion Error," Proceedings of the 20th annual ACM Symposium on Applied Computing (SAC):22-26. (proceedings, presentation)

  10. S. Martin, M. Kirby, and R. Miranda (2000), "Kernel/Feature Selection for Support Vector Machines Applied to Materials Design," Proceedings of 9th IFAC Symposium on Artificial Intelligence in Real Time Control (AIRTC):29-34. (pdf)

Extended Abstracts

  1. S. Martin, W. M. Brown, J.-L. Faulon, D. Weis, D. Visco, and J. Kenneke (2005), "Inverse Design of Large Molecules using Linear Diophantine Equations," Proceedings of the 4th IEEE Computational Systems Bioinformatics Workshops (CSBW):11-16. (proceedings, poster)

  2. S. Martin, G. S. Davidson, E. E. May, J.-L. Faulon, and M. Werner-Washburne (2004), "Inferring Genetic Networks from Microarray Data," Proceedings of the 3rd IEEE Computational Systems Bioinformatics (CSB):566-569. (proceedings, poster)

  3. J.-L. Faulon, S. Martin, and R. D. Carr (2004), "Dynamical Robustness in Gene Regulatory Networks," Proceedings of the 3rd IEEE Computational Systems Bioinformatics (CSB):626-627. (proceedings, pdf, poster)

Dissertation and M.S. Paper

  1. S. Martin (2001), Techniques in Support Vector Classification, Ph. D. Dissertation, Colorado State University. (pdf)

  2. S. Martin (1997), "Concerning the Quadratic Relations which define the Grassman Manifold," M.S. Paper, Colorado State University. (pdf)

Last Updated Jan. 24, 2013.