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Selected Publications

  1. J. D. MacCuish and N. E. MacCuish, "Clustering in Bioinformatics and Drug Discovery", Chapman & Hall, 2010 [link]
  2. John MacCuish, Norah E. MacCuish, Mitchell Chapman, Michael Hawrylycz, "quasi-Monte Carlo methods for the generation of molecular shape fingerprints", submitted for review Nov. 9th, 2010
  3. J. Pinto, X. Qin, J. He, E. Pontelli, D. Bevan, N. MacCuish, J. MacCuish, M. Chapman, D. Moreland, "BIOPS Interactive: An e-learning platform focused on protein structure and DNA, BioScene, Volume 35(2), 2009
  4. N. E. MacCuish, J. D. MacCuish, “Clustering Compound Data: Asymmetric Clustering of Chemical Datasets”, Chemometrics and Cheminfomatics, ACS Symposium Series, Vol 894, ed. B. K. Lavine, Oxford University Press, 2005
  5. TJ O'Donnell; Norah E. MacCuish; J. D. MacCuish; "Virtual Classrooms and E-Learning: Bringing Cheminformatics Training Into Academic and Industrial Settings", ChemAxon 2005 User Group Meeting Proceedings, Budapest, Hungary, May 19th, 2005
  6. A.Nicholls; Norah E. MacCuish; J. D. MacCuish, “Variable Selection and Model Validation of 2D and 3D Molecular Descriptors”, Journal of Computer-Aided Molecular Design, 18, 2004, pp. 451-474
  7. J.D. MacCuish, C.A. Nicolaou, N.E. MacCuish, "Ties in Proximity and Clustering Compound Data", Journal of Chemical Information and Computer Science, Vol. 41 (1), 2001, pp. 134-146
  8. John D. MacCuish, Christos A. Nicolaou, Assignee: Bioreason Inc., "Method and System for Artificial Intelligence Directed Lead Discovery Through Multi-Domain Agglomerative Clustering", United States Patent , MBHB Case No. 99,832.
  9. Christos A. Nicolaou, John D. MacCuish, Susan Y. Tamura, "A new multi-domain clustering algorithm for lead discovery that exploits ties in proximities", Proceedings from the 13th European Symposium on Quantitative Structure-Activity Relationships, Prous Science, September, 2000, pp.486-495.
  10. J.F. Cargill, N.E. MacCuish, "Object-relational databases: the next wave in pharmaceutical data management", Drug Discovery Today, 3(12), 1998, pp. 547-551
  11. N.E. Shemetulskis, D. Weininger, C.J. Blankley, J.J. Yang, C. Humblet, "Stigmata: An Algorithm To Determine Structural Commonalities in Diverse Datasets", Journal of Chemical Information and Computer Sciences , 36(4),1996, pp. 862-871
  12. J. MacCuish, A. McPherson, J. Barros, P. Kelly. "Interactive Layout Mechanisms for Image Database Retrieval". IS&T/SPIE Symposium on Electronic Imaging: Science & Technology, February, 1996
  13. J.Berry, N. Dean, P. Fasel, M. Golberg, E. Johnson, J. MacCuish, G. Shannon and S. Skiena. "LINK: A Combinatorics and Graph Theory Workbench, for Applications and Research", DIMACS Technical Report 95-15 and Los Alamos Unclassified Report 95-1982, 1995.
  14. Norah E. Shemetulskis, James B. Dunbar Jr., Bonnie W. Dunbar, David W. Moreland and Christine Humblet, "Enhancing the diversity of a corporate database using chemical database clustering and analysis", Journal of Computer-Aided Molecular Design, 9, 1995, pp. 407-416.
  15. J. MacCuish, S. Mniszewski, G. Shannon, and B. Yantis. "Digital Village". Los Alamos Science, Number 22, p. 150-155, 1994
  16. G. Shannon, J. MacCuish and E. Johnson. "A case study in algorithm animation: Maximum flow algorithms", DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 12, American Mathematical Society, 1993

Selected Presentations

  1. "Cluster Analysis is not Rocket Science but it can Blow Up: A brief survey of cluster analysis and its dangerous use in bioinformatics and drug discovery", John MacCuish, New Mexico State University Computer Science Colloquium, April 2010 [link]
  2. "quasi-Monte Carlo integration and molecular shape fingerprints", John D. MacCuish, Norah E. MacCuish, Michael Hawrylycz, and Mitch Chapman, ACS San Francisco COMP, March 21, 2010 [link]
  3. "Fragment Database Analysis Using Molecular Shape Fingerprints", John D. MacCuish,Norah E. MacCuish, Michael Hawrylycz, and Mitch Chapman, ACS San Francisco CINF, March 21, 2010 [link]
  4. "Interactive Maps: from h1n1 swine flu to solar power", John MacCuish, Ignite New Mexico, Santa Fe, September 15, 2009 [link]
  5. "Computational Tools in Dynamic Drug Design Workflows", Norah MacCuish, John MacCuish, and Mitch Chapman, ACS National Spring National Meeting in Philadelphia, COMP Session, August 18, 2008 [link]
  6. "Parallel tiered clustering for large data sets using a modified Taylor’s algorithm", John MacCuish, Norah MacCuish, and Mitch Chapman, (Poster)ICCS Noordwijkerhout, Holland, June 2, 2008 [link]
  7. "Dynamic web application for drug design research", Mitch Chapman, Norah MacCuish, John MacCuish, John Bradley, and John Blankley, (Poster) ICCS Noordwijkerhout, Holland, June 2, 2008 [link]
  8. "Where Bioinformatics and Cheminformatics Meet: A Virtual Classroom", John MacCuish, Norah MacCuish, Mitch Chapman, Enrico Pontelli, Jing He, Jorge Pinto, Xiaoxiao Qin, David Bevan, David Moreland, Biocomputing Day, March 30, 2007 [link]
  9. "Substructure commonality analysis and visualization with new key-based binary fingerprinter", Norah MacCuish and John MacCuish, ACS National Spring National Meeting in Chicago, CINF Session, March 24-28, 2007 [link]
  10. "Evaluating Asymmetry in Similarity Searching and Clustering via Multidimensional Scaling and Procrustes Analysis", John MacCuish and Norah MacCuish, ACS National Fall National Meeting in San Francisco, General Computational Chemistry Session, September 10, 2006 [link]
  11. "Web-based Computational Laboratory", Norah MacCuish and John MacCuish, ACS National Fall National Meeting in San Francisco, General Computational Chemistry Session, September 10, 2006
  12. "A Virtual Classroom in Cheminformatics", Norah MacCuish, Biennial Conference on Chemical Education, Purdue University, IN, August 1, 2006 (Workshop and Presentation)
  13. "Web-based Computational Laboratory", Norah MacCuish, American Chemical Society Mid-Atlantic Regional Meeting, Hershey, Penn. June 8, 2006
  14. "Cheminformatics Virtual Classroom", John MacCuish, Norah MacCuish, Mitch Chapman, and TJ O'Donnell, Biocomputing @ UNM, UNM Albuquerque, April 28, 2006
  15. "SAESAR: Software workbench for the interpretation and visualization of shape, electrostatics and structure activity relationships", Norah E. MacCuish, Anthony Nicholls, John D. MacCuish, and Mitch Chapman, 230th American Chemical Society National Meeting, Division of Computers in Chemistry, Washington, DC, August 28, 2005
  16. "Virtual Classrooms and e-Learning: Bringing Cheminformatics Training into Academic and Industrial Settings", TJ O'Donnell, Norah MacCuish, and John MacCuish, ChemAxon User Group Meeting, Budapest, Hungary, May 19, 2005
  17. "Cheminformatics Virtual Classroom", Norah MacCuish and John MacCuish, Biocomputing @ UNM, UNM Albuquerque, April 22, 2005
  18. "Virtual Classrooms and e-Learning: Bringing Cheminformatics Training into Academic and Industrial Settings", Norah MacCuish and John MacCuish, CUPVI - OpenEye Scientific Software's User Group Meeting, Santa Fe, February 22, 2005
  19. "Clustering Ambiguity: An Overview", J.MacCuish and N. MacCuish, 3rd Joint Sheffield Conference on Chemoinformatics, University of Sheffield, April 23, 2004
  20. "Variable Selection and Model Validation of 2D and 3D Molecular Descriptors", A.Nicholls, N.MacCuish, and J. MacCuish, 227th ACS, Anaheim, Ca., March 29, 2004
  21. "SAESAR Shape and Electrostatics in SAR", N.MacCuish, A.Nicholls, and J. MacCuish, CUPV - OpenEye Scientific Software's User Group Meeting, Santa Fe, NM March 1, 2004
  22. "OEChem Enabled: Data Mining Tools and Chemoinformatics Virtual Classroom", N.MacCuish, J. MacCuish, TJ O'Donnell, Tudor Oprea, Mitch Chapman, Poster CUPV - OpenEye Scientific Software User Group Meeting, Santa Fe, NM February 29, 2004
  23. "Clustering ambiguity and binary descriptors", J. MacCuish and N. MacCuish, 226th ACS, September 8, 2003, New York, NY
  24. "Investigations in shape clustering for lead hopping", N. MacCuish and J. MacCuish, 226th ACS New York September 8, 2003 New York, NY
  25. "Tversky Shape Clustering for Screening Data", N. MacCuish and J. MacCuish, OpenEye Scientific Software User Group Meeting CUPIV Santa Fe, NM February 2003
  26. "Russian Doll: Structure Clustering Using Asymmetry", N. MacCuish, J. MacCuish and J. Bradshaw, Daylight Chemical Information Systems User Group Meeting MUG'03, Santa Fe, NM, February 2003
  27. "Asymmetric Shape Clustering for Lead Hopping", Norah E. MacCuish and John D. MacCuish, Biology, Chemistry, and Computing for Drug Discovery in New Mexico, New Mexico Tech., Socorro, NM, January, 2003
  28. "Asymmetric and Symmetric Clustering Chemical Data Sets with the Tversky Measure", Norah E. MacCuish and John D. MacCuish, American Chemical Society 2002 Rocky Mountain Regional Meeting, October, 2002
  29. "Asymmetric Clustering of Chemical Data Sets: An Investigation", Norah E. MacCuish and John D. MacCuish, 224th American Chemical Society National Meeting, August, 2002
  30. "A new multi-domain clustering algorithm for lead discovery that exploits ties in proximities", Christos A. Nicolaou, John D. MacCuish, Susan Y. Tamura, 13th European Symposium on Quantitative Structure-Activity Relationships, Dusseldorf, August-September, 2000
  31. "Ambiguities due to ties in proximity in lead discovery clustering algorithms", J.D. MacCuish, C.A. Nicolaou, N.E. MacCuish, American Chemical Society National Meeting, San Francisco, March, 2000
  32. "Ties and Clustering", John MacCuish, Christos Nicolaou and Norah MacCuish, MUG2000, Daylight CIS User Group Meeting, February, 2000
  33. "The Daylight Datablade", N. MacCuish, EuroMug'98, Daylight European User Group Meeting, October, 1998
  34. "Database Integration", N. Shemetulskis, MUG'98 Daylight User Group Meeting, February, 1998
  35. "Extracting Structural Commonalities from Chemically Diverse Datasets", Norah Shemetulskis, Dave Weininger, C. John Blankley, J. Scott Dixon, Presentation made at the Second Annual Conference for the Society for Biomolecular Screening, Basel, Switzerland, October 1996
  36. "Interactive Layout Mechanisms for Image Database Retrieval", J. MacCuish, A. McPherson, J. Barros, and P. Kelly; IS&T/SPIE Symposium on Electronic Imaging: Science & Technology, February, 1996
  37. "Animating Network Flow Algorithms", G. Shannon, J. MacCuish, and E. Johnson, DIMACS Workshop on Computational Support for Discrete Mathematics, Rutgers University, New Jersey, March 1992
  38. "Animating Embedding Heuristics", K. Desch, C. Edge, K. Simonsen, G. Shannon, and J. MacCuish; DIMACS Workshop on Computational Support for Discrete Mathematics, Rutgers University, New Jersey, March 1992
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