1. Mario Latendresse, Efficiently Gap-Filling Reaction Networks, BMC Bioinformatics, 15:225, June 2014, DOI: 10.1186/1471-2105-15-225.

  2. Mario Latendresse, Markus Krummenacker, Peter D. Karp, Optimal metabolic route search based on atom mappings, Bioinformatics, March 2014, doi: 10.1093/bioinformatics/btu150 (full paper).
  3. Mario Latendresse, Jeremiah P. Malerich, Mike Travers, and Peter D. Karp, Accurate Atom-Mapping Computation for Biochemical Reactions, Journal of Chemical Information and Modeling, September 2012. JCIM
  4. Danny Dubé, Mario Latendresse, and Pascal Tesson, Conservative Groupoids Recognize only Regular Languages, Proceedings of the International Conference on Language and Automata Theory and Applications (LATA), Coruña, Spain, March 5-9, 2012. (See also the slides, written by Pascal Tesson, summarizing the work)
  5. Mario Latendresse, Markus Krummenacker, Miles Trupp, and Peter Karp, Construction and Completion of Flux-Balance Models from Pathway Databases, Bioinformatics, doi: 10.1093/bioinformatics/btr681, January 2012. Open access
  6. Mario Latendresse, Multiple Gap-Filling of Flux-Balance Models, 1st Conference on Constraint-based Reconstruction and Analysis (COBRA), Reykjavik, Iceland, June 24-26, 2011.
  7. Slides

  8. Mario Latendresse and Peter D. Karp, Web-based metabolic network visualization with a zooming user interface, BMC Bioinformatics, 12:176, 2011. PDF Open Access Version

  9. Mario Latendresse and Peter D. Karp, An Advanced Web Query Interface for Biological Databases, DATABASE - The Journal of Biological Databases and Curation, Oxford University Press, 2010. Open Access Version

  10. Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne M. Paley, Seung Y. Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang and Peter D. Karp, The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Research, Vol. 36, Database issue, 2008, pp. 623-631. Open Access Version

  11. Mario Latendresse, Simple and Efficient Compilation of List Comprehension in Common Lisp, in the Proceedings of the International Lisp Conference, Cambridge, UK, 1-4 April 2007, pp. 125-130. PDF, conference slides (PDF, 9MB)

  12. Mario Latendresse and Marc Feeley, Generation of fast interpreters for Huffman compressed bytecode, Science of Computer Programming, Volume 57, Issue 3, September 2005, (Advances in Interpreters, Virtual Machines and Emulators), pp. 295-317. (This is a modified and expanded version of the paper published at IVME 2003)

  13. Mario Latendresse, Masquerade Detection via Customized Grammars in Proceedings of Intrusion and Malware Detection and Vulnerability Assessment: Second International Conference, DIMVA 2005, Vienna, Austria, July 7-8, 2005. LNCS 3548, abstract, PDF
  14. Mario Latendresse, Rewrite Systems for Symbolic Evaluation of C-like Preprocessing, proceedings of CSMR'04, Tampere, Finland, pp.165-173, March 2004. PostScript, PDF, Slides in PDF
  15. Mario Latendresse, RegReg: a Lightweight Generator of Robust Parsers for Irregular Languages, Proc. of the 10th Working Conference on Reverse Engineering (WCRE), Victoria, Canada, November 2003. PostScript, PDF
  16. Mario Latendresse and Marc Feeley, Generation of Fast Interpreters for Huffman Compressed Bytecode, Proc. of the Workshop on Interpreters, Virtual Machines and Emulators, (IVME), San Diego, USA, ACM, June 2003. PostScript, PDF. This paper received the 2003 best DES/Northrop Grumman technical award DES award.
  17. Mario Latendresse, Fast Symbolic Evaluation of C/C++ Preprocessing Using Conditional Values, Proc. of the 7th European Conference on Software Maintenance and Reengineering (CSMR), Benevento, Italy, pp. 170-179, March 2003. PostScript, PDF
  18. Mario Latendresse, A persistent web application for distribution of weather information in Scheme, International Lisp Conference, San Francisco, USA, October 2002. PostScript, PDF
  19. Mario Latendresse and Marc Feeley, Fast and compact decoding of Huffman encoded virtual instructions, Technical Report DIRO 1219, November 2002. PostScript, PDF
  20. Findler, Latendresse, Felleisen. Behavioral Contracts and Behavioral Subtyping, FSE 2001, Vienna, Austria. PostScript, PDF
  21. Mario Latendresse, Automatic Generation of Compact Programs and Virtual Machines for Scheme, Scheme Workshop, Principles, Logics and Implementations of high-level programming Languages (PLI), Montréal, Canada, September 2000. PostScript, PDF
  22. Mario Latendresse, Génération de machines virtuelles pour l'exécution de programmes compressés, Thèse de Doctorat, Université de Montréal, Avril 2000. PostScript, PDF
  23. Mario Latendresse, Marc Feeley, Lazy Remote Procedure Call in C: Implementation and Performance , International Workshop on Parallel Algorithms and Software for Computational Fluid Dynamics, CERCA, Montréal, Canada, March 1997. PostScript, PDF
  24. Guy Lapalme, Mario Latendresse, A debugging environment for lazy functional languages, Lisp and Symbolic Computation, 5(3), pp. 271-287, September 1992. PostScript, PDF

Book Chapter

Mario Latendresse, Suzanne Paley and Peter D. Karp, Browsing Metabolic and Regulatory Networks with BioCyc, in Bacterial Molecular Networks Methods and Protocols, Methods in Molecular Biology, vol. 802, 2012. (DOI: 1007/978-1-61779-361-5)

Other Publications

  1. Peter Karp, Mario Latendresse, Ron Caspi, The Pathway Tools Pathway Prediction Algorithm, Standards in Genomic Sciences, Vol. 5, No. 3 (2011), Open Access (HTML)
  2. Caspi, R; Altman, T; Dale, JM; Dreher, K; Fulcher, CA; Gilham, F; Kaipa, P; Karthikeyan, AS; Kothari, A; Krummenacker, M; M. Latendresse, M; Mueller, LA; Paley, S; Popescu, L; Pujar, A; Shearer, AG; Zhang, P; Karp, PD, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Res., 38 (suppl_1): D473-479, 2010. Online Version
  3. Peter D. Karp , Suzanne M. Paley , Markus Krummenacker , Mario Latendresse , Joseph M. Dale , Thomas J. Lee , Pallavi Kaipa , Fred Gilham , Aaron Spaulding , Liviu Popescu , Tomer Altman , Ian Paulsen , Ingrid M. Keseler , and Ron Caspi Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology Briefings in Bioinformatics Advance Access published on January 1, 2010, Brief Bioinform 11: 40-79. Online Version

  4. Peifen Zhang, Kate Dreher, A. Karthikeyan, Anjo Chi, Anuradha Pujar, Ron Caspi, Peter Karp, Vanessa Kirkup, Mario Latendresse, Cynthia Lee, Lukas A. Mueller, Robert Muller, and Seung Yon Rhee, Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for PlantsPlant Physiology, vol. 153, no. 4, pp. 1479-1491, August 2010. Online version

  5. Peter D. Karp, Ingrid M. Keseler, Alexander G. Shearer, Mario Latendresse, Markus Krummenacker, Suzanne M. Paley, Ian Paulsen, Julio Collado-Vides, Socorro Gama-Castro, Martin Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, César Bonavides-Martinez and John Ingraham, Multidimensional annotation of the Escherichia coli K-12 genome, Nucleic Acids Research, Vol. 35, No. 22, 2007. Online Version

Mario Latendresse