Publications

1. Mario Latendresse.
   Efficiently Gap-Filling Reaction Networks,
   BMC Bioinformatics, 15:225 doi:10.1186/1471-2105-15-225, June 2014.
2. Mario Latendresse, Markus Krummenacker, and Peter D. Karp.
   Optimal Metabolic Route Search Based on Atom Mappings,
   Bioinformatics, doi: 10.1093/bioinformatics/btu150, March 2014.
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 (JCIM), September 2012.
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.
   Slides.
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.
6. Mario Latendresse.
   Multiple Gap-Filling of Flux-Balance Models,
   First Conference on Constraint-based Reconstruction and Analysis (COBRA), Reykjavik, Iceland, June 24-26, 2011.
7. Mario Latendresse and Peter D. Karp.
   Web-based metabolic network visualization with a zooming user interface,
   BMC Bioinformatics, 12:176, 2011.
8. 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.

9. 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, pp. 623-631, 2008.
10. Mario Latendresse.
    Simple and Efficient Compilation of List Comprehension in Common Lisp,
    Proceedings of the International Lisp Conference, Cambridge, UK, 1-4 April 2007, pp. 125-130.
    Conference slides.

11. Mario Latendresse and Marc Feeley.
    Generation of fast interpreters for Huffman compressed bytecode,
    Advances in Interpreters, Virtual Machines and Emulators,
    Science of Computer Programming, Volume 57, Issue 3, pp. 295-317, September 2005.
    

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

Book Chapter

Other Publications

1. Peter Karp, Mario Latendresse, Ron Caspi.
   The Pathway Tools Pathway Prediction Algorithm,
   Standards in Genomic Sciences, Vol. 5, No. 3, 2011.
2. Caspi, R; Altman, T; Dale, JM; Dreher, K; Fulcher, CA; Gilham, F; Kaipa, P; Karthikeyan, AS; Kothari, A; Krummenacker, 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.
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, January 1, pp. 40-79, 2010.

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 Plants,
   Plant Physiology, vol. 153, no. 4, pp. 1479-1491, August 2010.

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.