Publications
- 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
- 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 (by Pascal Tesson)
- 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
- Mario Latendresse, Multiple Gap-Filling of Flux-Balance
Models, 1st Conference on Constraint-based Reconstruction and
Analysis (COBRA), Reykjavik, Iceland, June 24-26, 2011.
Slides
- 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
- 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
- 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
- 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)
- 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)
- 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
- 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
- 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
- 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.
- 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
- Mario Latendresse, A persistent web application
for distribution of weather information in Scheme, International Lisp
Conference, San Francisco, USA, October 2002. PostScript,
PDF
- Mario Latendresse and Marc Feeley, Fast and compact decoding of
Huffman encoded virtual instructions, Technical Report DIRO 1219, November 2002.
PostScript,
PDF
- Findler, Latendresse, Felleisen. Behavioral Contracts and
Behavioral Subtyping, FSE 2001, Vienna, Austria.
PostScript,
PDF
- 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
- Mario Latendresse, Génération de machines virtuelles pour
l'exécution de programmes compressés, Thèse de Doctorat,
Université de Montréal, Avril 2000. PostScript,
PDF
- 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
- 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
- Peter Karp, Mario Latendresse, Ron Caspi, The Pathway Tools
Pathway Prediction Algorithm, Standards in Genomic Sciences,
Vol. 5, No. 3 (2011), Open Access (HTML)
- 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. Online Version
- 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
- 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
- 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