| Articles and Presentations |
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Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR
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Pierre Baldi, Daniel S. Hirschberg and Ramzi J. Nasr.
"Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR."
Submitted, (2008).
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| 100K random chemical data set |
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Discovery of Power-Laws in Chemical Space
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Ryan W. Benz, S. Joshua Swamidass, and Pierre Baldi.
"Discovery of Power-Laws in Chemical Space."
Submitted, (2008).
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Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction
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Jonathan H. Chen and Pierre Baldi.
"Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction."
Journal of Chemical Education, submitted, (2007).
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Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval
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Pierre Baldi, Ryan W. Benz, Daniel S. Hircshberg, and S. Joshua Swamidass.
"Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval."
Journal of Chemical Information and Modeling, 47, 6, 2098-2109, (2007).
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A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval
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S. Joshua Swamidass and Pierre Baldi.
"A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval."
Journal of Chemical Information and Modeling, 47, 3, 952-964, (2007).
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Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time
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S. Joshua Swamidass and Pierre Baldi.
"Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time."
Journal of Chemical Information and Modeling, 47, 2, 302-317, (2007).
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Virtual High-Throughput Screening with Two-Dimensional Kernels
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Chloe A. Azencott and Pierre Baldi.
"Virtual High-Throughput Screening with Two-Dimensional Kernels."
In: Hands-On Pattern Recognition. Challenges in Data Representation, Model Selection, and Performance Prediction,
I. Guyon, G. Cawley, G. Droor, and A. Saffari Editors, Lulu Press, (2007)
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Effective Compression of Monotone and Quasi-Monotone Sequences of Integers
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Daniel S. Hirschberg and Pierre Baldi.
"Effective Compression of Monotone and Quasi-Monotone Sequences of Integers."
Proceedings of the 2008 Data Compression Conference (DCC 08), Snowbird, UTA, IEEE Computer Society Press, (2008).
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ChemDB Update - Full-Text Search and Virtual Chemical Space
(Supplementary Materials)
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Jonathan H. Chen; Erik Linstead; S. Joshua Swamidass; Dennis Wang; Pierre Baldi
Bioinformatics Advance Access 2007; doi: 10.1093/bioinformatics/btm341.
Bioinformatics 23: 2348-2351.
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| Chemoinformatics Tutorial, ISMB 2006 |
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Prof. Pierre Baldi presents a tutorial on chemoinformatics at the
2006 ISMB Conference
in Fortaleza, Brazil.
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One-to-Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties
(Supplementary Materials)
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Chloe-Agathe Azencott, Alexandre Ksikes, S Joshua Swamidass, Jonathan H Chen, Liva Ralaivola and Pierre Baldi.
(2007).
"One-to-Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties."
Journal of Chemical Informatics and Modeling, 47(3):965-974, (2007)
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ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources
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Jonathan Chen*, S. Joshua Swamidass*, Yimeng Dou, Jocelyne Bruand, Pierre Baldi.
(2005).
ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources.
Bioinformatics, 21 (22): 4133-4139
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Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity
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S. Joshua Swamidass*, Jonathan Chen*, Peter Phung, Jocelyne Bruand, Liva Ralaivola, and Pierre Baldi.
"Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity."
Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05.
Bioinformatics, 21 (Supplement 1), i359-368, (2005).
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Graph Kernels for Chemical Informatics
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Liva Ralaivola, S. Joshua Swamidass, Hiroto Saigo, and Pierre Baldi.
(2005).
"Graph Kernels for Chemical Informatics."
Neural Networks, special issue on Neural Networks and Kernel Methods for Structured Domains,
18 (8): 1093-1110.
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* These authors contributed equally