| An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases | |
| Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi Recent Advances of Neural Network Models and Applications Smart Innovation, Systems and Technologies, 26, 63-74, (2014) | |
| Small-molecule 3D Structure Prediction Using Open Crystallography Data | |
| P. Sadowski and P. Baldi Journal of Chemical Information and Modeling, 53, 12, 3127-3130, (2013) | |
| A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Reactions | |
| I. Chang and P. Baldi. Bioinformatics, 29, 10, 1299-1307, (2013) | |
| Deep Architectures and Deep Learning in Chemoinformatics: the Prediction of Aqueous Solubility for Drug-Like Molecules | |
| A. Lusci, G. Pollastri, and P. Baldi. Journal of Chemical Information and Modeling , 53, 7, 1563–1575, (2013) | |
| COBRA: A Computational Brewing Application for Predicting the Molecular Composition of Organic Aerosols | |
| D. R. Fooshee, T. B. Nguyen, S. A. Nizkorodov, J. Laskin, A. Laskin, and P. Baldi. Environmental Science & Technology, 46, 11, 6048–6055, (2012). | |
| SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations | |
| K. Nagata, A. Randall, and P. Baldi. Protein: Structure, Function, and Bioinformatics, 80, 1, 142–153, (2012). | |
| Speeding Up Chemical Searches Using the Inverted Index: the Convergence of Chemoinformatics and Text Search Methods | |
| R. Nasr. R. Vernica, C. Li, and P. Baldi. Journal of Chemical Information and Modeling , 52, 4, 891—900, (2012). | |
| Deep Architectures for Protein Contact Map Prediction | |
| P. Di Lena, K. Nagata, and P. Baldi. Bioinformatics , 28, 2449-2457, (2012). | |
| ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning. | |
| M. Kayala, P. Baldi. Journal of Chemical Information and Modeling, 52, 10, American Chemical Society, 2526-2540 (2012). | |
| Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response to the Letter by the Cambridge Crystallographic Data Center | |
| P. Baldi. Journal of Chemical Information and Modeling , 51, 12, 3029–3029, (2011). | |
| Learning to Predict Chemical Reactions | |
| M. Kayala, C. Azencott, J. Chen, P. Baldi. Journal of CHemical Information and Modeling, 51, 9, 2209-2222, (2011). | |
| When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values | |
| P. Baldi and R. Nasr. Journal of Chemical Information and Modeling (2010). | |
| Supplementary Data | |
| No Electron Left-Behind: a Rule-Based Expert System to Predict Chemical Reactions and Reaction Mechanisms | |
| J. Chen and P. Baldi. Journal of Chemical Information and Modeling, 49, 9, 2034-2043, (2009). | |
| An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases | |
| P. Baldi and D. Hirschberg. Journal of Chemical Information and Modeling, in press, (2009). | |
| Large Scale Study of Multiple-molecule Queries | |
| R. Nasr*, S. Joshua Swamidass*, and P. Baldi. Journal of Cheminformatics 1, 7, (2009). | |
| Supplementary Data | |
| Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR | |
| P. Baldi, D. S. Hirschberg and R. J. Nasr. Journal of Chemical Information and Modeling 48 (7), 1367-1378, (2008). | |
| 100K random chemical data set | |
| Discovery of Power-Laws in Chemical Space | |
| R. W. Benz, S. Joshua Swamidass, and P. Baldi. Journal of Chemical Information and Modeling 48(6), 1138-1151, (2008). | |
| Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction | |
| J. H. Chen and P. Baldi. Journal of Chemical Education 2008(85):1699, (2008). | |
| Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval | |
| P. Baldi, R. W. Benz, D. S. Hircshberg, and S. Joshua Swamidass. Journal of Chemical Information and Modeling, 47, 6, 2098-2109, (2007). | |
| A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval | |
| S. Joshua Swamidass and P. Baldi. Journal of Chemical Information and Modeling, 47, 3, 952-964, (2007). | |
| Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time | |
| S. Joshua Swamidass and P. Baldi. Journal of Chemical Information and Modeling, 47, 2, 302-317, (2007). | |
| Virtual High-Throughput Screening with Two-Dimensional Kernels | |
| C. A. Azencott and P. Baldi. 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). | |
| Effective Compression of Monotone and Quasi-Monotone Sequences of Integers | |
| D. S. Hirschberg and P. Baldi. Proceedings of the 2008 Data Compression Conference (DCC 08), Snowbird, UTA, IEEE Computer Society Press, (2008). | |
| ChemDB Update - Full-Text Search and Virtual Chemical Space (Supplementary Materials) | |
| J. H. Chen, E. Linstead, S. Joshua Swamidass, D. Wang, P. Baldi. Bioinformatics Advance Access 2007; doi: 10.1093/bioinformatics/btm341. Bioinformatics 23: 2348-2351. | |
| Chemoinformatics Tutorial, ISMB 2006 | |
| P. Baldi presents a tutorial on chemoinformatics at the 2006 ISMB Conference in Fortaleza, Brazil. | |
| One-to-Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties (Supplementary Materials) | |
| C. Azencott, A. Ksikes, S. Joshua Swamidass, J. H Chen, L. Ralaivola and P. Baldi. Journal of Chemical Informatics and Modeling, 47(3):965-974, (2007). | |
| ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources | |
| J. Chen*, S. Joshua Swamidass*, Y. Dou, J. Bruand, P. Baldi. Bioinformatics, 21 (22): 4133-4139, (2005). | |
| Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity | |
| S. Joshua Swamidass*, J. Chen*, P. Phung, J. Bruand, L. Ralaivola, and P. Baldi. Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, 21 (Supplement 1), i359-368, (2005). | |
| Graph Kernels for Chemical Informatics | |
| L. Ralaivola, S. Joshua Swamidass, H. Saigo, and P. Baldi. Neural Networks, special issue on Neural Networks and Kernel Methods for Structured Domains, 18 (8): 1093-1110, (2005). | |
* These authors contributed equally
Disclaimer: Downloadable articles above may be slightly different from published versions.
Disclaimer: Downloadable articles above may be slightly different from published versions.