University of California in Irvine (UCI)
School of Information and Computer Sciences (ICS)
Institute for Genomics and Bioinformatics (IGB)
 
Publications

Publications

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2010

2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 |
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1986
 
  • Test   Test   Neuroscience

2009

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1986
 
  • Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability.   D. Guzman, A. Randall, P. Baldi, and Z. Guan.   Proceedings of the National Academy of Sciences USA, in press, (2009).

  • 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, in press, (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, 49, 8, 1866--1870, (2009).

  • Large Scale Study of Multiple-Molecule Queries.   R. J Nasr, S. J. Swamidass, and P.Baldi.   Journal of Chemoinformatics, 1:7, 2009.

  • SOLpro: Accurate Sequence-Based Prediction of Protein Solubility.   C. N. Magnan, A. Randall, and P. Baldi.   Bioinformatics, 25, 2200—2207, (2009).

  • Data Structures and Compression Algorithms for Genomic Sequence Data.   M. C. Brandon, D. C. Wallace, and P. Baldi.   Bioinformatics, 25, 1731--1738, (2009).

  • The Influence Relevance Voter: An Accurate and Interpretable Virtual High Throughput Screening Method.   S. J. Swamidass, C. Azencott, and P. Baldi.   Journal of Chemical Information and Modeling, 49, 4, 756--766, (2009).

  • Machine Learning Methods for Protein Structure Prediction.   J. Cheng, A. N. Tegge, and P. Baldi.   IEEE Reviews in Biomedical Engineering, 1, 1, in press, (2009).

  • MITOMASTER: A Bioinformatics Tool For the Analysis of Mitochondrial DNA Sequences.   M. Brandon, P. Baldi, and D. Wallace.   Human Mutation, Database Issue, 30, 1, 1-6, (2009).

  • Sourcerer: Mining and Searching Internet-Scale Software Repositories.   E. Linstead, S. Bajracharya, T. Ngo, P. Rigor, C. Lopes, P. Baldi.   Journal of Datamining and Knowledge Discovery, 18, 2, 300-336, (2009).

  • Bayesian Surprise Attracts Human Attention.   L. Itti and P. Baldi.   Vision Research, 49, 1295--1306, (2009).

  • COBEpro: A Novel System for Predicting Continuous B-cell Epitopes.   M. J. Sweredoski and P. Baldi.   Protein Engineering Design and Selection, 22, 3, 113-120, (2009).

  • A Burkholderia pseudomallei protein array reveals serodiagnostic and cross-reative antigens.   P.Felgner, M. Kayala, C. Burk, R. Nakajima-Sasaki, J. Pablo, D. Molina, S. Hirst, J. Chew, D. Wang, G. Tan, M. Duffield, R. Yang, J. Neel, N. Chantratita, G. Bancroft, G. Lertmemongkolchai, D. Davies, A. Vigil, P. Baldi, S. Peacock , and R. Titball.   Proceedings National Academy of Sciences USA, 106, 13499-13504, (2009).

  • MotifMap: a human genome-wide map of candidate regulatory motif sites.   Xiaohui Xie, Paul Rigor, and Pierre Baldi.   Bioinformatics, 15 January 2009; 25: 167 - 174.

2008

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1986
 
  • Mining Internet-Scale Software Repositories.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, and P. Baldi.   Advances in Neural Information Processing Systems 20, NIPS 2007 , Y. Weiss, B. Scholkopf, and J. Platt Editors, 929-936, MIT Press, Cambridge, MA, (2008).

  • A Theory of Aspects as Latent Topics.   P. Baldi, C. Lopes, E. Linstead, S. Bajracharya.   2008 ACM SIGPLAN Conference on Object-Oriented Programming Systems, Languages, and Applications. OOPSLA '08, October 19-23, Nashville, TN, (2008).

  • 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), 520, Snowbird, Utah, J. A. Storer and M.W. Marcellin Editors, IEEE Computer Society Press, 520, (2008).

  • Dysregulation of the Hypothalamic-Pituitary-Adrenal (HPA) Axis and its Association with Symptoms and Mucosal Cytokines in Irritable Bowel Syndrome.   L. Chang, S. Sundaresh, J. Elliott, P. A. Anton, P. Baldi, A. Licudine, M. Mayer, T. Vuong, M. Hirano, T. Olivas, C. Liu, B. D. Naliboff, V. Z. Ameen, and E. A. Mayer.   Neurogastroenterology and Motility, 21, 149-159, (2008).

  • Software-Driven Sensor Networks for Short-Range Shallow Water Applications.   R. Jurdak, P. Baldi, and C. Lopes.   Ad Hoc Networks Journal, 7, 837-848, (2008).

  • A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia bugdorferi.   A. G. Barbour, M. Kayala, A. Jasinskas, H. Davies, A. C. Steere, P. Baldi, and P. Felgner.   Infection and Immunity, 76, 3374-3389, (2008).

  • TMBpro: Secondary Structure, Beta-Contact, and Tertiary Structure Prediction of Transmembrane Beta-Barrel Proteins.   A. Randall, J. Cheng, M. Sweredoski, and P. Baldi.   Bioinformatics, 24, 513-520, (2008).

  • Learning to Play Go Using Recursive Neural Networks.   L. Wu and P. Baldi.   Neural Networks, 21, 1392-1400, (2008).

  • Discovery of Power-Laws in Chemical Space.   R. W. Benz, S. J. Swamidass, and P. Baldi.   Journal of Chemical Information and Modeling, 48, 6, 1138-1151, (2008).

  • Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR.   P. Baldi, D. S. Hirschberg and R. J. Nasr.   of Chemical Information and Modeling,48, 7, 1367-1378, (2008).

  • PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure.   M. J. Sweredoski and P. Baldi.   Bioinformatics, 24, 12, 1459-1460, (2008).

  • BLASTing Small Molecules: Statistics and Extreme Statistics of Chemical Similarity Scores.   P. Baldi and R. W. Benz.   Bioinformatics, 24(13):i357-i365, (2008).

  • Synthesis Explorer: Organic Chemistry Tutorial System for Multi-Step Synthesis Design and Reaction Prediction.   J. Chen and P. Baldi.   Journal of Chemical Education, 85, 12, 1699-1703, (2008).

  • Software-Driven Sensor Networks for Short-Range Shallow Water Applications.   R. Jurdak, P. Baldi, and C. Lopes.   Ad Hoc Networks Journal, 7, 837-848, (2008).

  • SELECTpro: Effective Protein Model Selection Using a Structure-Based Energy Function Resistant to Blunders.   A. Randall and P. Baldi.   BMC Structural Biology,8:52, (2008).

2007

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1986
 
  • Mining Concepts from Code with Probabilistic Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, and P. Baldi.   Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering, (ASE’07), 461-464, Atlanta, GA, November 2007.

  • Mining Eclipse Developer Contributions via Author-Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, and P. Baldi.   Proceedings of the MSR 2007: International Workshop on Mining Software Repositories, 30-33, Minneapolis, MN, (2007). Best Paper Award, MSR Scale Challenge.

  • Software Modems for Underwater Sensor Networks   R. Jurdak, P.M.Q. Aguiar, P. Baldi, and C.V. Lopes.   Proceedings of IEEE/OES Oceans'07

  • 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.

  • Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.   P. Baldi., R. W. Benz, D. S. Hirschberg, and S. Joshua Swamidass.   Journal of Chemical Information and Modeling, 47, 6, 2098-2109, (2007).

  • From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.   S. Sundaresh; A. Randall; B. Unal; J. M. Petersen; J. T. Belisle; M. Gill Hartley; M. Duffield; R. W. Titball; D. Huw Davies; P. L. Felgner; and P. Baldi.   Bioinformatics, 23, i508-i518, (2007).

  • ChemDB Update--Full-Text Search and Virtual Chemical Space.   J. Chen, E. Linstead, S. J. Swamidass, D. Wang, and P. Baldi.   Bioinformatics, 23, 2348-2351, (2007).

  • Assessment of Predictions Submitted for the CASP7 Domain Prediction Category.   M. Tress, J. Cheng, P. Baldi, K. Joo, J. Lee, J. Seo, J. Lee, D. Baker, D. Chivian, D. Kim, A. Valencia, I. Ezkurdia.   Proteins, 69, S8, 137-151, (2007).

  • Minimizing the Overlap Problem in Protein NMR: A Computational Framework for Precision Amino Acid Labeling.   M. Sweredoski, K. Donovan, B. Nguyen, A. J. Shaka, and P. Baldi   Bioinformatics, 23, 2829-2835, (2007).

  • On the Luria-Delbruck Model with a Nonzero Death Rate.   N. Komarova, L. Wu, and P. Baldi   Mathematical Biosciences, 210, 1, 253-290, (2007).

  • Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set.   J. Cheng and P. Baldi   BMC Bioinformatics, 8, 113-121, (2007).

  • Immunodominant Francisella tularensis antigens identified using proteome microarray.   J. E. Eyles, B. Unal, M. Gill Hartley, S. L. Newstead, H. Flick-Smith, J. L. Prior, P. C. F. Oyston, A. Randal, Y. Mu, S. Hirst, D. M. Molina, D. Huw Davies, T. Milne, K. F. Griffin, P. Baldi, R. W. Titball and P. L. Felgner.   Proteomics, 7, 13, 2172-2183, (2007).

  • A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition.   W. Einhäuser, T. N. Mundhenk, P. Baldi, C. Koch, and L. Itti   Journal of Vision, 7, 10, article 6, 1-13, (2007).

  • A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.   S. J. 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. J. Swamidass and P. Baldi   Journal of Chemical Information and Modeling, 47, 2, 302-317, (2007).

  • A Theoretical Study of the In Vivo Mechanical Properties of Angiosperm Roots: Constitutive Theories and Methods of Parameter Estimation.   A. Sadovsky, P. Baldi, and F. Wan   Journal of Engineering Materials and Technology, in press, (2007).

  • A Cross-Layer Optimization Framework for Sensor Networks.   R. Jurdak, C. Lopes, and P. Baldi   IEEE Transactions on Mobile Computing, in press, (2007).

  • Adaptive Low Power Listening for Wireless Sensor Network.   R. Jurdak, P. Baldi , and C. Lopes   IEEE Transactions on Mobile Computing, 6, 2, 988-1004, (2007).

  • An Enhanced MITOMAP with a Global mtDNA Mutational Philogeny.   E. Ruiz-Pesini, M. T. Lott, V. Procaccio, J. Poole, M. C. Brandon, D. Mishmar, C. Yi , J. Kreuziger, P. Baldi, D. C. Wallace   Nucleic Acids Research, i35 (Database Issue), D823-D828, (2007).

  • Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain.   L. Zicker-Larsen, M. Zhang, N. Beliakova-Bethell, V. Bilanchone, A. Lamsa, K. Nagashima, R. Najdi, K. Kosaka, V. Kovacevic, J. Cheng, P. Baldi, G. Wesley Hatfield, and S. Sandmeyer   The Journal of Virology, in press, 81, 3, 6957-6972, (2007).

  • Phylogenetic Analysis and Genome Evolution in the Herpesviridae.   N. Wang, P. Baldi, and B. Gaut   Molecular Phylogenetics and Evolution, , 43, 3, 1066-1075, (2007).

  • One- to Four- Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties   C. Azencott, A. Ksikes, S. Joshua Swamidass, J. Chen, L. Ralaivola, and P. Baldi   Journal of Chemical Information and Modeling, 47, 3, 965-974, (2007).

  • A Scalable Machine Learning Approach to Go   L. Wu and P. Baldi   Advances in Neural Information Processing Systems 19, NIPS 20065, Y. Weiss, B. Scholkopf, and J. Platt Editors, MIT Press, Cambridge, MA, (2007).

  • An Enhanced MITOMAP with a Global mtDNA Mutational Philogeny.   E. Ruiz-Pesini, M. T. Lott, V. Procaccio, J. Poole, M. C. Brandon, D. Mishmar, C. Yi , J. Kreuziger, P. Baldi, D. C. Wallace   Nucleic Acids Research, i35 (Database Issue), D823-D828, (2007).

2006

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1986
 
  • Genomic Splice-Site Analysis Reveals Frequent Alternative Splicing Close to the Dominant Splice Site   Y. Dou, K. Fox-Walsh, P. Baldi, and K. Hertel   RNA,12, 12, 2047-2056, (2006).

  • Identification of Humoral Immune Responses in Protein Microarrays using DNA Microarray Data Analysis Techniques   Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Phil Felgner, and Pierre Baldi   Bioinformatics, 22, 14, 1760-1766, (2006). (PubMed)

  • Mitochondrial Mutations in Cancer   M. Brandon, P. Baldi, and D. C. Wallace   Oncogene, 25, 4647-4662,, (2006). (PubMed)

  • A Machine Learning Information Retrieval Approach to Protein Fold Recognition   J. Cheng and P. Baldi   Bioinformatics, 22, 12, 1456-1463, (2006). (PubMed)

  • Localization of Off-the-Shelf Mobile Devices Using Audible Sound: Architectures, Protocols and Performance Assessment.   C. V. Lopes, A. Haghighat, A. Mandal, P. Baldi, and T. Givargis.   ACM SIGMOBILE Mobile Computing and Communications Review, 10, 2, 38-50, (2006).

  • A tandem-affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking.   C. Tagwerker, K. Flick1, M. Cui, C. Guerrero, Y. Dou, B. Auer, P. Baldi, L. Huang, and Peter Kaiser.   Molecular and Cellular Proteomics, 4, 737-748, (2006).

  • Structure-Based Inhibitor Design of AccD5, an Essential acyl-CoA Carboxylase Carboxyltransferase Domain of Mycobacterium tuberculosis.   T. Lin, M. Melgar, S. J. Swamidass, J. Purdon, T. Tseng, G. Gago, D. Kurth, P. Baldi, H. Gramajo, and S. Tsai.   Proceedings of the National Academy of Sciences USA, 103, 9, 3072-3077, (2006).

  • Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.   G. Pollastri, A. Vullo, P. Frasconi, and P. Baldi.   Journal of Computational Biology, 3, 631-650, (2006). (PubMed)

  • DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.   J. Cheng, M. J. Sweredoski, and P. Baldi.   Data Mining and Knowledge Discovery, 13, 1, 1-10, (2006).

  • Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines.   J. Cheng, A. Randall, and P. Baldi.   Proteins, i62, 4, 1125-1132, (2006). (PubMed)

  • Global Landscape of Recent Inferred Darwinian Selection for Homo Sapiens.   E. T. Wang, G. Kodama, P. Baldi, and R. K. Moyzis.   Proceedings of the National Academy of Sciences USA, 103, 135-140, (2006). (PubMed)

  • Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.   J. Cheng, H. Saigo, and P. Baldi.   Proteins, 62, 3, 617-629, (2006).

  • Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.   S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, Rainer K. Brachmann, and Richard H. Lathrop.   IEEE Transactions on Computational Biology and Bioinformatics, 3, 2, 114-125, (2006).

  • A Comparative Analysis and Experimental Study on Wireless Aerial and Underwater Acoustic Communications   R. Jurdak, C. V. Lopes, P. M. Q. Aguiar, and P. Baldi   Proceeding of the 2006 International Conference on Digital Telecommunications, IEEE Computer Society

  • Sourcerer: A Search Engine for Open Source Code Supporting Structure-Based Search   S. Bajracharya, T. Ngo, E. Linstead, Y. Dou, P. Baldi, and C. Lopes   OOPSALA

2005

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1986
 
  • The Architecture of pre-mRNAs Affects Mechanisms of Splice-Site Pairing.   Kristi L. Fox-Walsh1, Yimeng Dou, Bianca J. Lam1, She-pin Hung, Pierre F. Baldi, and Klemens J. Hertel.   Proceedings of the National Academy of Sciences USA, 102, 16176-16181, (2005). (PubMed)

  • ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources.   J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, and P. Baldi.   Bioinformatics, 21, 4133-4139, (2005). (PubMed)

  • The Absence of Favorable Aromatic Interactions between Beta-Sheet Peptides.   D. M. Chung, Y. Dou, P. Baldi, and J. S. Nowick.   Journal of the American Chemical Society,127 (28), 9998-9999, (2005). (PubMed)

  • Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng and P. Baldi.   Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, 21, Supplement 1, i75-84, (2005).

  • Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   S. J. 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).

  • Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.   J. Cheng, M. J. Sweredoski, and P. Baldi.   Data Mining and Knowledge Discovery, 11, 3, 213-222, (2005).

  • SCRATCH: a Protein Structure and Structural Feature Prediction Server.   J. Cheng, A. Z. Randall, M. Sweredoski, and P. Baldi.   Nucleic Acids Research, 33, 9, Web Server issue, W72-76, (2005). (PubMed)

  • On the Relationship Between Deterministic and Probabilistic Directed Graphical Models: from Bayesian Networks to Recursive Neural Networks.   P. Baldi and M. Rosen-Zvi.   Neural Networks, special issue on Neural Networks and Kernel Methods for Structured Domains, 18, 8, (2005).

  • Graph Kernels for Chemical Informatics.   L. Ralaivola, J. S. Swamidass, H. Saigo, and P. Baldi.   Neural Networks, special issue on Neural Networks and Kernel Methods for Structured Domains, 18, 8, 1093-1110, (2005). (PubMed)

  • Retroviruses and Yeast Retrotransposons Use Overlapping Sets of Host Genes.   B. Irwin, M. Aye, P. Baldi, N. Beliakova-Bethell, H. Cheng, Y. Dou, W. Liou, and S. Sandmeyer.   Genome Research, 15, 641-654, (2005). (PubMed)

  • Global Gene Expression Profiling in Escherichia coli K12: The Effects of Oxygen Availability and ArcA.   K. A. Salmon, S. Hung, N. R. Steffen, R. Krupp, P. Baldi, G. Wesley Hatfield, and R. P. Gunsalus.   Journal of Biological Chemistry, 280, 15, 15084-15096, (2005). (PubMed)

  • U-MAC: A Proactive and Adaptive UWB Medium Access Control Protocol.   R. Jurdak, P. Baldi, and C. Videira Lopes.   Wireless Communications and Mobile Computing Journal, Special Issue on UWB Communications, 5, 5, 551-566, (2005).

  • How Noisy and Replicable are DNA Microarray Data?   S. Sundaresh, S. Hung, G. W. Hatfield, and P. Baldi.   International Journal of Bioinformatics Research and Applications, 1, 1, 31-50, (2005).

  • Profiling the Humoral Response to Infection by Using Proteome Microarrays: High-Throughput Vaccine and Diagnostic Antigen Discovery.   H. Davies, X. Liang, J. E. Hernandez, K. M. Romero, T. T. Nguyen, M. Kalantari-Dehaghi, S. Hirst, Y. Mu, A. Randall, P. Baldi, L. Villarreal, P. L. Felgner.   Proceedings of the National Academy of Sciences USA, 102, 3, 547-552, (2005). (PubMed)

  • Sigmoid: Towards a Generative, Scalable Software Infrastructure for Pathway Bioinformatics and Systems Biology.   J. Cheng, L. Scharenbroich, P. Baldi, and E. Mjolsness.   IEEE Intelligent Systems,20, 3, 68-75, (2005).

  • MITOMAP: a human mitochondrial genome database - 2004 update.   M. Brandon, M. Lott, K. Nguyen, S. Spolim, S. Navathe, P. Baldi , and D. Wallace.   Nucleic Acids Research, 33 (Database issue), D611-613, (2005). (PubMed)

  • Polymodal sensory function of the C. elegans OCR-2 channel arises from distinct intrinsic determinants within the protein and is selectively conserved in human TRPV2.   I. Sokolchik, T. Tanabe, P. Baldi, and J. Y. Sze.   Journal of Neuroscience, 25, 4, 1015-1023, (2005).

  • Statistical Detection of Chromosomal Homology Using Shared-Gene Density Alone.   S. Hampson, B. S. Gaut, and P. Baldi.   Bioinformatics, 21, 8, 1339-1348, (2005). (PubMed)

  • Statistical Distribution of Chemical Fingerprints.   S. J. Swamidass and P. Baldi.   Proceedings of WILF 2005, Springer Verlag. Andrea Tattamanzi Editor.

  • Clustering Algorithms for Gene Expression Analysis.   P. Baldi, G. Wesley Hatfield, and Li M. Fu.   Handbook of Computational Molecular Biology. S. Aluru Editor, Chapman & Hall/CRC Press, Computer and Information Science Series, (2005).

  • Surprise: A Shortcut for Attention?   P. Baldi.   Neurobiology of Attention. L. Itti, G. Rees, and J. Tsotsos Editors, Elsevier, San Diego, CA, 24-28, (2005).

  • Chemoinformatics, Drug Design, and Systems Biology.   P. Baldi.   Proceedings of the 16th International Conference on Genome Informatics. (GIW 2005),Yokohama, Japan, December 2005.

  • Exploring Chemical Space with Computers: Informatics Challenges for AI and Machine Learning.   P. Baldi.   BIOMAT V Symposium, Petr¢polis, Brazil, December 2005, World Scientific Co.Pte.Ltd.

  • Attention: Bits versus Wows.   P. Baldi and L. Itti.   Proceedings of the International Conference on Neural Networks and Brain (ICNN&B05), Edited by Mingsheng Zhao and Zhongzhi Shi, Vol. 1, PL-56-PL61, Beijing, China, IEEE Press, October 2005.

  • Bayesian Surprise Attracts Human Attention.   L. Itti and P. Baldi.   Advances in Neural Information Processing Systems 18, NIPS 2005, in press, (2005).

  • Energy-Aware Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, P. Baldi, C. V. Lopes.   To appear in proceedings of the 2nd International Workshop on Networked Sensing Systems (INSS). San Diego, CA. June,ÿ2005.

  • Programming Model for Supporting Complex Optimizations in Sensor Networks.   R. Jurdak, C. V. Lopes, and P. Baldi.   Proceedings of the Fourth International IEEE/ACM Conference on Information Processing in Sensor Networks (IPSN?05). Los Angeles, CA. April, 2005.

  • Emergy-aware Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. V. Lopes, P. Baldi.   Second International Workshop on Networked Sensing Systems, San Diego, June 2005.

  • Programming Model for Supporting Complex Optimizations in Sensor Networks.   R. Jurdak, C. V. Lopes, P. Baldi.   The Fourth International Conference on Information Processing in Sensor Networks.

  • Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng and P. Baldi.   Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).

  • Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   L. Ralaivola, J. Chen, P. Phung, J. Bruand, S. J. Swamidass, and P. Baldi.   Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).

  • Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants.   S. Danziger, S. J. Swamidass, J. Zeng, L. Dearth, Q. Lu, J. H. Chen, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, R. K. Brachmann, and R. H. Lathrop.   N/A.

  • Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng and P. Baldi.   Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).

  • Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   L. Ralaivola, J. Chen, P. Phung, J. Bruand, S. J. Swamidass, and P. Baldi.   Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).

  • Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. V. Lopes, P. Baldi.   11th Annual International Conference on Mobile Computing and Networking.

  • A Principled Approach to Detecting Surprising Events in Video.   L. Itti, P. Baldi.   Proc. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Jun 2005.

  • SVM and Pattern-Enriched Common Fate Graphs for the Game of GO.   L. Ralaivola, L. Wu, and P. Baldi.   European Symposium on Artificial Neural Networks (ESANN), Bruges, Belgium, April 2005. Accepted for Oral Persentation.

2004

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1986
 
  • A Survey, Classification, and Comparative Analysis of Medium Access Control Protocols for Ad Hoc Networks.   R. Jurdak, C. Videira Lopes, and P. Baldi.   IEEE Communications Surveys and Tutorials, 6, 1, 2-16, (2004).

  • Structural Proteomics of the Poxvirus Family.   A. Z. Randall, P. Baldi, and L. P. Villareal.   Artificial Intelligence in Medicine, special issue on 'Data mining in Genomics and Proteomics', 31, 2, 105-115, (2004). (PubMed)

  • ICBS: A Database of Interactions Between Protein Chains Mediated by Beta-Sheet Formation.   Y. Dou, P. Baisnee, G. Pollastri, Y. Pecout, J. Nowick, and P. Baldi .   Bioinformatics, 20, 16, 2767-2777, (2004). (PubMed)

  • Battery Lifetime Estimation and Optimization for Underwater Sensor Networks.   R. Jurdak, C. V. Lopes, and P. Baldi.   Sensor Network Operations, published by IEEE Press, edited by Shashi Phoha, Thomas F. La Porta and Christopher Griffinÿ,ÿ(2004) in press. Edited volume resulting from overflow to special issue on Sensor Networks in IEEE Transactions on Mobile Computing

  • Hidden Markov Models and Neural Networks.   S. Kremer and P. Baldi.   Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley, (2004). (PubMed)

  • Beep: 3D Indoor Positioning Using Audible Sound.   A. Mandal, C. V. Lopes, T. Givargis, A. Haghighat, R. Jurdak, and P. Baldi.   Proceedings of the 2004 IEEE Consumer Communications and Networking Conference, 348?353, (2004).

  • Large-Scale Prediction of Disulphide Bond Connectivity.   P. Baldi, J. Cheng, and A. Vullo.   Advances in Neural Information Processing Systems 17, NIPS 2004, in press, (2004).

  • An Identfication Scheme for Location Systems Using Robust Acoustic Signals.   R. Jurdak, C. Videira Lopes, and P. Baldi.   Proceeding of the ACS/IEEE International Conference on Pervasive Services, Beirut, Lebanon. IEEE Computer Society Press, (2004).

2003

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1986
 
  • Extensive Gene Gain Associated With Adaptive Evolution of Poxviruses.   A. McLysaght, P. Baldi, and B. S. Gaut.   Proceedings of the National Academy of Sciences USA, 100, 26, 15655-15660, (2003). (PubMed)

  • Global Gene Expression Profiling in Escherichia coli K12: The Effects of Oxygen Availability and FNR.   K. Salmon, K. Mekjian, R. P. Gunsalus, S. Hung, P. Baldi, and G. Wesley Hatfield.   Journal of Biological Chemistry, 278, 32, 29837-29855, (2003). (PubMed)

  • LineUp : Statistical Detection of Chromosomal Homology with Applications to Plant Comparative Genomics.   S. Hampson, A. McLysaght, B. Gaut, and P. Baldi .   Genome Research, 13, 5, 999-1010, (2003).

  • Comprehensive Mutagenesis of the C-terminal Domain of the M13 Gene-3 Minor Coat Protein: The Requirements for Assembly into the Bacteriophage Particle.   G. A. Weiss, T. A. Roth, P. Baldi, and S. S. Sidhu.   Journal of Molecular Biology, 332, 4, 777-782, (2003). (PubMed)

  • The Principled Design of Large-Scale Recursive Neural Network Architectures ? DAG-RNNs and the Protein Structure Prediction Problem.   P. Baldi and G. Pollastri.   Journal of Machine Learning Research, 4, 575-602, (2003).

  • Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity.   Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy, and P. Baldi.   Neurocomputing, (partially presented at JOBIM 2001 conference), Vol. 56C, 305-327, (2003).

  • Bounds on Variances of Estimators for Multinomial Processing Tree Models.   P. Baldi and W. H. Batchelder.   Journal of Mathematical Psychology, 47, 467-470, (2003).

  • Differential Analysis of DNA Microarray Gene Expression Data.   G. Wesley Hatfield, S. Hung, and P. Baldi.   Molecular Microbiology, 47, 4, 871-877, (2003). (PubMed)

  • Modeling the Internet and the Web?Probabilistic Methods and Algorithms.   P. Baldi, P. Frasconi, and P. Smyth.   Wiley, (2003)

  • What Genes are Made Of.   P. Baldi.   Review of edited book entitled: The Genomic Revolution: Unveiling the Unity of Life. Pathways, (2003). (PubMed)

  • Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets.   S. P. Hung, G. Wesley Hatfield, S. Sundaresh, and P. Baldi.   Genomics, Proteomics, and Vaccines. G. Grandi Editor, John Wiley and Sons, (2003).

  • New Machine Learning Methods for the Prediction of Protein Topologies, in Artificial Intelligence and Heuristic Methods in Bioinformatics.   P. Baldi, G. Pollastri, P. Frasconi, and A. Vullo.   P. Frasconi and R. Shamir Editors, IOS Press, 51-73, (2003).

  • Prediction of Protein Topologies Using Generalized IOHMMs and RNNs.   G. Pollastri, P. Baldi, A. Vullo, and P. Frasconi.   Advances in Neural Information Processing Systems 15, S. Becker, S. Thrun, and K. Obermayer Editors, Volume 15, MIT Press, Cambridge, MA, (2003).

2002

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1986
 
  • Modeling and Optimization of UWB Communication Networks Through a Flexible Cost Function.   P. Baldi, L. De Nardis, and M. G. Di Benedetto.   IEEE Journal on Selected Areas in Communications, 20, 9, 1733-1744, (2002).

  • Global Gene Expression Profiling in Excherichia coli K12: The Effects of Leucine-responsive Regulatory Protein.   S. Hung, P. Baldi, and G. Wesley Hatfield.   Journal of Biological Chemistry, 277, 43, 40309-40323, (2002).

  • Why Are Complementary DNA Strands Symmetric?   P. Baisnee, S. Hampson, and P. Baldi.   Bioinformatics, 18, 1021-1033, (2002). (PubMed)

  • Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri and P. Baldi.   Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology, ISMB 02. Bioinformatics, 18, Supplement 1, S62-S70, (2002). Nominated for Best Paper Award. (PubMed)

  • A Machine Learning Strategy for Protein Analysis.   P. Baldi and G. Pollastri.   IEEE Intelligent Systems. Special Issue on Intelligent Systems in Biology, 17, 2, 28-35, (2002).

  • Distribution Patterns of Over-Represented k-mers in Non-Coding Yeast DNA.   S. Hampson, D. Kibler, and P. Baldi.   Bioinformatics, 18, 4, 611-626, (2002). (PubMed)

  • Prediction of Coordination Number and Relative Solvent Accessibility in Proteins.   G. Pollastri, P. Baldi, P. Fariselli, and R. Casadio.   Proteins, 47, 142-153, (2002). (PubMed)

  • Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles.   G. Pollastri, D. Przybylski, B. Rost, and P. Baldi.   Proteins, 47, 228-235, (2002). (PubMed)

  • DNA Microarrays and Gene Regulation?From Experiments to Data Analysis and Modeling.   P. Baldi and G. Wesley Hatfield.   Cambridge University Press, (2002). English version for China and electronic publishing version through eBrary in 2003 and 2004.

  • A Computational Theory of Surprise, in Information, Coding, and Mathematics.   P. Baldi.   M. Blaum Editor, Kluwer, 1-25, (2002).

  • Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri and P. Baldi.   Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology, ISMB 02. Bioinformatics, 18, Supplement 1, S62-S70, (2002). Nominated for Best Paper Award. (PubMed)

  • UWB Ad-Hoc Networks.   L. De Nardis, P. Baldi, and M. G. Di Benedetto.   Proceedings of the 2002 IEEE Conference on Ultra Wide Band Systems and Technologies (UWBST 2002), Baltimore, MD, 219-224, (2002).

2001

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1986
 
  • Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio.   Bioinformatics, 17, S234-S242, (2001). (PubMed)

  • Improved Statistical Inference from DNA Microarray Data Using Analysis of Variance and a Bayesian Statistical Framework.   A. D. Long, H. J. Mangalam, B. Y. P. Chan, L. Tolleri, G. W. Hatfield, and P. Baldi.   Journal of Biological Chemistry, 276, 23, 19937-19944, (2001). (PubMed)

  • A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Inference of Gene Changes.   P. Baldi and A. D. Long.   Bioinformatics, 17, 6, 509-519, (2001). (PubMed)

  • Flexibility of the Genetic Code with Respect to DNA Structure.   P. Baisn‚e, P. Baldi, S. Brunak, and A. Gorm Pedersen.   Bioinformatics, 17: 237-248, (2001). (PubMed)

  • The Shattered Self ? The End of Natural Evolution.   P. Baldi.   MIT Press, (2001). Paperback version in 2002.

  • Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollasti, P. Baldi, P. Fariselli, R. Casadio.   Proceedings of the 2001 Conference on Intelligent Systems for Molecular Biology, (ISMB01), Copenhagen, Denmark, AAAI Press (2001). (PubMed)

  • A Model for Self-Organizing Large Scale Wireless Networks.   M. G. Di Benedetto and P. Baldi.   International Symposium on 3G Infrastructure and Services. Athens, Greece, July 2001.

2000

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1986
 
  • Sequence Analysis by Additive Scales: DNA Structure for Sequences and Repeats of All Lenghts.   P. Baldi, and P. Baisn‚e.   Bioinformatics, Vol 16, 10, 865-889, (2000).

  • Assessing the Accuracy of Prediction Algorithms for Classification: An Overview.   P. Baldi, S. Brunak, Y. Chauvin, and H. Nielsen.   Bioinformatics, Vol. 16, 5, 412-424, (2000). (PubMed)

  • On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial Genomes.   P. Baldi.   Bioinformatics, Vol. 16, 4, 367-371, (2000). (PubMed)

  • Probabilistic Graphical Models in Computational Molecular Biology.   P. Baldi.   Journal of the Italian Association for Artificial Intelligence (AIIA), Vol. 1, 8-12, (2000).

  • Bidirectional Dynamics for Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, and G. Soda.   Sequence Learning: Paradigms, Algorithms, and Applications, R. Sun and C. L. Giles Editors, Springer Verlag, 99-120, (2000). (PubMed)

  • Bidirectional IOHMMs and recurrent neural networks for protein secondary structure prediction.   P. Baldi, S. Brunak, G. Pollastri, and P. Frasconi.   Protein Sequence Analysis in the Genomic Era, Rita Casadio and Lanfranco Masotti Editors, CLUEB, Bologna, Italy, (2000). (PubMed)

  • Matching Protein Beta-Sheet Partners by Feedforward and Recurrent Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, and S. Brunak.   Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology, (ISMB00), La Jolla, CA, 25-36, AAAI Press (2000). (PubMed)

  • Analysis of Yeast?s ORFs Upstream Regions by Parallel Processing, Microarrays, and Computational Methods.   S. Hampson, P. Baldi, D. Kibler, and S. Sandmeyer.   Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology, (ISMB00), La Jolla, CA, 190-201, AAAI Press (2000).

  • Protein Beta-Sheet Partner Prediction by Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, and S. Brunak.   Artifical Neural Networks in Medicine and Biology. Proceedings of the ANNIMAB-1 Conference, G”teborg, Sweden, H. Malmgren, M. Borga and L. Niklasson Editors, Springer Verlag, (2000).

1999

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1986
 
  • Structural Basis for Triplet Repeat Disorders: A Computational Analysis.   P. Baldi, S. Brunak, Y.Chauvin, and A. Gorm Pedersen.   Bioinformatics, Vol. 15, 11, 918-929, (1999). (PubMed)

  • Exploiting the Past and the Future in Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Soda, and G. Pollastri.   Bioinformatics, Vol. 15, 11, 937-946, (1999). (PubMed)

  • The Biology of Eukaryotic Promoter Prediction-a Review.   A. Gorm Pedersen, P. Baldi, S. Brunak, and Y. Chauvin.   Computers and Chemistry, Special Issue on Genome and Informatics, 23, 191-207, (1999). (PubMed)

1998

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1986
 
  • DNA Structure in Human RNA Polymerase II Promoters.   A. Gorm Pedersen, P. Baldi, Y. Chauvin, and S. Brunak.   Journal of Molecular Biology, 281, 663-673, (1998). (PubMed)

  • On the Use of Bayesian Methods for Evaluating Compartmental Neural Models.   P. Baldi, M. C. Vanier, and J. M. Bower.   Journal of Computational Neuroscience, 5, 285-314, (1998). (PubMed)

  • Bioinformatics: the Machine Learning Approach.   P. Baldi and S. Brunak.   MIT Press, (1998). Second revised edition (2001). Indian and Chinese versions in 2003. (PubMed)

  • Software Foundation Libraries for the Design of Intelligent Systems.   P. Baldi, Y. Chauvin, and V. Mittal Henkle.   Neural Nets WIRN Vietri 98. Proceedings of the 10-th Italian Workshop on Neural Nets. M. Marinaro and R. Tagliaferri Editors. Springer Verlag Series on Perspectives on Neural Computing Series, J. Taylor Series Editor, 17-39, (1998).

  • Probabilistic Models of Neuronal Spike Trains.   P. Baldi.   Adaptive Processing of Temporal Information. C.L. Giles and M. Gori Editors, Lecture Notes in Computer Science, Springer Verlag, New York, 198-228, (1998).

  • Computational Applications of DNA Structural Scales.   P. Baldi, S. Brunak, Y. Chauvin, and A. Gorm Pedersen.   Proceedings of the 1998 Conference on Intelligent Systems for Molecular Biology, (ISMB98), Montreal, Canada, 35-42, AAAI Press (1998). (PubMed)

1996

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1986
 
  • Naturally Occurring Nucleosome Positioning Signals in Human Exons and Introns.   P. Baldi, S. Brunak, Y. Chauvin, and A. Krogh.   Journal of Molecular Biology, Vol. 263, 5, 503-510, (1996). (PubMed)

  • Hybrid Modeling, HMM/NN Architectures, and Protein Applications.   P. Baldi and Y. Chauvin.   Neural Computation, Vol. 8, 7, 1541-1565, (1996).

  • Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models.   P. Baldi, A. Gorm Pedersen, S. Brunak, and Y. Chauvin.   Proceedings of the 1996 Conference on Intelligent Systems for Molecular Biology (ISMB96), Washington University, Saint Louis, 182-191, AAAI Press, (1996). (PubMed)

  • Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequences.   P. Baldi, S. Brunak, Y. Chauvin, and A. Krogh.   Theoretical and Computational Methods in Genome Research, S.Suhai Editor, Plenum, NY, (1996). (PubMed)

  • Universal Approximation and Learning of Trajectories Using Oscillators.   P. Baldi and K. Hornik.   Advances in Neural Information Processing Systems 8, D. S. Touretzky, M. C. Mozer, and M. E. Hasselmo Editors, MIT Press, Cambridge MA, 451-457, (1996).

1995

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1986
 
  • Substitution Matrices and Hidden Markov Models.   P. Baldi.   Journal of Computational Biology, Vol. 2, 3, 497-501, (1995). (PubMed)

  • Learning in Linear Networks: a Survey.   P. Baldi and K. Hornik.   IEEE Transactions on Neural Networks, Vol. 6, 4, 837-858, (1995)

  • Gradient Descent Learning Algorithms Overview: A General Dynamical Systems Perspective.   P. Baldi.   IEEE Transactions on Neural Networks, Vol. 6, 1, 182-195, (1995).

  • Back-propagation and unsupervised learning in linear networks.   P. Baldi, Y. Chauvin, and K. Hornik.   Back-Propagation: Theory, Architectures and Applications. Y. Chauvin and D.E. Rumelhart Editors, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 389-432, (1995).

  • Gradient Descent Learning Algorithms: A Unified Perspective.   P. Baldi.   Back-Propagation: Theory, Architectures and Applications. Y. Chauvin and D.E. Rumelhart Editors, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 509-541, (1995).

  • When Neural Networks Play Sherlock Holmes.   P. Baldi and Y. Chauvin.   Back-Propagation: Theory, Architectures and Applications. Y. Chauvin and D.E. Rumelhart Editors, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 487-507, (1995).

  • Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures.   P. Baldi and Y. Chauvin.   Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95), Cambridge (UK), 39-47, (1995). (PubMed)

  • Periodic Sequence Patterns in Human Exons.   P. Baldi, Y. Chauvin, S. Brunak, J. Engelbrecht, and A. Krogh.   Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95), Cambridge (UK), 30-38, (1995). (PubMed)

  • Inferring Ground Truth from Subjective Labelling of Venus Images.   P. Smyth, U. Fayadd, P. Perona, M. Burl, and P. Baldi.   Advances in Neural Information Processing Systems, G. Tesauro, D. S. Touretzky and T. K. Leen Editors, MIT Press, Cambridge MA, 1085-1092, (1995).

1994

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1986
 
  • Hidden Markov Models of the G-Protein Coupled Receptor Family.   P. Baldi and Y. Chauvin.   Journal of Computational Biology, Vol. 1, 4, 311-335, (1994). (PubMed)

  • Hidden Markov Models of Biological Primary Sequence Information.   P. Baldi, Y. Chauvin, T. Hunkapiller, and M. A. McClure.   PNAS USA, Vol. 91, 3, 1059-1063, (1994). (PubMed)

  • Smooth On-Line Learning Algorithms for Hidden Markov Models.   P. Baldi and Y. Chauvin.   Neural Computation, Vol. 6, 2, 305-316, (1994).

  • How Delays Affect Neural Dynamics and Learning.   P. Baldi and A. Atiya.   IEEE Transactions on Neural Networks, Vol. 5, 4, 626-635, (1994).

  • Statistical Models of Proteins: an Application to the G-Protein-Coupled Receptor Family.   P. Baldi and Y. Chauvin.   Modern Approaches in Molecular Bioinformatics. S. Schulze-Kremer Editor, IOS Press, Amsterdam/New York, 53-102 (1994).

  • Trading Decision Learning: from Theory to Personal Traders.   P. Baldi and Y. Chauvin.   Proceedings of the Second International Conference on Neural Networks in the Capital Markets, Pasadena, CA (1994).

  • Hidden Markov Models of Human Genes.   P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, and A. Krogh.   Advances in Neural Information Processing Systems, J. D. Cowan, G. Tesauro and J. Alspector Editors, Morgan Kauffmann Publishers, 761-768, (1994). (PubMed)

  • Discrimination of Tyrosine and Serine/Threonine Kinase Sub-Families by Hidden Markov Models.   P. Baldi and Y. Chauvin.   Proceedings of The Third International Conference on Bioinformatics and Genome Research, World Scientific Publishing Co., New Jersey, (1994).

  • Modeling Protein Families and Human Genes: Hidden Markov Models and a Little Beyond.   P. Baldi and Y. Chauvin.   Proceedings of the 1994 Fifth Generation Computing Symposium, Workshop on Fusion of Molecular Biology and Knowledge Processing, (Tokyo, Japan), (1994).

1993

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1986
 
  • Neural Networks for Fingerprint Recognition.   P. Baldi and Y. Chauvin.   Neural Computation, Vol. 5, 3, 402-418, (1993).

  • Random Interactions in Higher-Orders Neural Networks.   P. Baldi and S.S. Venkatesh.   IEEE Transactions on Information Theory, Vol. 39, 1, 274-283, (1993).

  • Hidden Markov Models in Molecular Biology: New Algorithms and Applications.   P. Baldi, Y. Chauvin, T. Hunkapiller, and M. A. McClure.   Advances in Neural Information Processing Systems, S. J. Hanson, J. D. Cowan and C. Lee Giles Editors, Morgan Kauffmann Publishers, 747-754, (1993).

  • Learning Trajectories with a Hierarchy of Oscillatory Modules.   P. Baldi and Nikzad Toomarian.   Proceedings of the 1993 IEEE International Conference on Neural Networks, San Francisco, CA, Volume III, 1172-1176, and also, in similar form, in Proceedings of the 1993 European Symposium on Artificial Neural Networks (ESANN93), Brussels, 183-188.

1992

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1986
 
  • Trading Decision Learning, Neural Networks for Computing Conference (abstract).   P. Baldi and Y. Chauvin.   Snowbird, UT, (1992).

  • A Modular Hierarchical Approach to Learning.   P. Baldi.   Proceedings of the 2nd International Conference on Fuzzy Logic and Neural Networks, (Iizuka, Japan), Vol. 2, 985-988, (1992).

1991

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1986
 
  • Contrastive Learning and Neural Oscillations.   P. Baldi and F. Pineda.   Neural Computation, Vol. 3, No. 4, 526-545, (1991).

  • Temporal Evolution of Generalization during Learning in Linear Networks.   P. Baldi and Y. Chauvin.   Neural Computation, Vol. 3, No. 4, 589-603, (1991).

  • Can Regulatory Peptides Be Regarded as Words of a Biological Language?   E. A. Mayer, J. Furness, and P. Baldi.   American Journal of Physiology, Vol. 261(2), G171-G184, (1991). (PubMed)

  • Programmed Interactions in Higher-Orders Neural Networks: II. The Outer-Product Algorithm.   S. S. Venkatesh and P. Baldi.   Journal of Complexity, Vol. 7, 443-479, (1991).

  • Programmed Interactions in Higher-Orders Neural Networks: I. Maximal Capacity.   S.S. Venkatesh and P. Baldi.   Journal of Complexity, Vol. 7, 316-337, (1991).

  • Computing with Arrays of Bell-Shaped and Sigmoid Functions. Bernstein Polynomials, the Heat Equation and Universal Approximation Properties.   P. Baldi.   Proceedings of the 1990 Conference on Neural Information Processing Systems, Denver, CO, Morgan Kauffman Publishers, 735-742, (1991).

1990

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1986
 
  • Computing with Arrays of Coupled Oscillators: an Application to Preattentive Texture Discrimination.   P. Baldi and R. Meir.   Neural Computation, Vol. 2, No. 4, 458-471, (1990).

  • On a Generalized Family of Colorings.   P. Baldi.   Graphs and Combinatorics, Vol. 6, 95-110, (1990).

  • Graph Coloring Bounds for Cellular Radio.   P. Baldi and E.C. Posner.   Computers and Mathematics with Applications, Vol. 19, No. 10, 91-97, (1990).

  • On the Distribution of the Number of Local Minima of a Random Function on a Graph.   P. Baldi, Y. Rinott, and C. Stein.   Proceedings of the 1989 Conference on Neural Information Processing Systems, Denver, CO, Morgan Kauffman Publishers, 727-732, (1990).

1989

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1986
 
  • Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis.   P. Baldi and A. Atiya.   International Journal of Neural Systems, Vol. 1, No. 2, 103-124, (1989).

  • On Normal Approximations of Distributions in Terms of Dependency Graphs.   P. Baldi and Y. Rinott.   Annals of Probability, Vol. 17, No. 4, 1646-1650, (1989).

  • Asymptotic Normality of Some Graph Related Statistics.   P. Baldi and Y. Rinott.   Journal of Applied Probability, Vol. 26, 171-175, (1989).

  • A Normal Approximation for the Number of Local Maxima of a Random Function on a Graph.   P. Baldi, Y. Rinott, and C. Stein.   Probability, Statistics and Mathematics: Papers in Honor of Samuel Karlin, T.W. Anderson, K.B. Athreya and D.L. Iglehart, Editors, Academic Press (1989).

  • Neural Networks and Principal Component Analysis: Landscapes and Algorithms.   P. Baldi.   Proceedings of the 1988 Conference on Neural Information Processing, Denver, CO, Morgan Kauffman Publishers, 65-72, (1989).

1988

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1986
 
  • Neural Networks and Principal Component Analysis: Learning from Examples without Local Minima.   P. Baldi and K. Hornik.   Neural Networks, Vol. 2, No. 1, 53-58, (1988).

  • How Sensory Maps Could Enhance Resolution Through Ordered Arrangements of Broadly Tuned Receivers.   P. Baldi and W. Heiligenberg.   Biological Cybernetics, Vol. 59, No. 4,5, 313-318, (1988). (PubMed)

  • Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal Vectors.   P. Baldi.   SIAM Journal of Discrete Mathematics, Vol. 1, No. 1 (1988).

  • Group Actions and Learning for a Family of Automata.   P. Baldi.   Journal of Computer and System Sciences, Vol. 36, No. 2, 1-15, (1988).

  • Neural Networks, Orientations of the Hypercube and Algebraic Threshold Functions.   P. Baldi.   IEEE Transactions on Information Theory, Vol. 34, No. 3, 523-530, (1988).

1987

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1986
 
  • Embeddings of Ultrametric Spaces in Finite Dimensional Structures.   M. Aschbacher, P. Baldi, E. B. Baum, and R.M. Wilson.   SIAM Journal of Algebraic and Discrete Methods, Vol. 8, No. 4, 564-577, (1987).

  • Symmetries and Learning in Neural Network Models.   P. Baldi.   Physical Review Letters, Vol. 59, No. 17, 1976-1978, (1987). (PubMed)

  • Number of Stable Points for Spin Glasses and Neural Networks of Higher Orders.   P. Baldi and S.S. Venkatesh.   Physical Review Letters, Vol. 58, No. 9, 913-916, (1987). (PubMed)

  • On Properties of Networks of Neuron-Like Elements: Complexity and Capacity.   P. Baldi and S.S. Venkatesh.   Proceedings of the IEEE Conference on Neural Information Processing Systems (Denver 1987), published by the American Institute of Physics, (D.Z. Anderson, Editor).

1986

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1998 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | 1989 | 1988 | 1987 |
1986
 
  • Bounds on the Size of Ultrametric Structures.   P. Baldi and E.B. Baum.   Physical Review Letters, Vol. 56, No. 15, 1598-1600, (1986). (PubMed)

  • Caging and Exhibiting Ultrametric Structures.   P. Baldi and E.B. Baum.   Proceedings of the Conference on Neural Networks for Computing, Snowbird, Utah, April 1986, published by the American Institute of Physics, 35-40, (1986), (John S. Denker, Editor).

© 2006 Pierre Baldi | pfbaldi@ics.uci.edu