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

Publications by Category

Publications

2016
Refereed Journals
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation   Baldi, P., Sadowski, P. Neural Networks. 2016.
What Time is it? Deep Learning Approaches for Circadian Rhythms   Agostinelli, F., Ceglia, N., Shahbaba, B., Sassone-Corsi, P., Baldi, P. Bioinformatics. 32, 12, i8-i17, 2016.
Sequence assembly of Yarrowia lipolytica strain W29/CLIB89 shows transposonable element diversity   Magnan, C., Yu, J., Chang, I., Jahn, E., Kanomata, Y., Wu, J., Zeller, M., Oakes, M., Baldi, P., Sandmeyer, S. B. PLOS ONE. 2016.
Gut microbiota directs PPAR ? driven reprogramming of the liver circadian clock by nutritional challenge   Murakami, M., Tognini, P., Liu, Y., Eckel-Mahan, K, Baldi, P., Sassone-Corsi, P. EMBO Reports. 2016.
Jet Substructure Classification in High-Energy Physics with Deep Neural Networks   Baldi, P., Bauer, K., Eng, C., Sadowski, P., Whiteson, D. Physical Review D. 93, 94034, 27 May 2016, 2016.
Parameterized Neural Networks for High-Energy Physics   Baldi, P., Cranmer, K., Faucett, T., Sadowski, P., Whiteson, D. The European Physical Journal C. 76, 235, 1-7, May 2016, 2016.
Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells   Borrego, S. L., Fahrmann, J., Datta, R., Stringari, C., Grapov, D., Zeller, M., Chen, Y., Wang, P., Baldi, P., Gratton, E., Fiehn, O., Kaiser, P. Cancer and Metabolism. 4, 9, 2016 May 2, 2016.
Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis   Masri, S., Papagiannakopoulos, T., Kinouchi, K., Liu, Y., Cervantes, M., Baldi, P., Jacks, T., Sassone-Corsi, P. Cell. 165, 4, 896-909, May 5, 2016, 2016.
Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver   Abbondante, S., Eckel-Mahan, K, Ceglia, N., Baldi, P., Sassone-Corsi, P. Journal of Biological Chemistry. 291, 6, 2812-28, 2016 Feb 5, 2016.
VIRALpro: a tool to identify viral capsid and tail sequences   Galiez, C., Magnan, C., Coste, F., Baldi, P. Bioinformatics. 32, 9, 1405-1407, 2016-04-27, 2016.
Jet Flavor Classification in High-Energy Physics with Deep Neural Networks   Guest, D., Collado, J., Baldi, P., Whiteson, D. Physical Review D. 94, 112002, 2016, 2016.
Gut microbiota directs PPAR ? driven reprogramming of the liver circadian clock by nutritional challenge   Murakami, M., Tognini, P., Liu, Y., Eckel-Mahan, K, Baldi, P., Sassone-Corsi, P. EMBO Reports. 2016.
Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction   Sadowski, P., Fooshee, D., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling. 56, 11, 2125-2128, 2016, 2016.
Other
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation   Baldi, P., Sadowski, P. Neural Networks. 83, 51-74, Nov. 2016, 2016.
2015
Refereed Journals
Enhanced Higgs to tau+tau- Search with Deep Learning   P. Baldi, P. Sadowski, D. Whiteson. Physical Review Letters. 114, 111801-1-111801-5, 2015.
Mitochondrial Mutations in Subjects with Psychiatric Disorders   Sequeira, A., Rollins, B., Magnan, C., van Oven, M., Baldi, P., Myers, R. M., Barchas, J. David, Schatzberg, A. F., Watson, S. J., Akil, H., Bunney, W. E., Vawter, M. P. PLOS ONE. 2015.
Deep Learning, Dark Knowledge, and Dark Matter   Sadowski, P., Collado, J., Whiteson, D., Baldi, P. Journal of Machine Learning Research. 2015.
The Pervasiveness and Plasticity of Circadian Oscillations: The Coupled Circadian-Oscillators Framework   Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., Baldi, P. Bioinformatics. June 2, 2015, 2015.
Towards a Systems View of Irritable Bowel Syndrome   Mayer, E. A., Labus, J., Tillisch, K., Cole, S., Baldi, P. Nature Reviews Gastroenterolog yand Hepatology. 2015.
Function and regulation of Cph2 in Candida albicans   Lane, S., Di Lena, P., Tormanen, K., Baldi, P. Eukaryotic Cell. 2015.
Atmospheric Oxidation of Squalene: Molecular Study Using COBRA Modeling and High-Resolution Mass Spectrometry   Fooshee, D. R., Aiona, P. K., Laskin, A., Laskin J., Nizkorodov, S. A., Baldi, P. Environmental Sciences and Technology. 2015.
Accurate and Efficient Target Prediction Using a Potency-Sensitive Influence-Relevance Voter   Lusci, A., Browning, M., Fooshee, D., Swamidass, S. Josh, Baldi, P. Journal of Cheminformatics. 7, 63-79, 29 December 201, 2015.
2014
The Dropout Learning Algorithm   P. Baldi, P. Sadowski. Artifical Intelligence. 210, 78-122, 2014.
A Genomic Analysis Pipeline and Its Application to Pediatric Cancers   M. Zeller, C. Magnan, V. R. Patel, P. Rigor, L. Sender, P. Baldi. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11, 5, 826-839, 2014.
Circadian Control of Fatty Acid Elongation by SIRT1-mediated Deacetylation of Acetyl-CoA Synthetase 1   S. Sahar, S. Masubuchi, K. Eckel-Mahan, S. Vollmer, L. Galla, N. Ceglia, S. Selma Masri, T. K. Barth, B. Grimaldi, O. Oluyemi, G. Astarita, W. C. Hallows, D. Piomelli, A. Imhof, P. Baldi, J. M. Denu, P. Sassone-Corsi. Journal of Biological Chemistry. 2014.
How Pervasive Are Circadian Oscillations?   V. R. Patel, K. Eckel-Mahan, P. Sassone-Corsi, P. Baldi. Trends in Cell Biology. 24, 329-331, 2014.
Incorporating Post-Translational Modifications and Unnatural Amino Acids into High-Throughput Modeling of Protein Structures   K. Nagata, A. Randall, P. Baldi. Bioinformatics. 30, 12, 1681-1689, 2014.
SIRT6 defines circadian transcription leading to control of lipid metabolism   S. Masri, P. Rigor, M. Cervantes, N. Ceglia, C. Sebastian, C. Xiao, M. Roqueta-Rivera, C. Deng, T. F. Osborne, R. Mostoslavsky, P. Baldi, P. Sassone-Corsi. Cell. 2014.
Sspro/ACCpro 5.0: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility. Problem Solved?   C. Magnan, P. Baldi. Bioinformatics. 30, 18, 2592-2597, 2014.
Muscle Insulin Sensitivity and Glucose Metabolism are Controlled by the Intrinsic Muscle Clock   K. A. Dyar, S. Ciciliot, L. E. Wright, R. S. Bienso, G. Malagpli Tagliazucchi, V. R. Patel, M. Forcato, M. I. Pena Paz, A. Gudiksen, F. Solagna, M. Albiero, I. Moretti, K. L. Eckel-Mahan, P. Baldi, P. Sassone-Corsi, R. Rizzuto, S. Bicciato, H. Pilegaard, . Molecular Metabolism. 3, 1, 29-41, February 2014, 2014.
Deep Learning in High-Energy Physics: Improving the Search for Exotic Particles   P. Baldi, P. Sadowski, D. Whiteson. Nature Communicaiton. 5, 4038, 2014.
A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia   W. Gordon, M. Zeller, R. Herndon, W. Swindell, H. Ho, F. Espetia, J.E. Gudjonsson, P. Baldi, B. Andersen. Journal of Clinical Inverstigation. 124, 12, 5205-5218, 2014.
The TCF C-clamp DNA Binding Domain Expands the Wnt Transcriptome via Alternative Target Recognition   N. P. Hoverter, M. Zeller, M. McQuade, A. Garibaldi, A. Busch, K. Hertel, P. Baldi, M. L. Waterman. Nucleic Acids Research. 42, 22, 13615-13632, 2014.
Enhanced Higgs to Tau-plus Tau-minus Search with Deep Learning   Baldi, P., Sadowski, P., Whiteson, D. Pyhsical Review letters. 2014.
Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   Chicco, D., Sadowski, P., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2014.
A Large-Scale Deep Learning Target-Prediction System for Diverse Molecules   Lusci, A., Browning, M., Swamidass, S. Josh, Baldi, P. Journal of Chemical Information and Modeling. 2014.
Towards a Systems View of Irritable Bowel Syndrome   Mayer, Emeran A., Labus, Jen, Cole, Steve, Baldi, P. Nature Reviews Gastroenterology. 2014.
The Pervasiveness and Plasticity of Circadian Oscillations   Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., Baldi, P. Bioinformatics. 2014.
Refereed Conference Proceedings
Massively Parallel Multicut Segmentation via Dual Decomposition   J. Yarkony, T. Beyer, B. Andres, B.S. Manjunath, P. Baldi, F. Hamprecht. ICML. 2014, 2014.
Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   D. Chicco, P. Sadowski, P. Baldi. 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Newport Beach, CA, September 2014, 2014.
Searching for Higgs Boson Decay Modes with Deep Learning   P. Sadowski, D. Whiteson, P. Baldi. NIPS. 2014.
2013
Refereed Journals
The Circadian Clock Regulates the Host Response to Salmonella   M. M. Bellet, E. Deriu, J. Liu, B. Grimaldi, C. Blaschitz, M. Zeller, R. A. Edwards, S. Sahar, S. Dandekar, P. Baldi, M. D. George, M. Raffatellu, P. Sassone-Corsi. Proceedings of the National Academy of Sciences USA. 110, 24, 9897-9902, 2013.
A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Reactions   I. Chang, P. Baldi. Bioinformatics. 29, 10, 1299-1307, 2013 May 15, 2013.
Cycles in Spatial and Temporal Chromosomal Organization Driven by the Circadian Clock   Lorena Aguilar-Arnal, Ofir Hakim, Vishal R. Patel, Pierre Baldi, Gordon L. Hager, Paolo Sassone-Corsi. Nature Structural and Molecular Biology. 2013.
An Efficient Atom-Mapping Algorithm   D. Fooshee, A. Andronico, P. Baldi. Journal of Chemical Information and Modeling. 2013.
Combining Docking Site and Phosphosite Predictions to Find New Substrates: Identification of Smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal Kinase (JNK) Substrate   E. A. Gordon, T. Whisenant, M. Zeller, R. Kaake, W. Gordon, P. Krotee, V. Patel, L. Huang, P. Baldi, L. Bardwell. Cellular Signalling. 2013.
Deep Architectures and Deep Learning in Chemoinformatics: the Prediction of Aqueous Solubility for Drug-Like Molecules   A. Lusci, G. Pollastri, P. Baldi. Journal of Chemical Information and Modeling. 53, 7, 1563–1575, June 24, 2013, 2013.
A 3-dimensional trimeric B-barrel model for Chlamydia MOMP contains conserved and novel elements of gram-negative bacterial porins   V. A. Feher, A. Randall, P. Baldi, R. M. Bush, L. M de la Maza, R. E. Amaro. PLOS One. 2013.
Leptin Engages a Hypothalamic Neurocircuitry to Permit Survival in the Absence of Insulin   Teppei Fujikawa, Eric D. Berglund, Vishal R. Patel, Giorgio Ramadori, Claudia R. Vianna, Linh Vong, Fabrizio Thorel, Simona Chera, Pedro L. Herrera, Bradford B. Lowell, Joel K. Elmquist, Pierre Baldi, Roberto Coppari. Cell Metabolism. 2013.
Small-molecule 3D Structure Prediction Using Open Crystallography Data   P. Sadowski, P. Baldi. Journal of Chemical Information and Modeling. 53, 12, 3127-3130, 2013.
Reprogramming of the Circadian Clock by Nutritional Challenge   K. L. Eckel-Mahan, V. R. Patel, S. de Mateo, N. J. Ceglia, S. Sahar, S. Dilag, K. A. Dyar, R. Orozco-Solis, P. Baldi, P. Sassone-Corsi. Cell. 155, 7, 1464-1478, 2013.
The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory   Vogel-Cierna, A.,Matheos, D.P., Barrett, R.M., Kramar, E, Azzaw, S. Chen, Y. Magnan, C. Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R. J., Chabrier, M. Babayan, A. Wu, J. I., Crabtree, G. R., Baldi, P., Baram, T. Z. Lynch, G. . Nature Neuroscience. 10, , , , , 552-561, May, 2013.
Neuron-Specific Nucleosome Remodeling Component BAF53b is Neccessary for Synaptic Plasticity and Memory   Vogel-Ciernia, A, Matheos, D. P., Barrett, R. M., Kramar, E., Chen, Y., Magnan, C., Zeller, M., Sylvain, A., Azzawi, S., Haettig, J., Tran, A., Post, R.J., Crabtree, G. R., Baram, T. Z., Baldi, P., Lynch, G., Wood, M. A. Nature Neuroscience. 16, 552-561, 2013.
Refereed Conference Proceedings
An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases   Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi. WIRN. Springer-Verlag, 2013.
Understanding Dropout   P. Sadowski, P. Baldi. NIPS. 26, C.J.C. Burges, L. Bottou, M. Welling, Z. Ghahrami, K.Q. Weinberger, Lake Tahoe, NV, 2814-2822, 2013.
Beyond Gradient Diffusion: New Algorithms for Training Deep Layers of Neural Networks   J. Yarkony, P. Sadowski, B.S. Manjunath, P. Baldi. NIPS. 2013.
Distributed training of very large networks   V. R. Patel,, N. Cegna, P. Sadowski, P. Baldi. NIPS. 2013.
2012
Refereed Journals
Rationally Selected Single-Site Mutants of the Thermoascus aurantiacus Endoglucanase Increase Hydrolytic Activity on Cellulosic Substrates.   S. Srikrishnan, A. Z. Randall, P. Baldi, N.A. Da Silva. Biotechnology and Bioengineering. 109, 6, 1595–1599, 2012.
Mitochondrial Mutations and Polymorphisms in Psychiatric Disorders.   A. Sequeira, M. V. Martin, B. Rollins, E. A. Moon, W. E. Bunney, F. Macciardi, S. Lupoli, E. Smith, J. Kelsoe, C. Magnan, M. van Oven, P. Baldi, D.C. Wallace, M. P. Vawter. Frontiers in Behavioral and Psychiatric Genetics. 3, 103, 2012.
Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport.   D. Ren, M. Dalmau, A. Randall, M. M. Shindel, P. Baldi, S. Wang. Advanced Functional Materials. 2012.
Retrotransposons Profiling of RNA Polymerase III Initiation Sites.   X. Qi, K. Daily, K. Nguyen, H. Wang, D. Mayhew, P. Rigor, S. Forouzan, M. Johnston, R. D. Mitra, P. Baldi, S. B. Sandmeyer. Genome Research. 681-692, 2012.
Speeding Up Chemical Searches Using the Inverted Index: the Convergence of Chemoinformatics and Text Search Methods.   R. Nasr, R. Vernica, C. Li, P. Baldi. Journal of Chemical Information and Modeling. 52, 4, 891-900, 2012.
SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations.   K. Nagata, A. Randall, P. Baldi. Protein: Structure, Function, and Bioinformaics. 80, 1, 142-153, 2012.
Cyber-T Webserver: Differential Analysis of High-Throughput Data.   M. Kayala, P. Baldi. Nucleic Acids Research. 1-7, 2012.
Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling.   Kao, Athit, Randall, Arlo, Yang, Yingying, Patel, Vishal R., Kandur, Wynne, Guan, Shenheng, Rychnovsky, Scott D., Baldi, Pierre, Huang, Lan. Molecular & Cellular Proteomics. 2012/12/11/23:3, 2012.
GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program.   Hopkin, Amelia Soto, Gordon, William, Klein, Rachel Herndon, Espitia, Francisco, Daily, Kenneth, Zeller, Michael, Baldi, Pierre, Andersen, Bogi. PLoS Genet. 8, 7, 2012/12/11/23:0, 2012.
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, P. Baldi. Environmental Science & Technology. 46, 11, 6048-6055, 2012.
Mapping the Protein Interaction Network of the Human COP9 Signalosome (CSN) Complex Using a Label-Free QTAX Strategy.   L. Fang, R. M. Kaake, V. Patel, P. Baldi, L. Huang. Molecular and Cellular Proteomics. 2012.
Coordination of Metabolome and Transcriptome by the Circadian Clock.   K. L. Eckel-Mahan, V. R. Patel, K. S.Vignola, R. P. Mohney, P. Baldi, P. Sassone-Corsi. PNAS. 2012, 2012.
Complex-Valued Autoencoders.   P. Baldi, Z. Lu. Neural Networks. 33, 136-147, 2012.
The Universal Campus: An Open 3D Virtual World Infrastructure for Research and Education.   P. Baldi, C. Lopes. ACM eLearn Magazine. 2012, 4, 6, 2012.
Boolean autoencoders and hypercube clustering complexity   Baldi, P. Designs, Codes and Cryptography. 1-21, 2012.
Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research. 2012.
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics.   Patel, Vishal R., Eckel-Mahan, Kristin, Sassone-Corsi, Paolo, Baldi, Pierre. Nature methods. 9, 8, 772-773, 2012.
Engineered Synthetic Polymer Nanoparticles as IgG Affinity Ligands.   Lee, Shih-Hui, Hoshino, Yu, Randall, Arlo, Zeng, Zhiyang, Baldi, Piere, Doong, Ruey-an, Shea, Kenneth J. Journal of the American Chemical Society. 134, 38, American Chemical Society, 15765-15772, 2012/12/11, 2012.
ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning   Kayala, Matthew A., Baldi, Pierre. Journal of Chemical Information and Modeling. 52, 10, American Chemical Society, 2526-2540, 2012/12/11, 2012.
A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs.   Hoverter, Nate P., Ting, Ju-Hui, Sundaresh, Suman, Baldi, Pierre, Waterman, Marian L. Molecular and cellular biology. 32, 18, 3648-3662, 2012.
Deep architectures for protein contact map prediction   Di Lena, Pietro, Nagata, Ken, Baldi, Pierre. Bioinformatics (Oxford, England). 28, 19, 2449-2457, 2012.
Boolean autoencoders and hypercube clustering complexity.   Baldi, P. Designs, Codes and Cryptography. 1-21, 2012.
GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Pprogram.   A. S. Hopkin, W. Gordon, R. H. Klein, F. Espitia, K. Daily, M. Zeller, P. Baldi, B. Andersen. PLoS Genetics. 2012.
Refereed Conference Proceedings
Deep Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS. 2012.
Deep Spatial-Temporal Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS. 25, Pereira, F., Burges, C. J. C., Bottou, L., Weinberger, K.Q., Curran Associates Inc., Lake Tahoo, NV, 512-520, 2012.
2011
Refereed Journals
Sterile Protective Immunity to Malaria is Associated with a Panel of Novel Plasmodium Falciparum Antigens.   Trieu, Angela, Kayala, Matthew A., Burk, Chad, Molina, Douglas M., Freilich, Daniel A., Richie, Thomas L., Baldi, Pierre, Felgner, Philip L., Doolan, Denise L. Molecular and Cellular Proteomics. 2011.
Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling.   B. Tang, P. Di Lena, L. Schaffer, S. R. Head, P. Baldi, E. A. Thomas. PLoS ONE. 6, 9, e23691, 2011.
Tree and Hashing Data Structures to Speedup Chemical Searches: Analysis and Experiments.   R. Nasr, T. Kristensen, P. Baldi. Molecular Informatics. 30, 9, 791-800, 2011.
SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations   K. Nagata, A. Randall, P. Baldi. Protein: Structure, Function, and Bioinformaics. 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.
Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes.   A. Kao, C. Chiu, D. Vellucci, Y. Yang, V. R. Patel, S. Guan, A. Randall, P. Baldi, S. Rychnowski, L. Huang. Molecular and Cellular Proteomics. 2011.
Identification of Immunodominant Antigens by Probing a Whole Chlamydia trachomatis Open Reading Frame Proteome Microarray Using Sera from Immunized Mice.   Cruz-Fisher, Maria I., Cheng, Chunmei, Sun, Guifeng, Pal, Sukumar, Teng, Andy, Molina, Douglas M., Kayala, Matthew A., Vigil, Adam, Baldi, Pierre, Felgner, Philip L., Liang, Xiaowu, de la Maza, Luis M. Infection and Immunity. 79, 1, 246-257, 2011.
The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating.   Clemens, Kristina, Larsen, Liza, Zhang, Min, Kuznetsov, Yurii, Bilanchone, Virginia, Randall, Arlo, Harned, Adam, DaSilva, Rhonda, Nagashima, Kunio, McPherson, Alexander, Baldi, Pierre, Sandmeyer, Suzanne. Journal of Virology. 85, 7, 3055-3066, 2011.
Visual Adaptation and Novelty Responses in the Superior Colliculus.   S. Boehnke, D. Berg, R. Marino, P. Baldi, L. Itti, D. Munoz. European Journal of Neuroscience. 34, 5, 766-779, 2011.
The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium Falciparum are Associated with Age in a Malaria Endemic Area.   A. E. Barry, A. Trieu, F. J. I. Fowkes, J. Pablo, M. Kalantari-Dehaghi, A. Jasinskas, X. Tan, M.A. Kayala, L. Tavul, P.M. Siba, K. P. Day, P. Baldi, P. L. Felgner, D. L. Doolan. Molecular and Cellular Proteomics. 2011.
Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research. 2011.
Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling. 51, 4, 760-776, 2011.
MotifMap: Integrative Genome-Wide Maps of Candidate Regulatory Motif Sites for Model Species.   K. Daily, V. Patel, P. Rigor, X. Xie, P. Baldi. BMC Bioinformatics. 12, 1, 495, 2011.
Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling. 51, 4, 760-776, 2011.
Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling. 51, 4, 760-776, 2011.
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, 2011.
Refereed Conference Proceedings
Countering GATTACA: Efficient and Secure Testing of Fully-Sequenced Human Genomes.   P. Baldi, R. Baronio, E. De Cristofaro, P. Gasti, G. Tsudik. ACM Computer and Communication Security Conference (CCS 2011). 2011.
Privacy-Enhanced Methods for Comparing Compressed DNA Sequences.   D. Eppstein, M. T. Goodrich, P. Baldi. Workshop on Privacy in the Electronic Society. 11, WPES, Chicago, USA, 2011.
A Machine Learning Approach to Predict Chemical Reactions.   M. Kayla, P. Baldi. Neural Information Processing Systems 2011 (NIPS 2011). Granada, Spain, 2011.
2010
Refereed Journals
Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli transcription Factors.   T. C. Whisenant, D. T. Ho, R. Benz, J. Rogers, R. Kaake, E. A. Gordon, L. Huang, P. Baldi, L. Bardwell. PLoS Computational Biology. 2010.
High-throughput Prediction of Protein Antigenicity Using Protein Microarray Data.   Magnan, Christophe N., Zeller, Michael, Kayala, Matthew A., Vigil, Adam, Randall, Arlo, Felgner, Philip L., Baldi, Pierre. Bioinformatics (Oxford, England). 26, 23, 2936-2943, 2010.
Data Structures and Compression Algorithms for High-throughput Sequencing Technologies   Daily, Kenny, Rigor, Paul, Christley, Scott, Xie, Xiaohui, Baldi, Pierre. BMC Bioinformatics. 11, 514-526, 2010.
Modeling of Mitochondrial Bioenergetics Based on a Composable Chemiosmotic Energy Transduction Rate Law: Theory and Experimental Validation.   I. Chang, M. Heiske, T. Letellier, D. C. Wallace, P. Baldi. PLoS ONE. 2010.
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, Z. Guan. Proceedings of the National Academy of Sciences USA. 107, 5, 1989-1994, February 2, 201, 2010.
An Antibody Signature Associated with Naturally-Acquired Malaria Immunity.   Peter D. Crompton, Matthew A. Kayala, Boubacar Traore, Kassoum Kayentao, Aissata Ongoiba, Greta Weiss, Douglas M. Molina, Chad R. Burk, Michael Waisberg, Algis Jasinskas, Safiatou Doumbo, Didier Doumtabe, Younoussou Kone, David L. Narum, Xiaowu Liang, Ogo. PNAS. 2010.
A CROC Stronger than ROC: Measuring, Visualizing, and Optimizing Early Retrieval.   S. J. Swamidass, C. Azencott, K. Daily, P. Baldi. Bioinformatics. 2010.
Modeling User Reputation in Wikis.   S. Javanmardi, C. Lopes, P. Baldi. Statistical Analysis and Data Mining. 3, 2, 126-139, 2010.
Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia.   A. B. Mochon1, J. Ye, M. A. Kayala, J. R. Wingard, C. J. Clancy, M. H. Nguyen, P. Felgner, P. Baldi, H. Liu. PLoS Pathogens. 6, 3, Public Library of Science, e1000827, 2010.
Of Bits and Wows: A Bayesian Theory of Surprise with Applications to Attention.   P. Baldi, L. Itti. Neural Networks. 23, 649-666, 2010.
Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors.   R. Nasr, D. Hirschberg, P. Baldi. Journal of Chemical Information and Modeling. 2010.
Large Scale Immune Profiling of Infected Humans and Goats Reveals Differential Recognition of Brucella melitensis Antigens.   Li Liang, Diana Leng, Chad Burk, Rie Nakajima-Sasaki, Matt Kayala, Vidya L. Atluri, Jozelyn Pablo, Berkay Unal, Thomas A. Ficht, Eduardo Gotuzzo, Mayuko Saito John Morrow, Xiaowu Liang, Pierre Baldi, Joseph M. Vinetz, Philip L. Felgner, Renee M. Tsolis. PLoS Neglected Tropical Diseases. 4, 5, 1-11, 2010.
A Prospective Analysis of the Antibody Response to Plasmodium falciparum Before and After a Malaria Season by Protein Microarray.   P. Crompton, M. Kayala, B. Traore, K. Kayentao, A. Ongoiba, G. Weiss, D. Molina, C. Burk, M. Waisberg, A. Jasinskas, X. Tan, S. Doumbo, D. Doumtabe, Y. Kone, D. Narum, X. Liang, O. Doumbo, L. Miller, D. Doolan, P. Baldi, P. Felgner, S. Pierce. PNAS. 15, 6958-6963, 2010.
When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values.   P. Baldi, R. Nasr. Journal of Chemical Information and Modeling. 2010.
Refereed Conference Proceedings
Autoencoders, Unsupervised Learning, and Deep Architectures.   P. Baldi. Workshop on Deep Learning and Unsupervised Feature Learning. Neural Information Processing Systems (NIPS), Whistler, Canada, 2010.
A Scalable Reference-Point Based Algorithm to Efficiently Search Large Chemical Databases.   F. Napolitano, R. Tagliaferri, P. Baldi. IEEE Proceedings of the 2010 International Joint Conference on Neural Networks (IJCNN 2010). 2010.
Information-Theoretic Metrics for Project-Level Scattering and Tangling.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. International Conference on Software Engineering and Knowledge Engineering (SEKE). Redwood City, CA, 2010.
Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery.   P. Baldi, C. Azencott, S. J. Swamidass. WIRN 2010. IOS Press, 2010.
Book Chapters
Transmembrane β-Barrel Protein Structure Prediction.   A. Randall, P. Baldi. Structural Bioinformatics of Membrane Proteins. Dmitrij Frishman, Springer, in press, 2010.
Enhancing Learning with Online Resources, Social Networking and Digital Libraries.   J. Chen, M. A. Kayala, P. Baldi. R. E. Belford, J. Moore, 2010.
2009
Refereed Journals
Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia.   A. B. Mochon1, J. Ye, M. A. Kayala, J. R. Wingard, C. J. Clancy, M. H. Nguyen, P. Felgner, P. Baldi, H. Liu. PLoS Pathogens. 2009.
MotifMap: a human genome-wide map of candidate regulatory motif sites.   X. Xie, P. Rigor, P. Baldi. Bioinformatics. 25, 2, 167-174, 2009.
A Burkholderia pseudomallei protein array reveals serodiagnostic and cross-reative antigens.   P.Felgner, M. Kayala, A. Vigil, 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, P. Baldi, S. Peacock, R. Titball. PNAS. 106, 32, 13499-13504, 2009.
COBEpro: A Novel System for Predicting Continuous B-cell Epitopes.   M. J. Sweredoski, P. Baldi. Protein Engineering Design and Selection. 22, 3, 113-120, 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.
MITOMASTER: A Bioinformatics Tool For the Analysis of Mitochondrial DNA Sequences.   M. Brandon, E. Ruiz-pesini, D. Mishmar, V. Procaccio, M.T. Lott, K. C. Nguyen, S. Spolim, U. Patil, P. Baldi, D. Wallace. Human Mutation (Database Issue). 30, 1, 16, 2009.
Software-Driven Sensor Networks for Short-Range Shallow Water Applications.   R. Jurdak, P. Baldi, C. Lopes. Ad Hoc Networks Journal. 7, 5, 837-848, 2009.
The Influence Relevance Voter: An Accurate and Interpretable Virtual High Throughput Screening Method.   S. J. Swamidass, C. Azencott, H. Gramajo, S. Tsai, P. Baldi. Journal of Chemical Information and Modeling. 49, 4, 756-766, 2009.
Data Structures and Compression Algorithms for Genomic Sequence Data.   M. C. Brandon, D. C. Wallace, P. Baldi. Bioinformatics. 25, 14, 1731-1738, July 15, 2009, 2009.
SOLpro: Accurate Sequence-Based Prediction of Protein Solubility.   C. N. Magnan, A. Randall, P. Baldi. Bioinformatics. 25, 17, 2200-2207, 2009.
Large Scale Study of Multiple-Molecule Queries.   R. J. Nasr, S. J. Swamidass, P. Baldi. Journal of Chemoinformatics. 1, 7, June 4, 2009, 2009.
An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases.   P. Baldi, D. Hirschberg. Journal of Chemical Information and Modeling. 49, 8, 1866-1870, 2009.
No Electron Left-Behind: a Rule-Based Expert System to Predict Chemical Reactions and Reaction Mechanisms.   J. Chen, P. Baldi. Journal of Chemical Information and Modeling. 49, 9, 2034-2043, 2009.
Identification of Immunodominant Antigens of Chlamydia Trachomatis Using Proteome Microarrays.   D. M. Molina, S. Pal, A. Teng, M. Kayala, P. Baldi, P. Felgner, X. Liang, L. M. de la Maza. Vaccine. December 28, 20, 2009.
Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Vision Research. 49, 10, 1295-1306, 2009.
Refereed Conference Proceedings
Exploring Java Software Vocabulary: A Search and Mining Perspective.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. SUITE 2009: Proceedings of the First International Workshop on Search-Driven Development - Users, Tools, and Applications. Vancouver, BC, Canada, 2009.
Software Analysis with Unsupervised Topic Models.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. Neural Information Processing Systems (NIPS) Conference. Whistler, Canada, 2009.
Information-Theoretic Metrics for Project-Level Scattering and Tangling.   E. Linstead, L. Hughes, P. Baldi. Third International Symposium on Empirical Software Engineering and Measurement (ESEM). Lake Buena Vista, Florida, 2009.
The Evolution of Concerns, Scattering, and Tangling in Eclipse and ArgoUML.   E. Linstead, L. Hughes, P. Baldi. Third International Symposium on Empirical Software Engineering and Measurement (ESEM). Lake Buena Vista, Florida, 2009.
Mining the Coherence of GNOME Bug Reports with Statistical Topic Models.   E. Linstead, P. Baldi. MSR '09: Proceedings of the Sixth International Working Conference on Mining Software Repositories. IEEE Computer Society, Vancouver, BC, Canada, 2009.
User Contribution and Trust in Wikipedia.   S. Javanmardi, C. Loes, P. Baldi. Proceedings of the 5th International Conference on Collaborative Computing: Networking, Applications and Worksharing. Washinton D.C., 2009.
An Empirical Analysis of User Contributions in Wikipedia.   S. Javanmardi, Y. Ganjisaffar, C. Lopes, P. Baldi. WikiSym. 2009.
2008
Refereed Journals
Profiling Humoral Immune Responses to P. falciparum Infection with Protein Microarrays.   D. L. Doolan, Y. Mu, B. Unal, S. Sundaresh, S. Hirst, C. Valdez, A. Randall, D. Molina, X. Liang, J. A. Oloo, P. L. Blair, J. C. Aguiar, P. Baldi, D. Huw Davies, P. L. Felgner. Proteomics. 8, 4680-4694, 2008.
SELECTpro: Effective Protein Model Selection Using a Structure-Based Energy Function Resistant to Blunders.   A. Randall, P. Baldi. BMC Structural Biology. 8, 52, 2008.
Machine Learning Methods for Protein Structure Prediction.   J. Cheng, A. N. Tegge, P. Baldi. IEEE Reviews in Biomedical Engineering. 1, 41-49, 2008.
Synthesis Explorer: Organic Chemistry Tutorial System for Multi-Step Synthesis Design and Reaction Prediction.   J. Chen, P. Baldi. Journal of Chemical Education. 85, 12, 1699-1703, 2008.
BLASTing Small Molecules—Statistics and Extreme Statistics of Chemical Similarity Scores.   P. Baldi, R. W. Benz. Bioinformatics. 24, 13, i357-i365, 2008.
PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure.   M. J. Sweredoski, P. Baldi. Bioinformatics. 24, 12, 1459-1460, 2008.
Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR.   P. Baldi, D. S. Hirschberg, R. J. Nasr. Journal of Chemical Information and Modeling. 48, 7, 1367-1378, 2008.
Discovery of Power-Laws in Chemical Space.   R. W. Benz, S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling. 48, 6, 1138-1151, 2008.
Learning to Play Go Using Recursive Neural Networks.   L. Wu, P. Baldi. Neural Networks. 21, 1392-1400, 2008.
TMBpro: Secondary Structure, β-Contact, and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins.   A. Randall, J. Cheng, M. Sweredoski, P. Baldi. Bioinformatics. 24, 4, 513-520, 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, A. Jasinskas, M. Kayala, D. Huw Davies, A. C. Steere, P. Baldi, P. Felgner. Infection and Immunity. 76, 3374-3389, 2008.
Dysregulation of the Hypothalamic-Pituitary-Adrenal (HPA) Axis in Irritable Bowel Syndrome.   L. Chang, S. Sundaresh, J. Elliott, P. A. Anton, P. Baldi, A. Licudine, M. Mayer, T. Vuong, M. Hirano, B. D. Naliboff, V. Z. Ameen, E. A. Mayer. Neurogastroenterology and Motility. 21, 2, 149-159, 2008.
Refereed Conference Proceedings
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers.   D. S. Hirschberg, P. Baldi. Proceedings of the 2008 Data Compression Conference (DCC 08). J. A. Storer, M.W. Marcellin, IEEE Computer Society Press, Snowbird, Utah, 520, 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. Nashville, TN, 2008.
An Application of Latent Dirichlet Allocation to Analyzing Software Evolution.   E. Linstead, C. Lopes, P. Baldi. International Conference on Machine Learning and Applications (ICMLA). San Diego, 2008.
2007
Refereed Journals
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. 35, D823-D828, 2007.
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.   C. Azencott, A. Ksikes, S. Joshua Swamidass, J. Chen, L. Ralaivola, P. Baldi. Journal of Chemical Information and Modeling. 47, 3, 965-974, 2007.
Phylogenetic Analysis, Genome Evolution and the Rate of Gene Gain in the Herpesviridae.   N. Wang, P. Baldi, B. Gaut. Molecular Phylogenetics and Evolution. 43, 3, 1066-1075, 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, S. Sandmeyer. The Journal of Virology. 81, 13, 6957-6972, 2007.
Adaptive Low Power Listening for Wireless Sensor Network.   R. Jurdak, P. Baldi, C. Lopes. IEEE Transactions on Mobile Computing. 6, 8, 988-1004, 2007.
A Theoretical Study of the In Vivo Mechanical Properties of Angiosperm Roots: Constitutive Theories and Methods of Parameter Estimation.   A. Sadovsky, P. Baldi, F. Wan. Journal of Engineering Materials and Technology. 129, 3, 483-487, 2007.
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time.   S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling. 47, 2, 302-317, 2007.
A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.   S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling. 47, 3, 952-964, 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, L. Itti. Journal of Vision. 7, 10, 1-13, 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, P. L. Felgner. Proteomics. 7, 13, 2172-2183, 2007.
Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set.   J. Cheng, P. Baldi. BMC Bioinformatics. 8, 113-121, 2007.
The fixed-size Luria–Delbruck model with a nonzero death rate.   N. Komarova, L. Wu, P. Baldi. Mathematical Biosciences. 210, 1, 253-290, 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, P. Baldi. Bioinformatics. 23, 21, 2829-2835, 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, I. Ezkurdia. Proteins. 69, 137-151, 2007.
ChemDB Update—Full-Text Search and Virtual Chemical Space.   J. Chen, E. Linstead, S. J. Swamidass, D. Wang, P. Baldi. Bioinformatics. 23, 2348-2351, 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, P. Baldi. Bioinformatics. 23, i508-i518, 2007.
Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.   P. Baldi, R. W. Benz, D. S. Hirschberg, S. Joshua Swamidass. Journal of Chemical Information and Modeling. 47, 6, 2098-2109, 2007.
Refereed Conference Proceedings
CodeGenie: Using Test-Cases to Search and Reuse Source Code.   O. Lemos, S. Bajracharya, J. Ossher, R. Morla, P. Masiero, P. Baldi, C. Lopes. Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering (ASE’07). Atlanta, GA, 525-526, 2007.
Software Modems for Underwater Sensor Networks.   R. Jurdak, P. Aguiar, P. Baldi, C. Lopes. Proceedings of IEEE/OES Oceans'07. Aberdeen, Scotland, 2007.
Mining Eclipse Developer Contributions via Author-Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the MSR 2007: International Workshop on Mining Software Repositories. Minneapolis, MN, 30-33, 2007.
Mining Concepts from Code with Probabilistic Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering. Atlanta, GA, 461-464, 2007.
Mining Internet-Scale Software Repositories.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Advances in Neural Information Processing Systems 20. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 929-936, 2007.
Book Chapters
Virtual High-Throughput Screening with Two-Dimensional Kernels.   A. Azencott, P. Baldi. Hands-On Pattern Recognition. Challenges in Data Representation, Model Selection, and Performance Prediction. I. Guyon, G. Cawley, G. Droor, A. Saffari, Lulu Press, 2007.
2006
Refereed Journals
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, Richard H. Lathrop. IEEE Transactions on Computational Biology and Bioinformatics. 3, 2, 114-125, 2006.
Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.   J. Cheng, H. Saigo, P. Baldi. Proteins. 62, 3, 617-629, 2006.
Global Landscape of Recent Inferred Darwinian Selection for Homo Sapiens.   E. T. Wang, G. Kodama, P. Baldi, R. K. Moyzis. Proceedings of the National Academy of Sciences USA. 103, 135-140, 2006.
Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines.   J. Cheng, A. Randall, P. Baldi. Proteins. 62, 4, 1125-1132, 2006.
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.   J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery. 13, 1, 1-10, 2006.
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.   G. Pollastri, A. Vullo, P. Frasconi, P. Baldi. Journal of Computational Biology. 3, 631-650, 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, S. Tsai. Proceedings of the National Academy of Sciences USA. 103, 9, 3072-3077, 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, Peter Kaiser. Molecular and Cellular Proteomics. 4, 737-748, 2006.
Localization of Off-the-Shelf Mobile Devices Using Audible Sound: Architectures, Protocols and Performance Assessment.   C. V. Lopes, A. Haghighat, A. Mandal, P. Baldi, T. Givargis. ACM SIGMOBILE Mobile Computing and Communications Review. 10, 2, 38-50, 2006.
A Machine Learning Information Retrieval Approach to Protein Fold Recognition.   J. Cheng, P. Baldi. Bioinformatics. 22, 12, 1456-1463, 2006.
Mitochondrial Mutations in Cancer.   M. Brandon, P. Baldi, D. C. Wallace. Oncogene. 25, 4647-4662, 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, Pierre Baldi. Bioinformatics. 22, 14, 1760-1766, 2006.
Genomic Splice-Site Analysis Reveals Frequent Alternative Splicing Close to the Dominant Splice Site.   Y. Dou, K. Fox-Walsh, P. Baldi, K. Hertel. RNA. 12, 12, 2047-2056, 2006.
Refereed Conference Proceedings
Software Acoustic Modems for Short Range Mote-Based Underwater Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. In Proceedings of IEEE Oceans – Asia Pacific. Singapore, 1-7, 2006.
A Comparative Analysis and Experimental Study on Wireless Aerial and Underwater Acoustic Communications.   R. Jurdak, C. Lopes, P. Aguiar, P. Baldi. Proceeding of the 2006 International Conference on Digital Telecommunications. IEEE Computer Society, 2006.
A Scalable Machine Learning Approach to Go.   L. Wu, P. Baldi. Advances in Neural Information Processing Systems 19. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 1521-1528, 2006.
2005
Refereed Journals
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, P. Baldi. Bioinformatics. 21, i359-368, 2005.
Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. Bioinformatics. 21, i75-84, 2005.
Statistical Detection of Chromosomal Homology Using Shared-Gene Density Alone.   S. Hampson, B. S. Gaut, P. Baldi. Bioinformatics. 21, 8, 1339-1348, 2005.
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, J. Y. Sze. Journal of Neuroscience. 25, 4, 1015-1023, 2005.
MITOMAP: a human mitochondrial genome database - 2004 update.   M. Brandon, M. Lott, K. Nguyen, S. Spolim, S. Navathe, P. Baldi, D. Wallace. Nucleic Acids Research. 33, D611-613, 2005.
Sigmoid: Towards a Generative, Scalable Software Infrastructure for Pathway Bioinformatics and Systems Biology.   J. Cheng, L. Scharenbroich, P. Baldi, E. Mjolsness. IEEE Intelligent Systems. 20, 3, 68-75, 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.
How Noisy and Replicable are DNA Microarray Data?   S. Sundaresh, S. Hung, G. W. Hatfield, P. Baldi. International Journal of Bioinformatics Research and Applications. 1, 1, 31-50, 2005.
U-MAC: A Proactive and Adaptive UWB Medium Access Control Protocol.   R. Jurdak, P. Baldi, C. Videira Lopes. Wireless Communications and Mobile Computing Journal (special Issue on "UWB Communications"). 5, 5, 551-566, 2005.
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, R. P. Gunsalus. Journal of Biological Chemistry. 280, 15, 15084-15096, 2005.
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, S. Sandmeyer. Genome Research. 15, 641-654, 2005.
Graph Kernels for Chemical Informatics.   L. Ralaivola, J. S. Swamidass, H. Saigo, P. Baldi. Neural Networks. 18, 8, 1093-1110, 2005.
On the Relationship Between Deterministic and Probabilistic Directed Graphical Models: from Bayesian Networks to Recursive Neural Networks.   P. Baldi, M. Rosen-Zvi. Neural Networks. 18, 8, 1080-1086, 2005.
SCRATCH: a Protein Structure and Structural Feature Prediction Server.   J. Cheng, A. Z. Randall, M. Sweredoski, P. Baldi. Nucleic Acids Research. 33, 9, W72-76, 2005.
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.   J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery. 11, 3, 213-222, 2005.
The Absence of Favorable Aromatic Interactions between β-Sheet Peptides.   D. M. Chung, Y. Dou, P. Baldi, J. S. Nowick. Journal of the American Chemical Society. 127, 28, 9998-9999, 2005.
ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources.   J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, P. Baldi. Bioinformatics. 21, 4133-4139, 2005.
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, Klemens J. Hertel. Proceedings of the National Academy of Sciences USA. 102, 16176-16181, 2005.
Refereed Conference Proceedings
Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking. 2005.
State-Driven Energy Optimization in Wireless Sensor Networks.   R. Jurdak, P. Baldi, C. Lopes. Proceedings of the IEEE/IEE International Conference on Sensor Networks (SENET). Montreal, Canada, 356-363, 2005.
SVM and Pattern-Enriched Common Fate Graphs for the Game of GO.   L. Ralaivola, L. Wu, P. Baldi. European Symposium on Artificial Neural Networks (ESANN). Bruges, Belgium, 2005.
A Principled Approach to Detecting Surprising Events in Video.   L. Itti, P. Baldi. Proc. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2005.
Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking. 2005.
Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   S. Swamidass, J. Chen, P. Phung, J. Bruand, L. Ralaivola, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05). 21, Bioinformatics, i359-368, 2005.
Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05). Bioinformatics, i75-84, 2005.
Programming Model for Supporting Complex Optimizations in Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. Fourth International IEEE/ACM Conference on Information Processing in Sensor Networks (IPSN’05). Los Angeles, CA, 2005.
Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Advances in Neural Information Processing Systems 18, NIPS 2005. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 547-554, 2005.
Attention: Bits versus Wows.   P. Baldi, L. Itti. Proceedings of the International Conference on Neural Networks and Brain. 1, Mingsheng Zhao, Zhongzhi Shi, IEEE Press, Beijing, China, PL56-PL61, 2005.
Exploring Chemical Space with Computers: Informatics Challenges for AI and Machine Learning.   P. Baldi. BIOMAT V Symposium. World Scientific Co.Pte.Ltd., Petrópolis, Brazil, 2005.
Chemoinformatics, Drug Design, and Systems Biology.   P. Baldi. Proceedings of the 16th International Conference on Genome Informatics, (GIW 2005). Yokohama, Japan, 2005.
Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking. 2005.
Book Chapters
Surprise: A Shortcut for Attention?   P. Baldi. Neurobiology of Attention. L. Itti, G. Rees, J. Tsotsos, Elsevier, San Diego, 24-28, 2005.
Clustering Algorithms for Gene Expression Analysis.   P. Baldi, G. Wesley Hatfield, Li M. Fu. Handbook of Computational Molecular Biology. S. Aluru, Chapman & Hall/CRC Press, 2005.
Battery Lifetime Estimation and Optimization for Underwater Sensor Networks.   R. Jurdak, C. V. Lopes, P. Baldi. Sensor Network Operations. Shashi Phoha, Thomas F. La Porta, Christopher Griffin, IEEE Press, 2005.
Statistical Distribution of Chemical Fingerprints.   S. J. Swamidass, P. Baldi. Proceedings of WILF2005. Springer Verlag, Andrea Tattamanzi, 2005.
2004
Refereed Journals
ICBS: A Database of Interactions Between Protein Chains Mediated by β-Sheet Formation.   Y. Dou, P. Baisnee, G. Pollastri, Y. Pecout, J. Nowick, P. Baldi. Bioinformatics. 20, 16, 2767-2777, 2004.
Structural Proteomics of the Poxvirus Family.   A. Z. Randall, P. Baldi, L. P. Villareal. Artificial Intelligence in Medicine (special issue on “Data mining in Genomics and Proteomics”). 31, 2, 105-115, 2004.
A Survey, Classification, and Comparative Analysis of Medium Access Control Protocols for Ad Hoc Networks.   R. Jurdak, C. Videira Lopes, P. Baldi. IEEE Communications Surveys and Tutorials. 6, 1, 2-16, 2004.
Refereed Conference Proceedings
An Identfication Scheme for Location Systems Using Robust Acoustic Signals.   R. Jurdak, C. Lopes, P. Baldi. Proceeding of the ACS/IEEE International Conference on Pervasive Services. IEEE Computer Society Press, Beirut, Lebanon, 2004.
Large-Scale Prediction of Disulphide Bond Connectivity.   P. Baldi, J. Cheng, A. Vullo. Advances in Neural Information Processing Systems 17 (NIPS 2004). 2004.
Beep: 3D Indoor Positioning Using Audible Sound.   A. Mandal, C. Lopes, T. Givargis, A. Haghighat, R. Jurdak, P. Baldi. Proceedings of the 2004 IEEE Consumer Communications and Networking Conference. 348-353, 2004.
Book Chapters
Hidden Markov Models and Neural Networks.   S. Kremer, P. Baldi. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley, 2004.
2003
Refereed Journals
What Genes are Made Of.   P. Baldi. Pathways. 2003.
Differential Analysis of DNA Microarray Gene Expression Data.   G. Wesley Hatfield, S. Hung, P. Baldi. Molecular Microbiology. 47, 4, 871-877, 2003.
Bounds on Variances of Estimators for Multinomial Processing Tree Models.   P. Baldi, W. H. Batchelder. Journal of Mathematical Psychology. 47, 467-470, 2003.
Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity.   Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy, P. Baldi. Neurocomputing. 56, 305-327, 2003.
The Principled Design of Large-Scale Recursive Neural Network Architectures—DAG-RNNs and the Protein Structure Prediction Problem.   P. Baldi, G. Pollastri. Journal of Machine Learning Research. 4, 575-602, 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, S. S. Sidhu. Journal of Molecular Biology. 332, 4, 777-782, 2003.
LineUp : Statistical Detection of Chromosomal Homology with Applications to Plant Comparative Genomics.   S. Hampson, A. McLysaght, B. Gaut, P. Baldi. Genome Research. 13, 5, 1999-1010, 2003.
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, G. Wesley Hatfield. Journal of Biological Chemistry. 278, 32, 29837-29855, 2003.
Extensive Gene Gain Associated With Adaptive Evolution of Poxviruses.   A. McLysaght, P. Baldi, B. S. Gaut. Proceedings of the National Academy of Sciences USA. 100, 26, 15655-15660, 2003.
Refereed Conference Proceedings
Prediction of Protein Topologies Using Generalized IOHMMs and RNNs.   G. Pollastri, P. Baldi, A. Vullo, P. Frasconi. Advances in Neural Information Processing Systems 15. 15, S. Becker, S. Thrun, K. Obermayer, MIT Press, Cambridge, MA, 2003.
Other
What Genes are Made Of.   P. Baldi. Review of edited book entitled: The Genomic Revolution: Unveiling the Unity of Life. Pathways, 2003.
Books
Modeling the Internet and the Web: Probabilistic Methods and Algorithms.   P. Baldi, P. Frasconi, P. Smyth. Wiley, 2003.
Book Chapters
New Machine Learning Methods for the Prediction of Protein Topologies.   P. Baldi, G. Pollastri, P. Frasconi, A. Vullo. Artificial Intelligence and Heuristic Methods in Bioinformatics. P. Frasconi, R. Shamir, IOS Press, 51-73, 2003.
Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets.   S. P. Hung, G. Wesley Hatfield, S. Sundaresh, P. Baldi. Genomics, Proteomics, and Vaccines. G. Grandi, John Wiley and Sons, 2003.
2002
Refereed Journals
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Bioinformatics. 18, S62-S70, 2002.
Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles.   G. Pollastri, D. Przybylski, B. Rost, P. Baldi. Proteins. 47, 228-235, 2002.
Prediction of Coordination Number and Relative Solvent Accessibility in Proteins.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proteins. 47, 142-153, 2002.
Distribution Patterns of Over-Represented k-mers in Non-Coding Yeast DNA.   S. Hampson, D. Kibler, P. Baldi. Bioinformatics. 18, 4, 611-626, 2002.
A Machine Learning Strategy for Protein Analysis.   P. Baldi, G. Pollastri. IEEE Intelligent Systems (special Issue on "Intelligent Systems in Biology"). 17, 2, 28-35, 2002.
Why Are Complementary DNA Strands Symmetric?   P. Baisnee, S. Hampson, P. Baldi. Bioinformatics. 18, 1021-1033, 2002.
Global Gene Expression Profiling in Excherichia coli K12: The Effects of Leucine-responsive Regulatory Protein.   S. Hung, P. Baldi, G. Wesley Hatfield. Journal of Biological Chemistry. 277, 43, 40309-40323, 2002.
Modeling and Optimization of UWB Communication Networks Through a Flexible Cost Function.   P. Baldi, L. De Nardis, M. G. Di Benedetto. IEEE Journal on Selected Areas in Communications. 20, 9, 1733-1744, 2002.
Refereed Conference Proceedings
UWB Ad-Hoc Networks.   L. De Nardis, P. Baldi, M. Di Benedetto. Proceedings of the 2002 IEEE Conference on Ultra Wide Band Systems and Technologies (UWBST 2002). Baltimore, MD, 219-224, 2002.
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology (ISMB 02). 18, Bioinformatics, S62-S70, 2002.
Books
DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling.   P. Baldi, G. Wesley Hatfield. Cambridge University Press, 2002.
Book Chapters
A Computational Theory of Surprise.   P. Baldi. Information, Coding, and Mathematics. M. Blaum, Kluwer, 1-25, 2002.
2001
Refereed Journals
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.
Flexibility of the Genetic Code with Respect to DNA Structure.   P. Baisnée, P. Baldi, S. Brunak, A. Gorm Pedersen. Bioinformatics. 17, 237-248, 2001.
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Inference of Gene Changes.   P. Baldi, A. D. Long. Bioinformatics. 17, 6, 509-519, 2001.
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, P. Baldi. Journal of Biological Chemistry. 276, 23, 19937-19944, 2001.
Refereed Conference Proceedings
A Model for Self-Organizing Large Scale Wireless Networks.   M. Di Benedetto, P. Baldi. International Symposium on 3G Infrastructure and Services. Athens, Greece, 2001.
Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proceedings of the 2001 Conference on Intelligent Systems for Molecular Biology, (ISMB01). AAAI Press, Copenhagen, Denmark, 2001.
Books
The Shattered Self: The End of Natural Evolution.   P. Baldi. MIT Press, 2001.
2000
Refereed Journals
Probabilistic Graphical Models in Computational Molecular Biology.   P. Baldi. Journal of the Italian Association for Artificial Intelligence. 1, 8-12, 2000.
On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial Genomes.   P. Baldi. Bioinformatics. 16, 4, 367-371, 2000.
Assessing the Accuracy of Prediction Algorithms for Classification: An Overview.   P. Baldi, S. Brunak, Y. Chauvin, H. Nielsen. Bioinformatics. 16, 5, 412-424, 2000.
Sequence Analysis by Additive Scales: DNA Structure for Sequences and Repeats of All Lenghts.   P. Baldi, P. Baisnée. Bioinformatics. 16, 10, 865-889, 2000.
Refereed Conference Proceedings
Protein β-Sheet Partner Prediction by Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Artifical Neural Networks in Medicine and Biology. Proceedings of the ANNIMAB-1 Conference. H. Malmgren, M. Borga, L. Niklasson, Springer Verlag, Göteborg, Sweden, 2000.
Analysis of Yeast’s ORFs Upstream Regions by Parallel Processing, Microarrays, and Computational Methods.   S. Hampson, P. Baldi, D. Kibler, S. Sandmeyer. Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology (ISMB00). AAAI Press, La Jolla, CA, 190-201, 2000.
Matching Protein β-Sheet Partners by Feedforward and Recurrent Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology (ISMB00). AAAI Press, La Jolla, CA, 25-36, 2000.
Book Chapters
Bidirectional IOHMMs and recurrent neural networks for protein secondary structure prediction.   P. Baldi, S. Brunak, G. Pollastri, P. Frasconi. Protein Sequence Analysis in the Genomic Era. Rita Casadio, Lanfranco Masotti, CLUEB, Bologna, Italy, 2000.
Bidirectional Dynamics for Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, G. Soda. Sequence Learning: Paradigms, Algorithms, and Applications. R. Sun, C. L. Giles, Springer Verlag, 99-120, 2000.
1999
Refereed Journals
The Biology of Eukaryotic Promoter Prediction-a Review.   A. Gorm Pedersen, P. Baldi, S. Brunak, Y. Chauvin. Computers and Chemistry, Special Issue on Genome and Informatics. 23, 191-207, 1999.
Exploiting the Past and the Future in Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri. Bioinformatics. 15, 11, 937-946, 1999.
Structural Basis for Triplet Repeat Disorders: A Computational Analysis.   P. Baldi, S. Brunak, Y.Chauvin, A. Gorm Pedersen. Bioinformatics. 15, 11, 918-929, 1999.
1998
On the Use of Bayesian Methods for Evaluating Compartmental Neural Models.   P. Baldi, M. C. Vanier, J. M. Bower. Journal of Computational Neuroscience. 5, 285-314, 1998.
DNA Structure in Human RNA Polymerase II Promoters.   A. Gorm Pedersen, P. Baldi, Y. Chauvin, S. Brunak. Journal of Molecular Biology. 281, 663-673, 1998.
Refereed Conference Proceedings
Computational Applications of DNA Structural Scales.   P. Baldi, S. Brunak, Y. Chauvin, A. Gorm Pedersen. Proceedings of the 1998 Conference on Intelligent Systems for Molecular Biology (ISMB98). AAAI Press, Montreal, Canada, 35-42, 1998.
Books
Bioinformatics: the Machine Learning Approach.   P. Baldi, S. Brunak. MIT Press, 1998.
Book Chapters
Probabilistic Models of Neuronal Spike Trains.   P. Baldi. Adaptive Processing of Temporal Information. C.L. Giles, M. Gori, Springer Verlag, New York, 198-228, 1998.
Software Foundation Libraries for the Design of Intelligent Systems.   P. Baldi, Y. Chauvin, V. Mittal Henkle. Neural Nets WIRN Vietri 98. Proceedings of the 10-th Italian Workshop on Neural Nets. M. Marinaro, R. Tagliaferri, 17-39, 1998.
1996
Refereed Journals
Hybrid Modeling, HMM/NN Architectures, and Protein Applications.   P. Baldi, Y. Chauvin. Neural Computation. 2, 3, 497-501, 1996.
Naturally Occurring Nucleosome Positioning Signals in Human Exons and Introns.   P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Journal of Molecular Biology. 263, 5, 503-510, 1996.
Refereed Conference Proceedings
Universal Approximation and Learning of Trajectories Using Oscillators.   P. Baldi, K. Hornik. Advances in Neural Information Processing Systems 8. D. S. Touretzky, M. C. Mozer, M. E. Hasselmo, MIT Press, Cambridge MA, 451-457, 1996.
Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequences.   P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Theoretical and Computational Methods in Genome Research. S.Suhai, Plenum, NY, 1996.
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models.   P. Baldi, A. Gorm Pedersen, S. Brunak, Y. Chauvin. Proceedings of the 1996 Conference on Intelligent Systems for Molecular Biology (ISMB96). AAAI Press, Washington University, Saint Louis, 182-191, 1996.
1995
Refereed Journals
Gradient Descent Learning Algorithms Overview: A General Dynamical Systems Perspective.   P. Baldi. IEEE Transactions on Neural Networks. 6, 1, 182-195, 1995.
Learning in Linear Networks: a Survey.   P. Baldi, K. Hornik. IEEE Transactions on Neural Networks. 6, 4, 837-858, 1995.
Substitution Matrices and Hidden Markov Models.   P. Baldi. Journal of Computational Biology. 2, 3, 497-501, 1995.
Refereed Conference Proceedings
Inferring Ground Truth from Subjective Labelling of Venus Images.   P. Smyth, U. Fayadd, P. Perona, M. Burl, P. Baldi. Advances in Neural Information Processing Systems. G. Tesauro, D. S. Touretzky, T. K. Leen, MIT Press, Cambridge, MA, 1085-1092, 1995.
Periodic Sequence Patterns in Human Exons.   P. Baldi, Y. Chauvin, S. Brunak, J. Engelbrecht, A. Krogh. Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95). Cambridge, UK, 30-38, 1995.
Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures.   P. Baldi, Y. Chauvin. Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95). Cambridge, UK, 39-47, 1995.
Book Chapters
When Neural Networks Play Sherlock Holmes.   P. Baldi, Y. Chauvin. Back-Propagation: Theory, Architectures and Applications. 487, Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 1995.
Gradient Descent Learning Algorithms: A Unified Perspective.   P. Baldi. Back-Propagation: Theory, Architectures and Applications. Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 509-541, 1995.
Back-propagation and unsupervised learning in linear networks.   P. Baldi, Y. Chauvin, K. Hornik. Back-Propagation: Theory, Architectures and Applications. Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 389-432, 1995.
1994
Refereed Journals
How Delays Affect Neural Dynamics and Learning.   P. Baldi, A. Atiya. IEEE Transactions on Neural Networks. 5, 4, 626-635, 1994.
Smooth On-Line Learning Algorithms for Hidden Markov Models.   P. Baldi, Y. Chauvin. Neural Computation. 6, 2, 305-316, 1994.
Hidden Markov Models of Biological Primary Sequence Information.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. PNAS USA. 91, 3, 1059-1063, 1994.
Hidden Markov Models of the G-Protein Coupled Receptor Family.   P. Baldi, Y. Chauvin. Journal of Computational Biology. 1, 4, 311-335, 1994.
Refereed Conference Proceedings
Trading Decision Learning: from Theory to Personal Traders.   P. Baldi, Y. Chauvin. Proceedings of the Second International Conference on Neural Networks in the Capital Markets. Pasadena, CA, 1994.
Modeling Protein Families and Human Genes: Hidden Markov Models and a Little Beyond.   P. Baldi, Y. Chauvin. Proceedings of the 1994 Fifth Generation Computing Symposium, Workshop on Fusion of Molecular Biology and Knowledge Processing. Tokyo, Japan, 1994.
Discrimination of Tyrosine and Serine/Threonine Kinase Sub-Families by Hidden Markov Models.   P. Baldi, Y. Chauvin. Proceedings of The Third International Conference on Bioinformatics and Genome Research. World Scientific Publishing Co., 1994.
Hidden Markov Models of Human Genes.   P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, A. Krogh. Advances in Neural Information Processing Systems. J. D. Cowan, G. Tesauro, J. Alspector, Morgan Kauffmann Publishers, 761-768, 1994.
Book Chapters
Statistical Models of Proteins: an Application to the G-Protein-Coupled Receptor Family.   P. Baldi, Y. Chauvin. Modern Approaches in Molecular Bioinformatics. S. Schulze-Kremer, IOS Press, Amsterdam/New York, 53-102, 1994.
1993
Refereed Journals
Random Interactions in Higher-Orders Neural Networks.   P. Baldi, S.S. Venkatesh. IEEE Transactions on Information Theory. 39, 1, 274-283, 1993.
Neural Networks for Fingerprint Recognition.   P. Baldi, Y. Chauvin. Neural Computation. 5, 3, 402-418, 1993.
Refereed Conference Proceedings
Learning Trajectories with a Hierarchy of Oscillatory Modules.   P. Baldi, Nikzad Toomarian. Proceedings of the 1993 IEEE International Conference on Neural Networks. San Francisco, CA, 1172-1176, 1993.
Hidden Markov Models in Molecular Biology: New Algorithms and Applications.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. Advances in Neural Information Processing Systems. S. J. Hanson, J. D. Cowan, C. Lee Giles, Morgan Kauffmann Publishers, 747-754, 1993.
1992
A Modular Hierarchical Approach to Learning.   P. Baldi. Proceedings of the 2nd International Conference on Fuzzy Logic and Neural Networks. 2, Iizuka, Japan, 985-988, 1992.
Trading Decision Learning.   P. Baldi, Y. Chauvin. Neural Networks for Computing Conference (abstract). Snowbird, UT, 1992.
1991
Refereed Journals
Programmed Interactions in Higher-Orders Neural Networks: I. Maximal Capacity.   S.S. Venkatesh, P. Baldi. Journal of Complexity. 7, 316-337, 1991.
Programmed Interactions in Higher-Orders Neural Networks: II. The Outer-Product Algorithm.   S. S. Venkatesh, P. Baldi. Journal of Complexity. 7, 443-479, 1991.
Can Regulatory Peptides Be Regarded as Words of a Biological Language?   E. A. Mayer, J. Furness, P. Baldi. American Journal of Physiology. 261, G171-G184, 1991.
Temporal Evolution of Generalization during Learning in Linear Networks.   P. Baldi, Y. Chauvin. Neural Computation. 3, 4, 589-603, 1991.
Contrastive Learning and Neural Oscillations.   P. Baldi, F. Pineda. Neural Computation. 3, 4, 526-545, 1991.
1990
Graph Coloring Bounds for Cellular Radio.   P. Baldi, E.C. Posner. Computers and Mathematics with Applications. 19, 10, 91-97, 1990.
On a Generalized Family of Colorings.   P. Baldi. Graphs and Combinatorics. 6, 95-110, 1990.
Computing with Arrays of Coupled Oscillators: an Application to Preattentive Texture Discrimination.   P. Baldi, R. Meir. Neural Computation. 2, 4, 458-471, 1990.
Refereed Conference Proceedings
Computing with Arrays of Bell-Shaped and Sigmoid Functions.   P. Baldi. Proceedings of the 1990 conference on Advances in neural information processing systems 3. Morgan Kaufmann Publishers Inc., Denver, CO, 735-742, 1990.
1989
Refereed Journals
Asymptotic Normality of Some Graph Related Statistics.   P. Baldi, Y. Rinott. Journal of Applied Probability. 26, 171-175, 1989.
On Normal Approximations of Distributions in Terms of Dependency Graphs.   P. Baldi, Y. Rinott. Annals of Probability. 17, 4, 1646-1650, 1989.
Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis.   P. Baldi, A. Atiya. International Journal of Neural Systems. 1, 2, 103-124, 1989.
Refereed Conference Proceedings
On the Distribution of the Number of Local Minima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Proceedings of the 1989 Conference on Neural Information Processing Systems. Morgan Kauffman Publishers Inc., Denver, CO, 727-732, 1989.
Book Chapters
A Normal Approximation for the Number of Local Maxima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Probability, Statistics and Mathematics: Papers in Honor of Samuel Karlin. T.W. Anderson, K.B. Athreya, D.L. Iglehart, Academic Press, 1989.
1988
Refereed Journals
Neural Networks and Principal Component Analysis: Learning from Examples without Local Minima.   P. Baldi, K. Hornik. Neural Networks. 2, 1, 53-58, 1988.
Neural Networks, Orientations of the Hypercube and Algebraic Threshold Functions.   P. Baldi. IEEE Transactions on Information Theory. 34, 3, 523-530, 1988.
Group Actions and Learning for a Family of Automata.   P. Baldi. Journal of Computer and System Sciences. 36, 2, 1-15, 1988.
Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal Vectors.   P. Baldi. SIAM Journal of Discrete Mathematics. 1, 1, 1-13, 1988.
How Sensory Maps Could Enhance Resolution Through Ordered Arrangements of Broadly Tuned Receivers.   P. Baldi, W. Heiligenberg. Biological Cybernetics. 59, 4, 313-318, 1988.
Refereed Conference Proceedings
Neural Networks and Principal Component Analysis.   P. Baldi. Proceedings of the 1988 Conference on Neural Information Processing. Morgan Kauffman Publishers Inc., Denver, CO, 65-72, 1988.
1987
Refereed Journals
Number of Stable Points for Spin Glasses and Neural Networks of Higher Orders.   P. Baldi, S.S. Venkatesh. Physical Review Letters. 58, 9, 913-916, 1987.
Symmetries and Learning in Neural Network Models.   P. Baldi. Physical Review Letters. 59, 17, 1976-1978, 1987.
Embeddings of Ultrametric Spaces in Finite Dimensional Structures.   M. Aschbacher, P. Baldi, E. B. Baum, R.M. Wilson. SIAM Journal of Algebraic and Discrete Methods. 8, 4, 564-577, 1987.
Refereed Conference Proceedings
On Properties of Networks of Neuron-Like Elements: Complexity and Capacity.   P. Baldi, S.S. Venkatesh. Proceedings of the IEEE Conference on Neural Information Processing Systems. D.Z. Anderson, American Institute of Physics, Denver, CO, 1987.
1986
Refereed Journals
Bounds on the Size of Ultrametric Structures.   P. Baldi, E.B. Baum. Physical Review Letters. 56, 15, 1598-1600, 1986.
Refereed Conference Proceedings
Caging and Exhibiting Ultrametric Structures.   P. Baldi, E.B. Baum. Proceedings of the Conference on Neural Networks for Computing. John S. Denker, American Institute of Physics, Snowbird, Utah, 35-40, 1986.

Deep Learning

2016
Refereed Journals
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation   Baldi, P., Sadowski, P. Neural Networks. 2016.
What Time is it? Deep Learning Approaches for Circadian Rhythms   Agostinelli, F., Ceglia, N., Shahbaba, B., Sassone-Corsi, P., Baldi, P. Bioinformatics. 32, 12, i8-i17, 2016.
Jet Substructure Classification in High-Energy Physics with Deep Neural Networks   Baldi, P., Bauer, K., Eng, C., Sadowski, P., Whiteson, D. Physical Review D. 93, 94034, 27 May 2016, 2016.
Parameterized Neural Networks for High-Energy Physics   Baldi, P., Cranmer, K., Faucett, T., Sadowski, P., Whiteson, D. The European Physical Journal C. 76, 235, 1-7, May 2016, 2016.
VIRALpro: a tool to identify viral capsid and tail sequences   Galiez, C., Magnan, C., Coste, F., Baldi, P. Bioinformatics. 32, 9, 1405-1407, 2016-04-27, 2016.
Jet Flavor Classification in High-Energy Physics with Deep Neural Networks   Guest, D., Collado, J., Baldi, P., Whiteson, D. Physical Review D. 94, 112002, 2016, 2016.
Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction   Sadowski, P., Fooshee, D., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling. 56, 11, 2125-2128, 2016, 2016.
Other
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation   Baldi, P., Sadowski, P. Neural Networks. 83, 51-74, Nov. 2016, 2016.
2015
Refereed Journals
Enhanced Higgs to tau+tau- Search with Deep Learning   P. Baldi, P. Sadowski, D. Whiteson. Physical Review Letters. 114, 111801-1-111801-5, 2015.
Mitochondrial Mutations in Subjects with Psychiatric Disorders   Sequeira, A., Rollins, B., Magnan, C., van Oven, M., Baldi, P., Myers, R. M., Barchas, J. David, Schatzberg, A. F., Watson, S. J., Akil, H., Bunney, W. E., Vawter, M. P. PLOS ONE. 2015.
Deep Learning, Dark Knowledge, and Dark Matter   Sadowski, P., Collado, J., Whiteson, D., Baldi, P. Journal of Machine Learning Research. 2015.
Towards a Systems View of Irritable Bowel Syndrome   Mayer, E. A., Labus, J., Tillisch, K., Cole, S., Baldi, P. Nature Reviews Gastroenterolog yand Hepatology. 2015.
Accurate and Efficient Target Prediction Using a Potency-Sensitive Influence-Relevance Voter   Lusci, A., Browning, M., Fooshee, D., Swamidass, S. Josh, Baldi, P. Journal of Cheminformatics. 7, 63-79, 29 December 201, 2015.
2014
The Dropout Learning Algorithm   P. Baldi, P. Sadowski. Artifical Intelligence. 210, 78-122, 2014.
Incorporating Post-Translational Modifications and Unnatural Amino Acids into High-Throughput Modeling of Protein Structures   K. Nagata, A. Randall, P. Baldi. Bioinformatics. 30, 12, 1681-1689, 2014.
Sspro/ACCpro 5.0: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility. Problem Solved?   C. Magnan, P. Baldi. Bioinformatics. 30, 18, 2592-2597, 2014.
Deep Learning in High-Energy Physics: Improving the Search for Exotic Particles   P. Baldi, P. Sadowski, D. Whiteson. Nature Communicaiton. 5, 4038, 2014.
Enhanced Higgs to Tau-plus Tau-minus Search with Deep Learning   Baldi, P., Sadowski, P., Whiteson, D. Pyhsical Review letters. 2014.
Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   Chicco, D., Sadowski, P., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2014.
A Large-Scale Deep Learning Target-Prediction System for Diverse Molecules   Lusci, A., Browning, M., Swamidass, S. Josh, Baldi, P. Journal of Chemical Information and Modeling. 2014.
Refereed Conference Proceedings
Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   D. Chicco, P. Sadowski, P. Baldi. 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Newport Beach, CA, September 2014, 2014.
Searching for Higgs Boson Decay Modes with Deep Learning   P. Sadowski, D. Whiteson, P. Baldi. NIPS. 2014.
2013
Refereed Journals
Deep Architectures and Deep Learning in Chemoinformatics: the Prediction of Aqueous Solubility for Drug-Like Molecules   A. Lusci, G. Pollastri, P. Baldi. Journal of Chemical Information and Modeling. 53, 7, 1563–1575, June 24, 2013, 2013.
Leptin Engages a Hypothalamic Neurocircuitry to Permit Survival in the Absence of Insulin   Teppei Fujikawa, Eric D. Berglund, Vishal R. Patel, Giorgio Ramadori, Claudia R. Vianna, Linh Vong, Fabrizio Thorel, Simona Chera, Pedro L. Herrera, Bradford B. Lowell, Joel K. Elmquist, Pierre Baldi, Roberto Coppari. Cell Metabolism. 2013.
The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory   Vogel-Cierna, A.,Matheos, D.P., Barrett, R.M., Kramar, E, Azzaw, S. Chen, Y. Magnan, C. Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R. J., Chabrier, M. Babayan, A. Wu, J. I., Crabtree, G. R., Baldi, P., Baram, T. Z. Lynch, G. . Nature Neuroscience. 10, , , , , 552-561, May, 2013.
Refereed Conference Proceedings
Understanding Dropout   P. Sadowski, P. Baldi. NIPS. 26, C.J.C. Burges, L. Bottou, M. Welling, Z. Ghahrami, K.Q. Weinberger, Lake Tahoe, NV, 2814-2822, 2013.
Beyond Gradient Diffusion: New Algorithms for Training Deep Layers of Neural Networks   J. Yarkony, P. Sadowski, B.S. Manjunath, P. Baldi. NIPS. 2013.
2012
Refereed Journals
SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations.   K. Nagata, A. Randall, P. Baldi. Protein: Structure, Function, and Bioinformaics. 80, 1, 142-153, 2012.
Cyber-T Webserver: Differential Analysis of High-Throughput Data.   M. Kayala, P. Baldi. Nucleic Acids Research. 1-7, 2012.
Complex-Valued Autoencoders.   P. Baldi, Z. Lu. Neural Networks. 33, 136-147, 2012.
Boolean autoencoders and hypercube clustering complexity   Baldi, P. Designs, Codes and Cryptography. 1-21, 2012.
Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research. 2012.
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics.   Patel, Vishal R., Eckel-Mahan, Kristin, Sassone-Corsi, Paolo, Baldi, Pierre. Nature methods. 9, 8, 772-773, 2012.
ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning   Kayala, Matthew A., Baldi, Pierre. Journal of Chemical Information and Modeling. 52, 10, American Chemical Society, 2526-2540, 2012/12/11, 2012.
Deep architectures for protein contact map prediction   Di Lena, Pietro, Nagata, Ken, Baldi, Pierre. Bioinformatics (Oxford, England). 28, 19, 2449-2457, 2012.
Refereed Conference Proceedings
Deep Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS. 2012.
Deep Spatial-Temporal Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS. 25, Pereira, F., Burges, C. J. C., Bottou, L., Weinberger, K.Q., Curran Associates Inc., Lake Tahoo, NV, 512-520, 2012.
2011
Refereed Journals
Learning to Predict Chemical Reactions   M. Kayala, C. Azencott, J. Chen, P. Baldi. Journal of Chemical Information and Modeling. 51, 9, 2209-2222, 2011.
Visual Adaptation and Novelty Responses in the Superior Colliculus.   S. Boehnke, D. Berg, R. Marino, P. Baldi, L. Itti, D. Munoz. European Journal of Neuroscience. 34, 5, 766-779, 2011.
Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research. 2011.
Refereed Conference Proceedings
A Machine Learning Approach to Predict Chemical Reactions.   M. Kayla, P. Baldi. Neural Information Processing Systems 2011 (NIPS 2011). Granada, Spain, 2011.
2010
Refereed Journals
A CROC Stronger than ROC: Measuring, Visualizing, and Optimizing Early Retrieval.   S. J. Swamidass, C. Azencott, K. Daily, P. Baldi. Bioinformatics. 2010.
Of Bits and Wows: A Bayesian Theory of Surprise with Applications to Attention.   P. Baldi, L. Itti. Neural Networks. 23, 649-666, 2010.
When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values.   P. Baldi, R. Nasr. Journal of Chemical Information and Modeling. 2010.
Refereed Conference Proceedings
Autoencoders, Unsupervised Learning, and Deep Architectures.   P. Baldi. Workshop on Deep Learning and Unsupervised Feature Learning. Neural Information Processing Systems (NIPS), Whistler, Canada, 2010.
Information-Theoretic Metrics for Project-Level Scattering and Tangling.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. International Conference on Software Engineering and Knowledge Engineering (SEKE). Redwood City, CA, 2010.
Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery.   P. Baldi, C. Azencott, S. J. Swamidass. WIRN 2010. IOS Press, 2010.
2009
Refereed Journals
COBEpro: A Novel System for Predicting Continuous B-cell Epitopes.   M. J. Sweredoski, P. Baldi. Protein Engineering Design and Selection. 22, 3, 113-120, 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.
The Influence Relevance Voter: An Accurate and Interpretable Virtual High Throughput Screening Method.   S. J. Swamidass, C. Azencott, H. Gramajo, S. Tsai, P. Baldi. Journal of Chemical Information and Modeling. 49, 4, 756-766, 2009.
SOLpro: Accurate Sequence-Based Prediction of Protein Solubility.   C. N. Magnan, A. Randall, P. Baldi. Bioinformatics. 25, 17, 2200-2207, 2009.
Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Vision Research. 49, 10, 1295-1306, 2009.
Refereed Conference Proceedings
Exploring Java Software Vocabulary: A Search and Mining Perspective.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. SUITE 2009: Proceedings of the First International Workshop on Search-Driven Development - Users, Tools, and Applications. Vancouver, BC, Canada, 2009.
Software Analysis with Unsupervised Topic Models.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. Neural Information Processing Systems (NIPS) Conference. Whistler, Canada, 2009.
The Evolution of Concerns, Scattering, and Tangling in Eclipse and ArgoUML.   E. Linstead, L. Hughes, P. Baldi. Third International Symposium on Empirical Software Engineering and Measurement (ESEM). Lake Buena Vista, Florida, 2009.
Mining the Coherence of GNOME Bug Reports with Statistical Topic Models.   E. Linstead, P. Baldi. MSR '09: Proceedings of the Sixth International Working Conference on Mining Software Repositories. IEEE Computer Society, Vancouver, BC, Canada, 2009.
2008
Refereed Journals
Machine Learning Methods for Protein Structure Prediction.   J. Cheng, A. N. Tegge, P. Baldi. IEEE Reviews in Biomedical Engineering. 1, 41-49, 2008.
BLASTing Small Molecules—Statistics and Extreme Statistics of Chemical Similarity Scores.   P. Baldi, R. W. Benz. Bioinformatics. 24, 13, i357-i365, 2008.
PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure.   M. J. Sweredoski, P. Baldi. Bioinformatics. 24, 12, 1459-1460, 2008.
Discovery of Power-Laws in Chemical Space.   R. W. Benz, S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling. 48, 6, 1138-1151, 2008.
Learning to Play Go Using Recursive Neural Networks.   L. Wu, P. Baldi. Neural Networks. 21, 1392-1400, 2008.
TMBpro: Secondary Structure, β-Contact, and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins.   A. Randall, J. Cheng, M. Sweredoski, P. Baldi. Bioinformatics. 24, 4, 513-520, 2008.
Refereed Conference Proceedings
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. Nashville, TN, 2008.
An Application of Latent Dirichlet Allocation to Analyzing Software Evolution.   E. Linstead, C. Lopes, P. Baldi. International Conference on Machine Learning and Applications (ICMLA). San Diego, 2008.
2007
Refereed Journals
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.   C. Azencott, A. Ksikes, S. Joshua Swamidass, J. Chen, L. Ralaivola, P. Baldi. Journal of Chemical Information and Modeling. 47, 3, 965-974, 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, L. Itti. Journal of Vision. 7, 10, 1-13, 2007.
Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set.   J. Cheng, P. Baldi. BMC Bioinformatics. 8, 113-121, 2007.
Refereed Conference Proceedings
Mining Eclipse Developer Contributions via Author-Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the MSR 2007: International Workshop on Mining Software Repositories. Minneapolis, MN, 30-33, 2007.
Mining Concepts from Code with Probabilistic Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering. Atlanta, GA, 461-464, 2007.
Mining Internet-Scale Software Repositories.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Advances in Neural Information Processing Systems 20. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 929-936, 2007.
Book Chapters
Virtual High-Throughput Screening with Two-Dimensional Kernels.   A. Azencott, P. Baldi. Hands-On Pattern Recognition. Challenges in Data Representation, Model Selection, and Performance Prediction. I. Guyon, G. Cawley, G. Droor, A. Saffari, Lulu Press, 2007.
2006
Refereed Journals
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, Richard H. Lathrop. IEEE Transactions on Computational Biology and Bioinformatics. 3, 2, 114-125, 2006.
Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.   J. Cheng, H. Saigo, P. Baldi. Proteins. 62, 3, 617-629, 2006.
Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines.   J. Cheng, A. Randall, P. Baldi. Proteins. 62, 4, 1125-1132, 2006.
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.   J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery. 13, 1, 1-10, 2006.
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.   G. Pollastri, A. Vullo, P. Frasconi, P. Baldi. Journal of Computational Biology. 3, 631-650, 2006.
Refereed Conference Proceedings
A Scalable Machine Learning Approach to Go.   L. Wu, P. Baldi. Advances in Neural Information Processing Systems 19. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 1521-1528, 2006.
2005
Refereed Journals
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, P. Baldi. Bioinformatics. 21, i359-368, 2005.
Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. Bioinformatics. 21, i75-84, 2005.
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, J. Y. Sze. Journal of Neuroscience. 25, 4, 1015-1023, 2005.
Graph Kernels for Chemical Informatics.   L. Ralaivola, J. S. Swamidass, H. Saigo, P. Baldi. Neural Networks. 18, 8, 1093-1110, 2005.
On the Relationship Between Deterministic and Probabilistic Directed Graphical Models: from Bayesian Networks to Recursive Neural Networks.   P. Baldi, M. Rosen-Zvi. Neural Networks. 18, 8, 1080-1086, 2005.
SCRATCH: a Protein Structure and Structural Feature Prediction Server.   J. Cheng, A. Z. Randall, M. Sweredoski, P. Baldi. Nucleic Acids Research. 33, 9, W72-76, 2005.
Refereed Conference Proceedings
SVM and Pattern-Enriched Common Fate Graphs for the Game of GO.   L. Ralaivola, L. Wu, P. Baldi. European Symposium on Artificial Neural Networks (ESANN). Bruges, Belgium, 2005.
A Principled Approach to Detecting Surprising Events in Video.   L. Itti, P. Baldi. Proc. IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2005.
Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   S. Swamidass, J. Chen, P. Phung, J. Bruand, L. Ralaivola, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05). 21, Bioinformatics, i359-368, 2005.
Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05). Bioinformatics, i75-84, 2005.
Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Advances in Neural Information Processing Systems 18, NIPS 2005. Y. Weiss, B. Scholkopf, J. Platt, MIT Press, Cambridge, MA, 547-554, 2005.
Attention: Bits versus Wows.   P. Baldi, L. Itti. Proceedings of the International Conference on Neural Networks and Brain. 1, Mingsheng Zhao, Zhongzhi Shi, IEEE Press, Beijing, China, PL56-PL61, 2005.
Book Chapters
Surprise: A Shortcut for Attention?   P. Baldi. Neurobiology of Attention. L. Itti, G. Rees, J. Tsotsos, Elsevier, San Diego, 24-28, 2005.
2004
Refereed Conference Proceedings
Large-Scale Prediction of Disulphide Bond Connectivity.   P. Baldi, J. Cheng, A. Vullo. Advances in Neural Information Processing Systems 17 (NIPS 2004). 2004.
Book Chapters
Hidden Markov Models and Neural Networks.   S. Kremer, P. Baldi. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley, 2004.
2003
Refereed Journals
Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity.   Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy, P. Baldi. Neurocomputing. 56, 305-327, 2003.
The Principled Design of Large-Scale Recursive Neural Network Architectures—DAG-RNNs and the Protein Structure Prediction Problem.   P. Baldi, G. Pollastri. Journal of Machine Learning Research. 4, 575-602, 2003.
Refereed Conference Proceedings
Prediction of Protein Topologies Using Generalized IOHMMs and RNNs.   G. Pollastri, P. Baldi, A. Vullo, P. Frasconi. Advances in Neural Information Processing Systems 15. 15, S. Becker, S. Thrun, K. Obermayer, MIT Press, Cambridge, MA, 2003.
Book Chapters
New Machine Learning Methods for the Prediction of Protein Topologies.   P. Baldi, G. Pollastri, P. Frasconi, A. Vullo. Artificial Intelligence and Heuristic Methods in Bioinformatics. P. Frasconi, R. Shamir, IOS Press, 51-73, 2003.
2002
Refereed Journals
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Bioinformatics. 18, S62-S70, 2002.
Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles.   G. Pollastri, D. Przybylski, B. Rost, P. Baldi. Proteins. 47, 228-235, 2002.
Prediction of Coordination Number and Relative Solvent Accessibility in Proteins.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proteins. 47, 142-153, 2002.
A Machine Learning Strategy for Protein Analysis.   P. Baldi, G. Pollastri. IEEE Intelligent Systems (special Issue on "Intelligent Systems in Biology"). 17, 2, 28-35, 2002.
Refereed Conference Proceedings
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology (ISMB 02). 18, Bioinformatics, S62-S70, 2002.
Book Chapters
A Computational Theory of Surprise.   P. Baldi. Information, Coding, and Mathematics. M. Blaum, Kluwer, 1-25, 2002.
2001
Refereed Journals
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.
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Inference of Gene Changes.   P. Baldi, A. D. Long. Bioinformatics. 17, 6, 509-519, 2001.
Refereed Conference Proceedings
Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proceedings of the 2001 Conference on Intelligent Systems for Molecular Biology, (ISMB01). AAAI Press, Copenhagen, Denmark, 2001.
2000
Refereed Journals
Probabilistic Graphical Models in Computational Molecular Biology.   P. Baldi. Journal of the Italian Association for Artificial Intelligence. 1, 8-12, 2000.
On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial Genomes.   P. Baldi. Bioinformatics. 16, 4, 367-371, 2000.
Assessing the Accuracy of Prediction Algorithms for Classification: An Overview.   P. Baldi, S. Brunak, Y. Chauvin, H. Nielsen. Bioinformatics. 16, 5, 412-424, 2000.
Refereed Conference Proceedings
Protein β-Sheet Partner Prediction by Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Artifical Neural Networks in Medicine and Biology. Proceedings of the ANNIMAB-1 Conference. H. Malmgren, M. Borga, L. Niklasson, Springer Verlag, Göteborg, Sweden, 2000.
Matching Protein β-Sheet Partners by Feedforward and Recurrent Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology (ISMB00). AAAI Press, La Jolla, CA, 25-36, 2000.
Book Chapters
Bidirectional IOHMMs and recurrent neural networks for protein secondary structure prediction.   P. Baldi, S. Brunak, G. Pollastri, P. Frasconi. Protein Sequence Analysis in the Genomic Era. Rita Casadio, Lanfranco Masotti, CLUEB, Bologna, Italy, 2000.
Bidirectional Dynamics for Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, G. Soda. Sequence Learning: Paradigms, Algorithms, and Applications. R. Sun, C. L. Giles, Springer Verlag, 99-120, 2000.
1999
Refereed Journals
Exploiting the Past and the Future in Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri. Bioinformatics. 15, 11, 937-946, 1999.
1998
On the Use of Bayesian Methods for Evaluating Compartmental Neural Models.   P. Baldi, M. C. Vanier, J. M. Bower. Journal of Computational Neuroscience. 5, 285-314, 1998.
Book Chapters
Probabilistic Models of Neuronal Spike Trains.   P. Baldi. Adaptive Processing of Temporal Information. C.L. Giles, M. Gori, Springer Verlag, New York, 198-228, 1998.
Software Foundation Libraries for the Design of Intelligent Systems.   P. Baldi, Y. Chauvin, V. Mittal Henkle. Neural Nets WIRN Vietri 98. Proceedings of the 10-th Italian Workshop on Neural Nets. M. Marinaro, R. Tagliaferri, 17-39, 1998.
1996
Refereed Journals
Hybrid Modeling, HMM/NN Architectures, and Protein Applications.   P. Baldi, Y. Chauvin. Neural Computation. 2, 3, 497-501, 1996.
Refereed Conference Proceedings
Universal Approximation and Learning of Trajectories Using Oscillators.   P. Baldi, K. Hornik. Advances in Neural Information Processing Systems 8. D. S. Touretzky, M. C. Mozer, M. E. Hasselmo, MIT Press, Cambridge MA, 451-457, 1996.
Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequences.   P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Theoretical and Computational Methods in Genome Research. S.Suhai, Plenum, NY, 1996.
1995
Refereed Journals
Gradient Descent Learning Algorithms Overview: A General Dynamical Systems Perspective.   P. Baldi. IEEE Transactions on Neural Networks. 6, 1, 182-195, 1995.
Learning in Linear Networks: a Survey.   P. Baldi, K. Hornik. IEEE Transactions on Neural Networks. 6, 4, 837-858, 1995.
Substitution Matrices and Hidden Markov Models.   P. Baldi. Journal of Computational Biology. 2, 3, 497-501, 1995.
Refereed Conference Proceedings
Inferring Ground Truth from Subjective Labelling of Venus Images.   P. Smyth, U. Fayadd, P. Perona, M. Burl, P. Baldi. Advances in Neural Information Processing Systems. G. Tesauro, D. S. Touretzky, T. K. Leen, MIT Press, Cambridge, MA, 1085-1092, 1995.
Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures.   P. Baldi, Y. Chauvin. Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95). Cambridge, UK, 39-47, 1995.
Book Chapters
When Neural Networks Play Sherlock Holmes.   P. Baldi, Y. Chauvin. Back-Propagation: Theory, Architectures and Applications. 487, Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 1995.
Gradient Descent Learning Algorithms: A Unified Perspective.   P. Baldi. Back-Propagation: Theory, Architectures and Applications. Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 509-541, 1995.
Back-propagation and unsupervised learning in linear networks.   P. Baldi, Y. Chauvin, K. Hornik. Back-Propagation: Theory, Architectures and Applications. Y. Chauvin, D.E. Rumelhart, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 389-432, 1995.
1994
Refereed Journals
How Delays Affect Neural Dynamics and Learning.   P. Baldi, A. Atiya. IEEE Transactions on Neural Networks. 5, 4, 626-635, 1994.
Smooth On-Line Learning Algorithms for Hidden Markov Models.   P. Baldi, Y. Chauvin. Neural Computation. 6, 2, 305-316, 1994.
Hidden Markov Models of Biological Primary Sequence Information.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. PNAS USA. 91, 3, 1059-1063, 1994.
Hidden Markov Models of the G-Protein Coupled Receptor Family.   P. Baldi, Y. Chauvin. Journal of Computational Biology. 1, 4, 311-335, 1994.
Refereed Conference Proceedings
Trading Decision Learning: from Theory to Personal Traders.   P. Baldi, Y. Chauvin. Proceedings of the Second International Conference on Neural Networks in the Capital Markets. Pasadena, CA, 1994.
Modeling Protein Families and Human Genes: Hidden Markov Models and a Little Beyond.   P. Baldi, Y. Chauvin. Proceedings of the 1994 Fifth Generation Computing Symposium, Workshop on Fusion of Molecular Biology and Knowledge Processing. Tokyo, Japan, 1994.
Discrimination of Tyrosine and Serine/Threonine Kinase Sub-Families by Hidden Markov Models.   P. Baldi, Y. Chauvin. Proceedings of The Third International Conference on Bioinformatics and Genome Research. World Scientific Publishing Co., 1994.
Hidden Markov Models of Human Genes.   P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, A. Krogh. Advances in Neural Information Processing Systems. J. D. Cowan, G. Tesauro, J. Alspector, Morgan Kauffmann Publishers, 761-768, 1994.
Book Chapters
Statistical Models of Proteins: an Application to the G-Protein-Coupled Receptor Family.   P. Baldi, Y. Chauvin. Modern Approaches in Molecular Bioinformatics. S. Schulze-Kremer, IOS Press, Amsterdam/New York, 53-102, 1994.
1993
Refereed Journals
Random Interactions in Higher-Orders Neural Networks.   P. Baldi, S.S. Venkatesh. IEEE Transactions on Information Theory. 39, 1, 274-283, 1993.
Neural Networks for Fingerprint Recognition.   P. Baldi, Y. Chauvin. Neural Computation. 5, 3, 402-418, 1993.
Refereed Conference Proceedings
Learning Trajectories with a Hierarchy of Oscillatory Modules.   P. Baldi, Nikzad Toomarian. Proceedings of the 1993 IEEE International Conference on Neural Networks. San Francisco, CA, 1172-1176, 1993.
Hidden Markov Models in Molecular Biology: New Algorithms and Applications.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. Advances in Neural Information Processing Systems. S. J. Hanson, J. D. Cowan, C. Lee Giles, Morgan Kauffmann Publishers, 747-754, 1993.
1992
A Modular Hierarchical Approach to Learning.   P. Baldi. Proceedings of the 2nd International Conference on Fuzzy Logic and Neural Networks. 2, Iizuka, Japan, 985-988, 1992.
Trading Decision Learning.   P. Baldi, Y. Chauvin. Neural Networks for Computing Conference (abstract). Snowbird, UT, 1992.
1991
Refereed Journals
Programmed Interactions in Higher-Orders Neural Networks: I. Maximal Capacity.   S.S. Venkatesh, P. Baldi. Journal of Complexity. 7, 316-337, 1991.
Programmed Interactions in Higher-Orders Neural Networks: II. The Outer-Product Algorithm.   S. S. Venkatesh, P. Baldi. Journal of Complexity. 7, 443-479, 1991.
Temporal Evolution of Generalization during Learning in Linear Networks.   P. Baldi, Y. Chauvin. Neural Computation. 3, 4, 589-603, 1991.
1990
Computing with Arrays of Coupled Oscillators: an Application to Preattentive Texture Discrimination.   P. Baldi, R. Meir. Neural Computation. 2, 4, 458-471, 1990.
Refereed Conference Proceedings
Computing with Arrays of Bell-Shaped and Sigmoid Functions.   P. Baldi. Proceedings of the 1990 conference on Advances in neural information processing systems 3. Morgan Kaufmann Publishers Inc., Denver, CO, 735-742, 1990.
1989
Refereed Journals
Asymptotic Normality of Some Graph Related Statistics.   P. Baldi, Y. Rinott. Journal of Applied Probability. 26, 171-175, 1989.
On Normal Approximations of Distributions in Terms of Dependency Graphs.   P. Baldi, Y. Rinott. Annals of Probability. 17, 4, 1646-1650, 1989.
Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis.   P. Baldi, A. Atiya. International Journal of Neural Systems. 1, 2, 103-124, 1989.
Refereed Conference Proceedings
On the Distribution of the Number of Local Minima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Proceedings of the 1989 Conference on Neural Information Processing Systems. Morgan Kauffman Publishers Inc., Denver, CO, 727-732, 1989.
Book Chapters
A Normal Approximation for the Number of Local Maxima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Probability, Statistics and Mathematics: Papers in Honor of Samuel Karlin. T.W. Anderson, K.B. Athreya, D.L. Iglehart, Academic Press, 1989.
1988
Refereed Journals
Neural Networks and Principal Component Analysis: Learning from Examples without Local Minima.   P. Baldi, K. Hornik. Neural Networks. 2, 1, 53-58, 1988.
Neural Networks, Orientations of the Hypercube and Algebraic Threshold Functions.   P. Baldi. IEEE Transactions on Information Theory. 34, 3, 523-530, 1988.
Group Actions and Learning for a Family of Automata.   P. Baldi. Journal of Computer and System Sciences. 36, 2, 1-15, 1988.
Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal Vectors.   P. Baldi. SIAM Journal of Discrete Mathematics. 1, 1, 1-13, 1988.
How Sensory Maps Could Enhance Resolution Through Ordered Arrangements of Broadly Tuned Receivers.   P. Baldi, W. Heiligenberg. Biological Cybernetics. 59, 4, 313-318, 1988.
Refereed Conference Proceedings
Neural Networks and Principal Component Analysis.   P. Baldi. Proceedings of the 1988 Conference on Neural Information Processing. Morgan Kauffman Publishers Inc., Denver, CO, 65-72, 1988.
1987
Refereed Journals
Number of Stable Points for Spin Glasses and Neural Networks of Higher Orders.   P. Baldi, S.S. Venkatesh. Physical Review Letters. 58, 9, 913-916, 1987.
Symmetries and Learning in Neural Network Models.   P. Baldi. Physical Review Letters. 59, 17, 1976-1978, 1987.
Embeddings of Ultrametric Spaces in Finite Dimensional Structures.   M. Aschbacher, P. Baldi, E. B. Baum, R.M. Wilson. SIAM Journal of Algebraic and Discrete Methods. 8, 4, 564-577, 1987.
Refereed Conference Proceedings
On Properties of Networks of Neuron-Like Elements: Complexity and Capacity.   P. Baldi, S.S. Venkatesh. Proceedings of the IEEE Conference on Neural Information Processing Systems. D.Z. Anderson, American Institute of Physics, Denver, CO, 1987.
1986
Refereed Journals
Bounds on the Size of Ultrametric Structures.   P. Baldi, E.B. Baum. Physical Review Letters. 56, 15, 1598-1600, 1986.
Refereed Conference Proceedings
Caging and Exhibiting Ultrametric Structures.   P. Baldi, E.B. Baum. Proceedings of the Conference on Neural Networks for Computing. John S. Denker, American Institute of Physics, Snowbird, Utah, 35-40, 1986.

Nueroscence

2015
Refereed Journals
Mitochondrial Mutations in Subjects with Psychiatric Disorders   Sequeira, A., Rollins, B., Magnan, C., van Oven, M., Baldi, P., Myers, R. M., Barchas, J. David, Schatzberg, A. F., Watson, S. J., Akil, H., Bunney, W. E., Vawter, M. P. PLOS ONE. 2015.
Towards a Systems View of Irritable Bowel Syndrome   Mayer, E. A., Labus, J., Tillisch, K., Cole, S., Baldi, P. Nature Reviews Gastroenterolog yand Hepatology. 2015.
2013
Leptin Engages a Hypothalamic Neurocircuitry to Permit Survival in the Absence of Insulin   Teppei Fujikawa, Eric D. Berglund, Vishal R. Patel, Giorgio Ramadori, Claudia R. Vianna, Linh Vong, Fabrizio Thorel, Simona Chera, Pedro L. Herrera, Bradford B. Lowell, Joel K. Elmquist, Pierre Baldi, Roberto Coppari. Cell Metabolism. 2013.
The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory   Vogel-Cierna, A.,Matheos, D.P., Barrett, R.M., Kramar, E, Azzaw, S. Chen, Y. Magnan, C. Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R. J., Chabrier, M. Babayan, A. Wu, J. I., Crabtree, G. R., Baldi, P., Baram, T. Z. Lynch, G. . Nature Neuroscience. 10, , , , , 552-561, May, 2013.
2012
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics.   Patel, Vishal R., Eckel-Mahan, Kristin, Sassone-Corsi, Paolo, Baldi, Pierre. Nature methods. 9, 8, 772-773, 2012.
2011
Visual Adaptation and Novelty Responses in the Superior Colliculus.   S. Boehnke, D. Berg, R. Marino, P. Baldi, L. Itti, D. Munoz. European Journal of Neuroscience. 34, 5, 766-779, 2011.
2010
Of Bits and Wows: A Bayesian Theory of Surprise with Applications to Attention.   P. Baldi, L. Itti. Neural Networks. 23, 649-666, 2010.
© 2017 Pierre Baldi | pfbaldi [at] uci [dot] edu