Pierre Baldi
University of California, Irvine (UCI)
School of Information and Computer Sciences (ICS)
Center for Machine Learning and Intelligent Systems (CML)
Institute for Genomics and Bioinformatics (IGB)
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Publications
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Deep Learning in Science P. Baldi.
Population-Wide Analysis of Differences in Disease Progression Patterns in Men and Women Westergaard, D., Moseley, P., Sorup, F. K. H., Baldi, P., Brunak, S. Nature Communications.
Neural Network Gradient Hamiltonian Monte Carlo Li, L., Holbrook, A.J., Shahbaba, B., Baldi, P. Computational Statistics.
Improved energy reconstruction in NOvA with regression convolutional neural network Baldi, P., Bian, J., Hertel, L., et al. Physical Review D.
The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction Li, X., Zhou, Q., Wei, W., Lin, Q., Magnan, C., Emami, M., Wearick da Silva, L.E., Viola, T.W., Marshall, P., Edmunds, J., Nainar, S., Broberg Vagbo, C., Leighton, L., Zajackowski, E., Ke, K., Grassi-Oliveira, R., Bojoras, M., Balvdi, P., Spitale, C., Bre. Nature Neuroscience.
First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA Acero, M.A., et al. Physical Review Letters.
Solving the Rubik’s cube with deep reinforcement learning and search Agostinelli, F., McAleer, S., Shmakov, A.K., Baldi, P. Nature Machine Intelligence.
Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons Aras, E., Ramadori, G., Kinouchi, K., Liu, Y., Ioris, R.M., Brenachot, X., Ljubicic, S., Veyrat-Durebex, C., Mannucci, S., Galie, M., Baldi, P., Sassone-Corsi, P., Coppari, R. Cell Reports.
Bayesian Causality Baldi, P., Shahbaba, B. The American Statistician.
Neuronal Capacity Baldi, P., Vershynin, R. Journal of Statistical Mechanics, Theory and Experiment.
Polynomial threshold functions, hyperplane arrangements, and random tensors Baldi, P., Vershynin, R. SIAM Journal of Mathematics of Data Science.
The capacity of feedforward neural networks Baldi, P., Vershynin, R. Neural Networks.
Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells Chen, Y-H., Su, C-C., Deng, W., Lock, L., Donovan, P., Kayala, M., Baldi, P., Lee, H-C., Chen, Y., Wang, P.H. Scientific Reports.
Defining the Independence of the Liver Circadian Clock Koronowski, K.B., Kinouchi, K., Welz,P-S., Zinna, V.M., Shi, J., Samad, M., Chen, S., Magnan, C., Kinchen, J., Li, W., Baldi, P., Benitah, S.A., Sassone-Corsi, P. Cell.
Functional conservation of lncRNA JPX despite sequence and structural divergence Kraner, H., Webb, C-H., Carmona, S., Liu, Y., Lin, B., Erhard, M., Chen, D., Baldi, P., Spitale, R.C., Sun, S. Journal of Molecular Biology.
Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives Sanchez, A., Castro, C., Flores, D-L., Gutierrez, E., Baldi, P. International Journal of Molecular Science.
Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis Sato, S., Linde, A., Schonke, M., Chen, S., Samad, M., Altintas, A., Laker, R.C., Dalbram, E., Barres, R., Baldi, P., Treebak, J.T., Zierath, J. R., Sassone-Corsi, P. Cell Metabolism.
Towards Automating Precision Studies of Clone Detectors Saini, V., Farahani, F.F., Lu, Y., Yand, D., Maritns, P., Sainani, H., Baldi, P., Lopes, C. ICSE 2019.
Solving the Rubik's Cube with Approximate Policy Iteration McAleer, S., Agostinelli, F., Shmakov, A.K., Baldi, P. ICLR 2019.
ClusterCAD: a computational platform for type I modular polyketide synthase design Eng, C. H., Backman, W.H., Bailey, C. B., Magnan, C., Marin, H. G., Katz, L., Baldi, P., Keasling, J. D. Nucleic Acid Research.
Deep Learning in Biomedical Data Science Baldi, P. Annual Review of Biomedical Data Science.
Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-Hospital Mortality Lee, C. K., Hofer, I., Gabel, E., Baldi, P., Cannesson, M. Anestgesiology.
Inner and Outer Recursive Neural Networks for Chemoinformatics Applications Urban, G., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling.
Deep learning convolutional neural networks accurately classify genetic mutation in gliomas Chang, P., Su, L., Baldi, P., Choi, D. American Journal of Neuroradiolog.
Learning in the Machine: Random Backpropagation and the Learning Channel Baldi, P., Sadowski, P., Lu, Z. Artifical Intelligence.
Longitudinal Monitoring of Biofilm Formation via Robust SERS Quantification of Pseudomonas aeruginosa-Produced Metabolite Nguyen, C., Thrift, W. J., Bhattacharjee, A., Ranjbar, S., Gallagher, T., Darvishzadeh-Varcheie, M., Sandersion, R., Capolimo, F., Whiteson, K., Baldi, P., Hochbaum, A., Ragan, R. ACS, Applied Materilas and Interfaces.
Learning in the Machine: Random Backpropagation and the Deep Learning Channel Baldi, P., Sadowski, P., Lu, Z. Artificial Intelligence.
CircadiOmics: Circadian Omic Data Web Portal Ceglia, N., Liu, Y., Chen, S., Agostinelli, F., Eckel-Mahan, K, Sassone-Corsi, P., Baldi, P. Nuclei Acids Research.
Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images Urban, G., Bache, K., Phan, D.T.T., Sorbrino, A., Shmakov, A.K., Hachey, S.J., Hughes, C.W., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas Chang, P., Grinband, J., Winberg, B.D., Bardis, M., Khy, M., Cadena, G., Su, M.-Y., Cha, S., Filippi, C.G., Bota, D., Baldi, P., Poisson, L.M., Jain, R., Chow, D. American Journal of Neuroradiology.
Deep Learning Localizes and Identifies Polyps in Real Time with 96% Accuracy in Screening Colonoscopy Urban, G., Tripathi, P., Alkayali, T., Mittal, M., Jalali, F., Karnes, W., Baldi, P. Gastroenterology,.
A circadian metabolomics atlas reveals systems-wide coordination and communication between clocks Dyar, K. A., Lutter, D., Artati, A., Ceglia, N., Liu, Y., Armenta, D., Jastroch, M., Schneider, S., de Maeo, S., Abbondante, S., Tognini, P., Orozco-Solis, R., Sahar, S., Wang, C., Swerdloff, R.S., Nadeef, S., Orlando, V., Uhlenhaut, N. H., Masri, S., Mai. Cell.
Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming Liu, S., Chen, H., Ronquist, S., Seaman, L., Ceglia, N., Meixner, W., Muir, L.A., Chen, P., Higgins, G., Baldi, P., Smale, S., Hero, A., Rajapakse, I. ISCIENCE.
Epigenetic Regulation of the Circadian Gene Per1 in the Hippocampus Contributes to Age-Related Changes in Memory and Synaptic Plasticity Kwapis, J.L., Alaghband, Y., Kramar, E., Lopez, A., Vogel-Ciernia, A., White, A., Shu, G., Rhee, D., Michael, C.M., Montellier, E., Liu, Y., Magnan, C., Chen, S., Sassone-Corsi, P., Baldi, P., Matheos, D. P., Wood, M. A. Nature Communicaitons.
Highly-Accurate Machine Fault Diagnosis Using Deep Transfer Learning Shao, S., McAleer, S., Yan, R., Baldi, P. IEEE Transactions on Industrial Informatics.
Learning in the machine: Recirculation is random backpropagation Baldi, P., Sadowski, P. Neural Networks.
Fasting Imparts a Switch to Alternative Circadian Pathways in Liver and Muscle Kinouchi, K., Magnan, C., Ceglia, N., Liu, Y., Cervantes, M., Baldi, P., Masri, S. Cell Reports.
On the Capacity of Shallow and Deep Learning Architectures Baldi, P., Vershynin, R. COLT.
The Asymptotic Number of Boolean Polynomial Threshold Functions Baldi, P., Vershynin, R. FOCS.
Oreo: Detection of Clones in the Twilight Zone Saini, V., Farahani, F.F., Lu, Y., Baldi, P., Lopes, C. ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering ESEC/FSE 2018.
On Neuronal Capacity. Advances in Neural Information Processing Systems Baldi, P., Vershynin, R. NIPS 2018.
Deep Learning in the Natural Sciences: Applications to Physics. Sadowski, P., Baldi, P. Key Ideas in Learning Theory from Inception to Current State: Emmanuel Braverman's Legacy.
From Reinforcement Learning to Deep Reinforcement Learning: An Overview. Agostinelli, F., Hocquet, G., Singh, S., Baldi, P. Key Ideas in Learning Theory from Inception to Current State: Emmanuel Braverman's Legacy.
A Multi-Resolution Approach to Spinal Metastasis Detection using Dep Siamese Neural Networks Wang, J., Fang, Z., Lang, N., Yuan, H., Su, M., Baldi, P. Computers in Biology and Medicine.
Detecting Cardiovascular Disease from Mammograms with Deep Learning Wang, J., Ding, H., Azamian, F., Zhou, B., Iribarren, C., Molloi, S., Baldi, P. IEEE Transactions onBiomedical Imaging.
Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet Tognini, P., Murakami, M., Liu, Y., Eckel-Mahan, K, Newmand, J. C., Verdind, E., Baldi, P., Sassone-Corsi, P. Cell Metabolism.
Efficient Antihydrogen Detection in Antimater Physics by Deep Learning Sadowski, P., Radics, B., Ananya, A., Yamazaki, Y., Baldi, P. Journal of Physics Communications.
Mir-132/212 is Required for Maturation of Binocular Matching Orientation Prference and Depth Perception Mazziotti, R., Baroncelli, L., Ceglia, N., Chelini, G., Della Sala, G., Magnan, C., Napoli, D., Putugnano, E., Silingardi, D., Tola, J., Tognini, P., Baldi, P., Pizzorusso, T. Nature Communicaiton.
MotifMap-RNA: A Gnome-Wide Map of RBP Binding Sites Liu, Y., Sun, S., Bredy, T., Wood, M. A., Spitale, R. C., Baldi, P. Bioinformatics.
SIRT6 Hindrs Stemness of Tumors Bearing PI3K Activation Irois, R. M., Galie, M., Ramadori, G., Anderson, J. G., Charollais, A., Konstantinidou, G., Brenachot, X., Aras, E., Goga, A., Ceglia, N., Sebastian, C., Martinvalet, D., Baldi, P., Coppari, R. Cell Reports.
Mutation of neuron-specific chromatin remodeling subunit BAF53b: Rescue of plasticity and memory by manipulating actin remodeling Ciernial, A. V., Kramar, E. A., Matheos, D. P., Havekes, R., Hemstedt, T. J., Magnan, C., Sakata, K., Tran, A., Azzawi, S., Lopez, A., Dang, R., Wang, W., Trieu, B., Tong, J., Barrett, R. M., Post, R.J., Baldi, P., Abel, T., Lynch, G., Wood, M. A. Learning and Memory.
Learning in the Machine: the Symmetries of the Deep Learning Channel Baldi, P., Sadowski, P., Lu, Z. Neural Networks.
The Inner and Outer Approaches for the Design or Recursive Neural Networks Architctures Baldi, P. Data Mining and Knowledg Discovery.
Guidelines for Genome-Scale Analysis of Biological Rhythms Hughes, M. E., Baldi, P., Hogenesh, J.B., et al. Journal of Biological Rhythms.
Decorrelated Jet Substructure Tagging using Adversarial Neural Networks Shimmin, C., Sadowski, P., Baldi, P., Weik, E., Whiteson, D., Goul, E., Sogaard, A. Physical Review D.
Deep learning for chemical reaction prediction Fooshee, D., Mood, A., Gutman, E., Tavakoli, A., Urban, G., Liu, F., Huynh, N., Van Vranken, D., Baldi, P. Molecular Systems Design & Engineering.
Deep Learning for Predicitng Postoperative Outcomes: AKI, Reintubation, and In-Hospital Mortality Lee, C., Hofer, I., Baldi, P., Cannesson, M. American Society of Anesthesiologists Conference.
Deep Learning in Prediciting in Hospital Mortality Lee, C., Hofer, I., Cannesson, M., Baldi, P. Society for Technology in Anesthesia.
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation Baldi, P., Sadowski, P. Neural Networks.
What Time is it? Deep Learning Approaches for Circadian Rhythms Agostinelli, F., Ceglia, N., Shahbaba, B., Sassone-Corsi, P., Baldi, P. Bioinformatics.
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.
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.
Jet Substructure Classification in High-Energy Physics with Deep Neural Networks Baldi, P., Bauer, K., Eng, C., Sadowski, P., Whiteson, D. Physical Review D.
Parameterized Neural Networks for High-Energy Physics Baldi, P., Cranmer, K., Faucett, T., Sadowski, P., Whiteson, D. The European Physical Journal C.
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.
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.
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.
VIRALpro: a tool to identify viral capsid and tail sequences Galiez, C., Magnan, C., Coste, F., Baldi, P. Bioinformatics.
Jet Flavor Classification in High-Energy Physics with Deep Neural Networks Guest, D., Collado, J., Baldi, P., Whiteson, D. Physical Review D.
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.
Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction Sadowski, P., Fooshee, D., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling.
Enhanced Higgs to tau+tau- Search with Deep Learning P. Baldi, P. Sadowski, D. Whiteson. Physical Review Letters.
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.
Deep Learning, Dark Knowledge, and Dark Matter Sadowski, P., Collado, J., Whiteson, D., Baldi, P. Journal of Machine Learning Research.
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.
Towards a Systems View of Irritable Bowel Syndrome Mayer, E. A., Labus, J., Tillisch, K., Cole, S., Baldi, P. Nature Reviews Gastroenterolog yand Hepatology.
Function and regulation of Cph2 in Candida albicans Lane, S., Di Lena, P., Tormanen, K., Baldi, P. Eukaryotic Cell.
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.
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.
The Dropout Learning Algorithm P. Baldi, P. Sadowski. Artifical Intelligence.
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.
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.
How Pervasive Are Circadian Oscillations? V. R. Patel, K. Eckel-Mahan, P. Sassone-Corsi, P. Baldi. Trends in Cell Biology.
Incorporating Post-Translational Modifications and Unnatural Amino Acids into High-Throughput Modeling of Protein Structures K. Nagata, A. Randall, P. Baldi. Bioinformatics.
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.
Sspro/ACCpro 5.0: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility. Problem Solved? C. Magnan, P. Baldi. Bioinformatics.
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.
Deep Learning in High-Energy Physics: Improving the Search for Exotic Particles P. Baldi, P. Sadowski, D. Whiteson. Nature Communicaiton.
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.
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.
Enhanced Higgs to Tau-plus Tau-minus Search with Deep Learning Baldi, P., Sadowski, P., Whiteson, D. Pyhsical Review letters.
Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions Chicco, D., Sadowski, P., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
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.
Towards a Systems View of Irritable Bowel Syndrome Mayer, Emeran A., Labus, Jen, Cole, Steve, Baldi, P. Nature Reviews Gastroenterology.
The Pervasiveness and Plasticity of Circadian Oscillations Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., Baldi, P. Bioinformatics.
Massively Parallel Multicut Segmentation via Dual Decomposition J. Yarkony, T. Beyer, B. Andres, B.S. Manjunath, P. Baldi, F. Hamprecht. ICML.
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.
Searching for Higgs Boson Decay Modes with Deep Learning P. Sadowski, D. Whiteson, P. Baldi. NIPS.
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.
A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Reactions I. Chang, P. Baldi. Bioinformatics.
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.
An Efficient Atom-Mapping Algorithm D. Fooshee, A. Andronico, P. Baldi. Journal of Chemical Information and Modeling.
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.
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.
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.
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.
Small-molecule 3D Structure Prediction Using Open Crystallography Data P. Sadowski, P. Baldi. Journal of Chemical Information and Modeling.
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.
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.
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.
An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi. WIRN.
Understanding Dropout P. Sadowski, P. Baldi. NIPS.
Beyond Gradient Diffusion: New Algorithms for Training Deep Layers of Neural Networks J. Yarkony, P. Sadowski, B.S. Manjunath, P. Baldi. NIPS.
Distributed training of very large networks V. R. Patel,, N. Cegna, P. Sadowski, P. Baldi. NIPS.
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.
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.
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.
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.
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.
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.
Cyber-T Webserver: Differential Analysis of High-Throughput Data. M. Kayala, P. Baldi. Nucleic Acids Research.
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.
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.
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.
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.
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.
Complex-Valued Autoencoders. P. Baldi, Z. Lu. Neural Networks.
The Universal Campus: An Open 3D Virtual World Infrastructure for Research and Education. P. Baldi, C. Lopes. ACM eLearn Magazine.
Boolean autoencoders and hypercube clustering complexity Baldi, P. Designs, Codes and Cryptography.
Autoencoders, Unsupervised Learning, and Deep Architectures. Baldi, P. Journal of Machine Learning Research.
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Patel, Vishal R., Eckel-Mahan, Kristin, Sassone-Corsi, Paolo, Baldi, Pierre. Nature methods.
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.
ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning Kayala, Matthew A., Baldi, Pierre. Journal of Chemical Information and Modeling.
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.
Deep architectures for protein contact map prediction Di Lena, Pietro, Nagata, Ken, Baldi, Pierre. Bioinformatics (Oxford, England).
Boolean autoencoders and hypercube clustering complexity. Baldi, P. Designs, Codes and Cryptography.
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.
Deep Architectures and Learning for Protein Structure Prediction P. Di Lena, K. Nagata, P. Baldi. NIPS.
Deep Spatial-Temporal Architectures and Learning for Protein Structure Prediction P. Di Lena, K. Nagata, P. Baldi. NIPS.
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.
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.
Tree and Hashing Data Structures to Speedup Chemical Searches: Analysis and Experiments. R. Nasr, T. Kristensen, P. Baldi. Molecular Informatics.
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.
Learning to Predict Chemical Reactions M. Kayala, C. Azencott, J. Chen, P. Baldi. Journal of Chemical Information and Modeling.
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.
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.
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.
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.
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.
Autoencoders, Unsupervised Learning, and Deep Architectures. Baldi, P. Journal of Machine Learning Research.
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.
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.
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.
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.
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.
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).
Privacy-Enhanced Methods for Comparing Compressed DNA Sequences. D. Eppstein, M. T. Goodrich, P. Baldi. Workshop on Privacy in the Electronic Society.
A Machine Learning Approach to Predict Chemical Reactions. M. Kayla, P. Baldi. Neural Information Processing Systems 2011 (NIPS 2011).
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.
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).
Data Structures and Compression Algorithms for High-throughput Sequencing Technologies Daily, Kenny, Rigor, Paul, Christley, Scott, Xie, Xiaohui, Baldi, Pierre. BMC Bioinformatics.
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.
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.
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.
A CROC Stronger than ROC: Measuring, Visualizing, and Optimizing Early Retrieval. S. J. Swamidass, C. Azencott, K. Daily, P. Baldi. Bioinformatics.
Modeling User Reputation in Wikis. S. Javanmardi, C. Lopes, P. Baldi. Statistical Analysis and Data Mining.
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.
Of Bits and Wows: A Bayesian Theory of Surprise with Applications to Attention. P. Baldi, L. Itti. Neural Networks.
Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors. R. Nasr, D. Hirschberg, P. Baldi. Journal of Chemical Information and Modeling.
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.
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.
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.
Autoencoders, Unsupervised Learning, and Deep Architectures. P. Baldi. Workshop on Deep Learning and Unsupervised Feature Learning.
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).
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).
Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery. P. Baldi, C. Azencott, S. J. Swamidass. WIRN 2010.
Transmembrane β-Barrel Protein Structure Prediction. A. Randall, P. Baldi. Structural Bioinformatics of Membrane Proteins.
Reaction Explorer: Towards a Knowledge Map of Organic Chemistry to Support Dynamic Assessment and Personalized Instruction J. Chen, M. A. Kayala, P. Baldi. Enhancing Learning with Online Resources, Social Networking and Digital Libraries.
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.
MotifMap: a human genome-wide map of candidate regulatory motif sites. X. Xie, P. Rigor, P. Baldi. Bioinformatics.
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.
COBEpro: A Novel System for Predicting Continuous B-cell Epitopes. M. J. Sweredoski, P. Baldi. Protein Engineering Design and Selection.
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.
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).
Software-Driven Sensor Networks for Short-Range Shallow Water Applications. R. Jurdak, P. Baldi, C. Lopes. Ad Hoc Networks Journal.
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.
Data Structures and Compression Algorithms for Genomic Sequence Data. M. C. Brandon, D. C. Wallace, P. Baldi. Bioinformatics.
SOLpro: Accurate Sequence-Based Prediction of Protein Solubility. C. N. Magnan, A. Randall, P. Baldi. Bioinformatics.
Large Scale Study of Multiple-Molecule Queries. R. J. Nasr, S. J. Swamidass, P. Baldi. Journal of Chemoinformatics.
An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases. P. Baldi, D. Hirschberg. Journal of Chemical Information and Modeling.
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.
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.
Bayesian Surprise Attracts Human Attention. L. Itti, P. Baldi. Vision Research.
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.
Software Analysis with Unsupervised Topic Models. E. Linstead, L. Hughes, C. Lopes, P. Baldi. Neural Information Processing Systems (NIPS) Conference.
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).
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).
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.
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.
An Empirical Analysis of User Contributions in Wikipedia. S. Javanmardi, Y. Ganjisaffar, C. Lopes, P. Baldi. WikiSym.
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.
SELECTpro: Effective Protein Model Selection Using a Structure-Based Energy Function Resistant to Blunders. A. Randall, P. Baldi. BMC Structural Biology.
Machine Learning Methods for Protein Structure Prediction. J. Cheng, A. N. Tegge, P. Baldi. IEEE Reviews in Biomedical Engineering.
Synthesis Explorer: Organic Chemistry Tutorial System for Multi-Step Synthesis Design and Reaction Prediction. J. Chen, P. Baldi. Journal of Chemical Education.
BLASTing Small Molecules—Statistics and Extreme Statistics of Chemical Similarity Scores. P. Baldi, R. W. Benz. Bioinformatics.
PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure. M. J. Sweredoski, P. Baldi. Bioinformatics.
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.
Discovery of Power-Laws in Chemical Space. R. W. Benz, S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling.
Learning to Play Go Using Recursive Neural Networks. L. Wu, P. Baldi. Neural Networks.
TMBpro: Secondary Structure, β-Contact, and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins. A. Randall, J. Cheng, M. Sweredoski, P. Baldi. Bioinformatics.
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.
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.
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. D. S. Hirschberg, P. Baldi. Proceedings of the 2008 Data Compression Conference (DCC 08).
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.
An Application of Latent Dirichlet Allocation to Analyzing Software Evolution. E. Linstead, C. Lopes, P. Baldi. International Conference on Machine Learning and Applications (ICMLA).
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.
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.
Phylogenetic Analysis, Genome Evolution and the Rate of Gene Gain in the Herpesviridae. N. Wang, P. Baldi, B. Gaut. Molecular Phylogenetics and Evolution.
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.
Adaptive Low Power Listening for Wireless Sensor Network. R. Jurdak, P. Baldi, C. Lopes. IEEE Transactions on Mobile Computing.
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.
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.
A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling.
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.
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.
Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set. J. Cheng, P. Baldi. BMC Bioinformatics.
The fixed-size Luria–Delbruck model with a nonzero death rate. N. Komarova, L. Wu, P. Baldi. Mathematical Biosciences.
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.
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.
ChemDB Update—Full-Text Search and Virtual Chemical Space. J. Chen, E. Linstead, S. J. Swamidass, D. Wang, P. Baldi. Bioinformatics.
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.
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.
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).
Software Modems for Underwater Sensor Networks. R. Jurdak, P. Aguiar, P. Baldi, C. Lopes. Proceedings of IEEE/OES Oceans'07.
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.
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.
Mining Internet-Scale Software Repositories. E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Advances in Neural Information Processing Systems 20.
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.
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.
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.
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.
Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines. J. Cheng, A. Randall, P. Baldi. Proteins.
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.
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. G. Pollastri, A. Vullo, P. Frasconi, P. Baldi. Journal of Computational Biology.
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.
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.
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.
A Machine Learning Information Retrieval Approach to Protein Fold Recognition. J. Cheng, P. Baldi. Bioinformatics.
Mitochondrial Mutations in Cancer. M. Brandon, P. Baldi, D. C. Wallace. Oncogene.
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.
Genomic Splice-Site Analysis Reveals Frequent Alternative Splicing Close to the Dominant Splice Site. Y. Dou, K. Fox-Walsh, P. Baldi, K. Hertel. RNA.
Software Acoustic Modems for Short Range Mote-Based Underwater Sensor Networks. R. Jurdak, C. Lopes, P. Baldi. In Proceedings of IEEE Oceans – Asia Pacific.
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.
A Scalable Machine Learning Approach to Go. L. Wu, P. Baldi. Advances in Neural Information Processing Systems 19.
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.
Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms. J. Cheng, P. Baldi. Bioinformatics.
Statistical Detection of Chromosomal Homology Using Shared-Gene Density Alone. S. Hampson, B. S. Gaut, P. Baldi. Bioinformatics.
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.
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.
Sigmoid: Towards a Generative, Scalable Software Infrastructure for Pathway Bioinformatics and Systems Biology. J. Cheng, L. Scharenbroich, P. Baldi, E. Mjolsness. IEEE Intelligent Systems.
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.
How Noisy and Replicable are DNA Microarray Data? S. Sundaresh, S. Hung, G. W. Hatfield, P. Baldi. International Journal of Bioinformatics Research and Applications.
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").
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.
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.
Graph Kernels for Chemical Informatics. L. Ralaivola, J. S. Swamidass, H. Saigo, P. Baldi. Neural Networks.
On the Relationship Between Deterministic and Probabilistic Directed Graphical Models: from Bayesian Networks to Recursive Neural Networks. P. Baldi, M. Rosen-Zvi. Neural Networks.
SCRATCH: a Protein Structure and Structural Feature Prediction Server. J. Cheng, A. Z. Randall, M. Sweredoski, P. Baldi. Nucleic Acids Research.
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery.
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.
ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources. J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, P. Baldi. Bioinformatics.
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.
Adaptive Low Power Listening for Sensor Networks. R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking.
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).
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).
A Principled Approach to Detecting Surprising Events in Video. L. Itti, P. Baldi. Proc. IEEE Conference on Computer Vision and Pattern Recognition (CVPR).
Adaptive Low Power Listening for Sensor Networks. R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking.
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).
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).
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).
Bayesian Surprise Attracts Human Attention. L. Itti, P. Baldi. Advances in Neural Information Processing Systems 18, NIPS 2005.
Attention: Bits versus Wows. P. Baldi, L. Itti. Proceedings of the International Conference on Neural Networks and Brain.
Exploring Chemical Space with Computers: Informatics Challenges for AI and Machine Learning. P. Baldi. BIOMAT V Symposium.
Chemoinformatics, Drug Design, and Systems Biology. P. Baldi. Proceedings of the 16th International Conference on Genome Informatics, (GIW 2005).
Adaptive Low Power Listening for Sensor Networks. R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking.
Surprise: A Shortcut for Attention? P. Baldi. Neurobiology of Attention.
Clustering Algorithms for Gene Expression Analysis. P. Baldi, G. Wesley Hatfield, Li M. Fu. Handbook of Computational Molecular Biology.
Battery Lifetime Estimation and Optimization for Underwater Sensor Networks. R. Jurdak, C. V. Lopes, P. Baldi. Sensor Network Operations.
Statistical Distribution of Chemical Fingerprints. S. J. Swamidass, P. Baldi. Proceedings of WILF2005.
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.
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”).
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.
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.
Large-Scale Prediction of Disulphide Bond Connectivity. P. Baldi, J. Cheng, A. Vullo. Advances in Neural Information Processing Systems 17 (NIPS 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.
Hidden Markov Models and Neural Networks. S. Kremer, P. Baldi. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.
What Genes are Made Of. P. Baldi. Pathways.
Differential Analysis of DNA Microarray Gene Expression Data. G. Wesley Hatfield, S. Hung, P. Baldi. Molecular Microbiology.
Bounds on Variances of Estimators for Multinomial Processing Tree Models. P. Baldi, W. H. Batchelder. Journal of Mathematical Psychology.
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.
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.
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.
LineUp : Statistical Detection of Chromosomal Homology with Applications to Plant Comparative Genomics. S. Hampson, A. McLysaght, B. Gaut, P. Baldi. Genome Research.
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.
Extensive Gene Gain Associated With Adaptive Evolution of Poxviruses. A. McLysaght, P. Baldi, B. S. Gaut. Proceedings of the National Academy of Sciences USA.
Prediction of Protein Topologies Using Generalized IOHMMs and RNNs. G. Pollastri, P. Baldi, A. Vullo, P. Frasconi. Advances in Neural Information Processing Systems 15.
What Genes are Made Of. P. Baldi. Review of edited book entitled: The Genomic Revolution: Unveiling the Unity of Life.
Modeling the Internet and the Web: Probabilistic Methods and Algorithms. P. Baldi, P. Frasconi, P. Smyth.
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.
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.
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners. G. Pollastri, P. Baldi. Bioinformatics.
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.
Prediction of Coordination Number and Relative Solvent Accessibility in Proteins. G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proteins.
Distribution Patterns of Over-Represented k-mers in Non-Coding Yeast DNA. S. Hampson, D. Kibler, P. Baldi. Bioinformatics.
A Machine Learning Strategy for Protein Analysis. P. Baldi, G. Pollastri. IEEE Intelligent Systems (special Issue on "Intelligent Systems in Biology").
Why Are Complementary DNA Strands Symmetric? P. Baisnee, S. Hampson, P. Baldi. Bioinformatics.
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.
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.
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).
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).
DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling. P. Baldi, G. Wesley Hatfield.
A Computational Theory of Surprise. P. Baldi. Information, Coding, and Mathematics.
Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks. G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Bioinformatics.
Flexibility of the Genetic Code with Respect to DNA Structure. P. Baisnée, P. Baldi, S. Brunak, A. Gorm Pedersen. Bioinformatics.
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Inference of Gene Changes. P. Baldi, A. D. Long. Bioinformatics.
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.
A Model for Self-Organizing Large Scale Wireless Networks. M. Di Benedetto, P. Baldi. International Symposium on 3G Infrastructure and Services.
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).
The Shattered Self: The End of Natural Evolution. P. Baldi.
Probabilistic Graphical Models in Computational Molecular Biology. P. Baldi. Journal of the Italian Association for Artificial Intelligence.
On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial Genomes. P. Baldi. Bioinformatics.
Assessing the Accuracy of Prediction Algorithms for Classification: An Overview. P. Baldi, S. Brunak, Y. Chauvin, H. Nielsen. Bioinformatics.
Sequence Analysis by Additive Scales: DNA Structure for Sequences and Repeats of All Lenghts. P. Baldi, P. Baisnée. Bioinformatics.
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.
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).
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).
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.
Bidirectional Dynamics for Protein Secondary Structure Prediction. P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, G. Soda. Sequence Learning: Paradigms, Algorithms, and Applications.
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.
Exploiting the Past and the Future in Protein Secondary Structure Prediction. P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri. Bioinformatics.
Structural Basis for Triplet Repeat Disorders: A Computational Analysis. P. Baldi, S. Brunak, Y.Chauvin, A. Gorm Pedersen. Bioinformatics.
On the Use of Bayesian Methods for Evaluating Compartmental Neural Models. P. Baldi, M. C. Vanier, J. M. Bower. Journal of Computational Neuroscience.
DNA Structure in Human RNA Polymerase II Promoters. A. Gorm Pedersen, P. Baldi, Y. Chauvin, S. Brunak. Journal of Molecular Biology.
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).
Bioinformatics: the Machine Learning Approach. P. Baldi, S. Brunak.
Probabilistic Models of Neuronal Spike Trains. P. Baldi. Adaptive Processing of Temporal Information.
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.
Hybrid Modeling, HMM/NN Architectures, and Protein Applications. P. Baldi, Y. Chauvin. Neural Computation.
Naturally Occurring Nucleosome Positioning Signals in Human Exons and Introns. P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Journal of Molecular Biology.
Universal Approximation and Learning of Trajectories Using Oscillators. P. Baldi, K. Hornik. Advances in Neural Information Processing Systems 8.
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.
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).
Gradient Descent Learning Algorithms Overview: A General Dynamical Systems Perspective. P. Baldi. IEEE Transactions on Neural Networks.
Learning in Linear Networks: a Survey. P. Baldi, K. Hornik. IEEE Transactions on Neural Networks.
Substitution Matrices and Hidden Markov Models. P. Baldi. Journal of Computational Biology.
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.
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).
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).
When Neural Networks Play Sherlock Holmes. P. Baldi, Y. Chauvin. Back-Propagation: Theory, Architectures and Applications.
Gradient Descent Learning Algorithms: A Unified Perspective. P. Baldi. Back-Propagation: Theory, Architectures and Applications.
Back-propagation and unsupervised learning in linear networks. P. Baldi, Y. Chauvin, K. Hornik. Back-Propagation: Theory, Architectures and Applications.
How Delays Affect Neural Dynamics and Learning. P. Baldi, A. Atiya. IEEE Transactions on Neural Networks.
Smooth On-Line Learning Algorithms for Hidden Markov Models. P. Baldi, Y. Chauvin. Neural Computation.
Hidden Markov Models of Biological Primary Sequence Information. P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. PNAS USA.
Hidden Markov Models of the G-Protein Coupled Receptor Family. P. Baldi, Y. Chauvin. Journal of Computational Biology.
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.
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.
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.
Hidden Markov Models of Human Genes. P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, A. Krogh. Advances in Neural Information Processing Systems.
Statistical Models of Proteins: an Application to the G-Protein-Coupled Receptor Family. P. Baldi, Y. Chauvin. Modern Approaches in Molecular Bioinformatics.
Random Interactions in Higher-Orders Neural Networks. P. Baldi, S.S. Venkatesh. IEEE Transactions on Information Theory.
Neural Networks for Fingerprint Recognition. P. Baldi, Y. Chauvin. Neural Computation.
Learning Trajectories with a Hierarchy of Oscillatory Modules. P. Baldi, Nikzad Toomarian. Proceedings of the 1993 IEEE International Conference on Neural Networks.
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.
A Modular Hierarchical Approach to Learning. P. Baldi. Proceedings of the 2nd International Conference on Fuzzy Logic and Neural Networks.
Trading Decision Learning. P. Baldi, Y. Chauvin. Neural Networks for Computing Conference (abstract).
Programmed Interactions in Higher-Orders Neural Networks: I. Maximal Capacity. S.S. Venkatesh, P. Baldi. Journal of Complexity.
Programmed Interactions in Higher-Orders Neural Networks: II. The Outer-Product Algorithm. S. S. Venkatesh, P. Baldi. Journal of Complexity.
Can Regulatory Peptides Be Regarded as Words of a Biological Language? E. A. Mayer, J. Furness, P. Baldi. American Journal of Physiology.
Temporal Evolution of Generalization during Learning in Linear Networks. P. Baldi, Y. Chauvin. Neural Computation.
Contrastive Learning and Neural Oscillations. P. Baldi, F. Pineda. Neural Computation.
Graph Coloring Bounds for Cellular Radio. P. Baldi, E.C. Posner. Computers and Mathematics with Applications.
On a Generalized Family of Colorings. P. Baldi. Graphs and Combinatorics.
Computing with Arrays of Coupled Oscillators: an Application to Preattentive Texture Discrimination. P. Baldi, R. Meir. Neural Computation.
Computing with Arrays of Bell-Shaped and Sigmoid Functions. P. Baldi. Proceedings of the 1990 conference on Advances in neural information processing systems 3.
Asymptotic Normality of Some Graph Related Statistics. P. Baldi, Y. Rinott. Journal of Applied Probability.
On Normal Approximations of Distributions in Terms of Dependency Graphs. P. Baldi, Y. Rinott. Annals of Probability.
Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis. P. Baldi, A. Atiya. International Journal of Neural Systems.
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.
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.
Neural Networks and Principal Component Analysis: Learning from Examples without Local Minima. P. Baldi, K. Hornik. Neural Networks.
Neural Networks, Orientations of the Hypercube and Algebraic Threshold Functions. P. Baldi. IEEE Transactions on Information Theory.
Group Actions and Learning for a Family of Automata. P. Baldi. Journal of Computer and System Sciences.
Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal Vectors. P. Baldi. SIAM Journal of Discrete Mathematics.
How Sensory Maps Could Enhance Resolution Through Ordered Arrangements of Broadly Tuned Receivers. P. Baldi, W. Heiligenberg. Biological Cybernetics.
Neural Networks and Principal Component Analysis. P. Baldi. Proceedings of the 1988 Conference on Neural Information Processing.
Number of Stable Points for Spin Glasses and Neural Networks of Higher Orders. P. Baldi, S.S. Venkatesh. Physical Review Letters.
Symmetries and Learning in Neural Network Models. P. Baldi. Physical Review Letters.
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.
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.
Bounds on the Size of Ultrametric Structures. P. Baldi, E.B. Baum. Physical Review Letters.
Caging and Exhibiting Ultrametric Structures. P. Baldi, E.B. Baum. Proceedings of the Conference on Neural Networks for Computing.
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© 2024 Pierre Baldi | pfbaldi [at] uci [dot] edu
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