Refereed
Journals - Book
Chapters
- Refereed Conference Proceedings
This page was last updated on
05/16/06.
(Downloadable versions may differ slightly from published
versions)
Refereed
Journals
93. 93.
Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay
Unal, D. Huw Davies, Phil Felgner, and Pierre Baldi. Identification of
Humoral Immune Responses in Protein Microarrays using DNA Microarray Data
Analysis Techniques. Bioinformatics, in press, (2006).
92. M. Brandon, P. Baldi, and D. C.
Wallace. Mitochondrial Mutations in Cancer. Oncogene, in press,
(2006).
91. J. Cheng and P. Baldi. A Machine
Learning Information Retrieval Approach to Protein Fold Recognition.
Bioinformatics, in press, (2006).
90 C. V. Lopes, A. Haghighat, A.
Mandal, P. Baldi, and T. Givargis. Localization of Off-the-Shelf Mobile
Devices Using Audible Sound: Architectures, Protocols and Performance
Assessment. ACM SIGMOBILE Mobile Computing and Communications Review,
in press, (2006).
89. C. Tagwerker, K. Flick1, M. Cui,
C. Guerrero, Y. Dou, B. Auer, P. Baldi, L. Huang, and Peter Kaiser. 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. Molecular and
Cellular Proteomics, in press, (2006).
88. T. Lin, M. Melgar, S. J.
Swamidass, J. Purdon, T. Tseng, G. Gago, D. Kurth, P. Baldi, H. Gramajo,
and S. Tsai. Structure-Based Inhibitor Design of AccD5, an Essential
acyl-CoA Carboxylase Carboxyltransferase Domain of Mycobacterium
tuberculosis. Proceedings of the National Academy of Sciences USA,
103, 9, 3072-3077, (2006).
87. G. Pollastri, A. Vullo, P.
Frasconi, and P. Baldi. Modular DAG-RNN Architectures for Assembling Coarse
Protein Structures. Journal of Computational Biology, in press,
(2006).
86. J. Cheng, M. J. Sweredoski, and P.
Baldi. DOMpro: Protein Domain Prediction Using Profiles, Secondary
Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Data Mining and Knowledge Discovery. In press, (2006).
85. J. Cheng, A. Randall, and P.
Baldi. Prediction of Protein Stability Changes for Single Site Mutations
Using Support Vector Machines. Proteins, 62, 4, 1125-1132, (2006).
84. E. T. Wang, G. Kodama, P. Baldi,
and R. K. Moyzis. Global Landscape of Recent Inferred Darwinian Selection
for Homo Sapiens. Proceedings of the National Academy of Sciences USA,
103, 135-140, (2006).
83. J. Cheng, H. Saigo, and P.
Baldi. Large-Scale Prediction of Disulphide Bridges Using Kernel Methods,
Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.
Proteins, 62, 3, 617-629, (2006).
82. Kristi L. Fox-Walsh1, Yimeng Dou,
Bianca J. Lam1, She-pin Hung, Pierre F. Baldi, and Klemens J. Hertel.
The
Architecture of pre-mRNAs Affects Mechanisms of Splice-Site Pairing.. Proceedings of the
National Academy of Sciences USA, 102, 16176-16181, (2005).
81. J. Chen, S. J. Swamidass, Y.
Dou, J. Bruand, and P. Baldi. ChemDB: A Public Database of Small Molecules and
Related Chemoinformatics Resourrces. Bioinformatics, 21, 4133-4139, (2005).
80. S. A. Danziger, S. J. Swamidass,
J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo,
R. Luo, P. Baldi, Rainer K. Brachmann, and Richard H. Lathrop. Functional
census of mutation sequence spaces: The example of p53 cancer rescue
mutants. IEEE Transactions on Computational Biology and Bioinformatics.
In press, (2005).
79. D. M. Chung, Y. Dou, P. Baldi,
and J. S. Nowick. The Absence of Favorable Aromatic Interactions between
Beta-Sheet Peptides. Journal of the American Chemical Society, 127
(28) 9998-9999,
(2005).
78. J. Cheng and P. Baldi.
Three-Stage Prediction of Protein Beta-Sheets by Neural Networks,
Alignments, and Graph Algorithms. Proceedings of the 2005 Conference on
Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics,
21,
Supplement 1, i75-84, (2005).
77. S. J. Swamidass, J. Chen, P. Phung,
J. Bruand, L. Ralaivola, and P. Baldi. Kernels for Small Molecules and
the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.
Proceedings of the 2005 Conference on Intelligent Systems for Molecular
Biology, ISMB 05. Bioinformatics,
21, Supplement 1, i359-368, (2005).
76. J. Cheng, M. J. Sweredoski, and P.
Baldi. Accurate Prediction of Protein Disordered Regions by Mining Protein
Structure Data. Data Mining and Knowledge Discovery, 11, 3, 213-222,
(2005).
75. J. Cheng, A. Z. Randall, M.
Sweredoski, and P. Baldi. SCRATCH: a Protein Structure and Structural
Feature Prediction Server. Nucleic Acids Research, Special Issue on
Servers., 33, 9, W72-76, (2005).
74.
P. Baldi and M. Rosen-Zvi. On the
Relationship Between Deterministic and Probabilistic Directed Graphical
Models: from Bayesian Networks to Recursive Neural Networks. Neural
Networks, special issue on Neural Networks and Kernel Methods for
Structured Domains, 18, 8, (2005).
Article.
Technical Report (long
version).
73. L. Ralaivola, J. S.
Swamidass, H. Saigo, and P. Baldi. Graph Kernels for Chemical Informatics.
Neural Networks, special issue on Neural Networks and Kernel Methods
for Structured Domains, 18, 8, 1093-1110, (2005).
72. B. Irwin, M. Aye, P. Baldi, N. Beliakova-Bethell, H. Cheng, Y. Dou, W. Liou, and S. Sandmeyer. Retroviruses
and Yeast Retrotransposons Use Overlapping Sets of Host Genes. Genome
Research, 15, 641-654, (2005).
71. K. A. Salmon, S. Hung, N. R.
Steffen, R. Krupp, P. Baldi, G. Wesley Hatfield, and R. P. Gunsalus. Global
Gene Expression Profiling in Escherichia coli K12: The Effects of Oxygen
Availability and ArcA. Journal of Biological Chemistry, 280, 15,
15084-15096,
(2005).
70. R. Jurdak, C. Videira Lopes,
and P. Baldi. U-MAC: A Proactive and Adaptive UWB Medium Access Control
Protocol. Wireless Communications and Mobile Computing Journal,
Special Issue on UWB Communications, in press, (2004).
69. S. Sundaresh, S. Hung, G. W.
Hatfield, and P. Baldi. How Noisy and Replicable are DNA Microarray Data?
International Journal of Bioinformatics Research and Applications, 1,1,
31-50, (2005).
68 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. Vaccine Antigen
Discovery from Vaccinia and F. Tularensis Proteome Microarrays: H3L Envelope
Protein Is a Target for Vaccinia-Neutralizing Antibodies and Elicits
Neutralizing Antibodies In Vivo. Proceedings of the National Academy of
Sciences USA, 102, 3, 547-552, (2005).
67 J. Cheng, L.
Scharenbroich, P. Baldi, and E. Mjolsness. Sigmoid: Towards a Generative,
Scalable Software Infrastructure for Pathway Bioinformatics and Systems
Biology. IEEE Intelligent Systems, in press, (2005).
66 M. Brandon, M.
Lott, K. Nguyen, S. Spolim, S. Navathe, P. Baldi , and D. Wallace. MITOMAP:
a human mitochondrial genome database - 2004 update. Nucleic Acids
Research, 33 (Database issue), D611-613, (2005).
65 I. Sokolchik,
T. Tanabe, P. Baldi, and J. Y. Sze. 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. Journal of
Neuroscience, 25, 4, 1015-1023, (2005).
64 S.
Hampson, B. S. Gaut, and P. Baldi. Statistical Detection of Chromosomal
Homology Using Density Alone. Bioinformatics, 21, 8, 1339-1348, (2005).
63
R. Jurdak, C. Videira Lopes, and P. Baldi. A Survery, Classification, and
Comparative Analysis of Medium Access
Control Protocols for Ad Hoc Networks. IEEE Communications Surveys and
Tutorials, 6, 1, 2-16, (2004).
·62
A. Z. Randall, P. Baldi, and L. P. Villareal. Structural Proteomics of the
Poxvirus Family. Artificial Intelligence in Medicine Journal, special
issue on “Data mining in Genomics and Proteomics”, 31, 2, 105-115, (2004).
61
Y. Dou, P. Baisnee, G. Pollastri, Y. Pecout, J. Nowick, and P. Baldi ICBS: A
Database of Protein-Protein Interactions Mediated by Beta-Sheet
Formation. Bioinformatics, 20 16. 2767-2777, (2004).
60
A. McLysaght, P. Baldi, and B. S. Gaut. Extensive Gene Gain Associated
With Adaptive Evolution of Poxvirus. Proceedings of the National
Academy of Sciences USA, 100, 26, 15655-15660, (2003).
59
K. Salmon, K. Mekjian, R. P. Gunsalus, S. Hung, P. Baldi, and G. Wesley
Hatfield. Global Gene Expression Profiling in Escherichia coli K12: The
Effects of Oxygen Availability and FNR. Journal of Biological Chemistry,
278, 32, 29837-29855, (2003).
58
S. Hampson, A. McLysaght, B. Gaut, and P. Baldi . LineUp : Statistical
Detection of Chromosomal Homology with Applications to Plant Comparative
Genomics. Genome Research, 13, 5, 999-1010, (2003).
57
G. A. Weiss, T. A. Roth, P. Baldi, and S. S. Sidhu Comprehensive Mutagenesis
of the C-terminal Domain of the M13 Gene-3 Minor Coat Protein: The
Requirement for Assembly into the Bacteriophage Particle. Journal of
Molecular Biology, 332, 4, 777-782, (2003).
56 P.
Baldi and G. Pollastri.The Principled Design of Large-Scale Recursive Neural
Network Architectures--DAG-RNNs and the Protein Structure Prediction
Problem. Journal of Machine Learning Research, 4, 575-602, (2003)..
55
Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy,and P.
Baldi. Combining Protein Secondary Structure Prediction Models With Ensemble
Methods of Optimal Complexity. Neurocomputing, in press, (2003).
Presented during
JOBIM01 Conference.
54 P. Baldi
and W. H. Batchelder.Bounds on Variances of Estimators
for Multinomial Processing Tree Models. Journal of Mathematical Psychology,
47, 467-470, (2003).
53·
P. Baldi, L. De Nardis, and M. G. Di Benedetto. Modelization and
Optimization of Ultra Wide Band
Communication Networks Through a Flesible Cost Function.. IEEE Journal on Selected Areas in Communications,
20, 9, (2002).
52·
S. Hung, P. Baldi, and G. Wesley Hatfield. Global Gene Expression Profiling
in Excherichia coli K12: The Effects of Leucine-responsive Regulatory
Protein. Journal of Biological Chemistry, 277, 43, 40309-40323, (2002).
51·
P. Baisnee, S. Hampson, and P. Baldi. Why Are Complementary DNA Strands
Symmetric? Bioinformatics, 18, 1021-1033, (2002).
50·
G. Wesley Hatfield, S. Hung, and P. Baldi. Differential Analysis of DNA
Microarray Gene Expression Data. Molecular Microbiology, in press,
(2002).
49·
G. Pollastri and P. Baldi. Prediction of Contact Maps by GIOHMMs and
Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal
Corners. Proceedings of the 2002 Conference on Intelligent Systems for
Molecular Biology, ISMB 02. Bioinformatics, 18, Supplement 1, S62-S70,
(2002).
48·
P. Baldi and G. Pollastri. Machine Learning Structural and Functional Proteomics.
IEEE Intelligent Systems. Special Issue on Intelligent Systems in Biology,
17, 2, 28-35, (20002). Article
47·
S. Hamspon, D. Kibler, and P. Baldi. Distribution Patterns of Over-Represented k-mers in Non-Coding Yeast DNA. Bioinformatics,
18, 4, 611-626, (2002).Article
46·
G. Pollastri, P. Baldi, P. Fariselli, and R. Casadio. Prediction of Coordination Number and Relative Solvent Accessibility in Proteins. Proteins,
47, 142-153, (2002).
Article
45·
G. Pollastri, D. Przybylski, B. Rost, and P. Baldi. Improving the Prediction of Protein Secondary Strucure in Three and Eight Classes Using Recurrent Neural Networks and Profiles. Proteins,
47, 228-235, (2002).Article
44·
G. Pollasti, P. Baldi, P. Fariselli, R. Casadio. Improved
Prediction of the Number of Residue Contacts in Proteins by Recurrent
Neural Networks. Bioinformatics, in press (2001).Article
43· A.
D. Long, H. J. Mangalam, B. Y. P. Chan, L. Tolleri, G. W. Hatfield, and P.
Baldi. Improved Statistical Inference from DNA Microarray Data Using Analysis of
Variance and a Bayesian Statistical Framework. Journal of Biological Chemistry, 276,23,19937-19944, (2001). Article
42·
P. Baldi and
A. D. Long A Bayesian Framework for the Analysis of Microarray Expression Data:
Regularized t-Test and Statistical Inferences of Gene Changes.
Bioinformatics, 17, 6, 509-519, (2001). Article
41·
P. Baisnée, P. Baldi, S. Brunak, and A. Gorm Pedersen. Flexibility of the Genetic Code with Respect to DNA Structure. Bioinformatics, 17, 237-248, (2001).
Article
40·
P. Baldi and P. Baisnee.
Sequence Analysis by Additive Scales: DNA Structure for Sequence and Repeats of All Lenghts. Bioinformatics, 16, 10, 865-889, (2000).
Abstract
- Article
39·
P. Baldi, S. Brunak, Y. Chauvin, and H. Nielsen.
Assessing the Accuracy of Prediction Algorithms for Classification: An
Overview. Bioinformatics, 16, 5, 412-424, (2000).
Abstract
- Article
38·
P. Baldi. On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial
Genomes. Bioinformatics, 16,
4, 367-371, (2000).
Abstract
- Article
37·
P. Baldi. Probabilistic Graphical Models in Computational Molecular Biology, Journal of the Italian Association for Artificial Intelligence (AIIA), Vol. 1, 8-12, (2000).
Abstract
- Article
36·
P. Baldi, S. Brunak, Y. Chauvin, A. Gorm
Pedersen. Structural Basis for Triplet Repeat Disorders: A Computational
Analysis. Bioinformatics, 15,
918-929, (1999).
Abstract
- Article
35·
P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri
Pedersen. Exploiting the Past and the Future in Protein Secondary Structure
Prediction. Bioinformatics, 15,
937-946, (1999).
Abstract
- Article
34·
A. Gorm
Pedersen, P. Baldi, S. Brunak, and Y. Chauvin. The Biology of Eukaryotic
Promoter Prediction-a Review. Computers
and Chemistry, Special Issue on Genome and Informatics, 23,
191-207, (1999).
Abstract
33·
A. Gorm
Pedersen, P. Baldi, Y. Chauvin, and S. Brunak. DNA Structure in Human RNA
Polymerase II Promoters, Journal of
Molecular Biology, 281, 663-673, (1998).
32·
P. Baldi,
M. C. Vanier, and J. M. Bower. On the Use of Bayesian Methods for Evaluating
Compartmental Neural Models, Journal of
Computational Neuroscience, 5, 285-314, (1998).
31·
P. Baldi,
S. Brunak, Y. Chauvin, and A. Krogh. Naturally Occurring Nucleosome Positioning
Signals in Human Exons and Introns, Journal of Molecular Biology, Vol. 263, 5, 503-510, (1996).
30·
P. Baldi
and Y. Chauvin. Hybrid Modeling, HMM/NN
Architectures, and Protein Applications, Neural Computation, Vol. 8, 7, 1541-1565, (1996).
29·
P. Baldi.
Substitution Matrices and Hidden Markov Models, Journal of Computational Biology, Vol. 2, 3, 497-501, (1995).
28·
P.
Baldi and K. Hornik. Learning in Linear Networks: a Survey, IEEE
Transactions on Neural Networks, Vol. 6, 4, 837-858, (1995)
27·
P. Baldi.
Gradient Descent Learning Algorithms Overview: A General Dynamical Systems
Perspective, IEEE Transactions on Neural
Networks, Vol. 6, 1, 182-195, (1995).
26·
P. Baldi
and Y. Chauvin. Hidden Markov Models of the G-Protein Coupled Receptor Family, Journal
of Computational Biology, Vol. 1, 4, 311-335, (1994).
25·
P. Baldi,
Y. Chauvin, T. Hunkapiller, and M. A. McClure. Hidden Markov Models
of Biological Primary Sequence Information, PNAS
USA, Vol. 91, 3, 1059-1063, (1994).
24·
P. Baldi
and Y. Chauvin. Smooth On-Line
Learning Algorithms for Hidden Markov Models, Neural Computation, Vol. 6, 2, 305-316, (1994).
23·
P. Baldi
and A. Atiya. How Delays Affect Neural Dynamics and Learning, IEEE
Transactions on Neural Networks, Vol. 5, 4, 626-635, (1994).
22·
P. Baldi
and Y. Chauvin. Neural Networks for Fingerprint Recognition, Neural
Computation, Vol. 5, 3, 402-418, (1993).
21·
P. Baldi
and S.S. Venkatesh. Random Interactions in Higher-Orders Neural Networks, IEEE
Transactions on Information Theory, Vol. 39, 1, 274-283, (1993).
20·
P. Baldi
and F. Pineda. Contrastive Learning and Neural Oscillations, Neural
Computation, Vol. 3, No. 4, 526-545, (1991).
19·
P. Baldi
and Y. Chauvin. Temporal Evolution of Generalization during Learning in Linear
Networks, Neural Computation, Vol. 3,
No. 4, 589-603, (1991).
18·
E. A.
Mayer, J. Furness, and P. Baldi. Can
Regulatory Peptides Be Regarded as Words of a Biological Language?, American
Journal of Physiology, Vol. 261(2), G171-G184, (1991).
17·
S. S.
Venkatesh and P. Baldi. Programmed Interactions in Higher-Orders Neural
Networks: II. The Outer-Product Algorithm, Journal
of Complexity, Vol. 7, 443-479, (1991).
16·
S.S.
Venkatesh and P. Baldi. Programmed
Interactions in Higher-Orders Neural Networks: I. Maximal Capacity, Journal
of Complexity, Vol. 7, 316-337, (1991).
15·
P. Baldi
and R. Meir. Computing with Arrays of Coupled Oscillators: an Application to
Preattentive Texture Discrimination, Neural
Computation, Vol. 2, No. 4, 458-471, (1990).
14·
P. Baldi.
On a Generalized Family of Colorings, Graphs and Combinatorics, Vol. 6, 95-110, (1990).
13·
P. Baldi
and E.C. Posner. Graph Coloring
Bounds for Cellular Radio, Computers and
Mathematics with Applications, Vol. 19, No. 10, 91-97, (1990).
12·
P. Baldi
and A. Atiya. Oscillations and Synchronizations in Neural Networks: an
Exploration of the Labeling Hypothesis, International
Journal of Neural Systems, Vol. 1, No. 2, 103-124, (1989).
11·
P. Baldi
and Y. Rinott. On Normal Approximations of Distributions in Terms of Dependency
Graphs, Annals of Probability, Vol.
17, No. 4, 1646-1650, (1989).
10·
P. Baldi
and Y. Rinott. Asymptotic Normality of Some Graph Related Statistics, Journal
of Applied Probability, Vol. 26, 171-175, (1989).
9·
P. Baldi
and K. Hornik. Neural Networks and Principal Component Analysis: Learning from
Examples without Local Minima, Neural
Networks, Vol. 2, No. 1, 53-58, (1988).
8·
P. Baldi
and W. Heiligenberg. How Sensory Maps Could Enhance Resolution Through Ordered
Arrangements of Broadly Tuned Receivers, Biological Cybernetics, Vol. 59, No. 4,5, 313-318, (1988).
7·
P. Baldi.
Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal
Vectors, SIAM Journal of Discrete
Mathematics, Vol. 1, No. 1 (1988).
6·
P. Baldi.
Group Actions and Learning for a Family of Automata, Journal
of Computer and System Sciences, Vol. 36, No. 2, 1-15, (1988).
5·
P. Baldi.
Neural Networks, Orientations of the Hypercube and Algebraic Threshold
Functions, IEEE Transactions on
Information Theory, Vol. 34, No. 3, 523-530, (1988).
4·
M.
Aschbacher, P. Baldi, E. B. Baum, and R.M. Wilson. Embeddings of Ultrametric Spaces in Finite Dimensional Structures, SIAM
Journal of Algebraic and Discrete Methods, Vol. 8, No. 4, 564-577, (1987).
3·
P. Baldi.
Symmetries and Learning in Neural Network Models, Physical Review Letters, Vol. 59, No. 17, 1976-1978, (1987).
2·
P. Baldi
and S.S. Venkatesh. Number of Stable Points for Spin Glasses and Neural Networks
of Higher Orders, Physical Review Letters,
Vol. 58, No. 9, 913-916, (1987).
1·
P. Baldi
and E.B. Baum. Bounds on the Size of Ultrametric Structures, Physical
Review Letters, Vol. 56, No. 15, 1598-1600, (1986).
refereed
journals - refereed
conference proceedings
Book
Chapters
16
R.
Jurdak, C. V. Lopes, and P. Baldi. Battery Lifetime Estimation and
Optimization for Underwater Sensor Networks. In Sensor Network Operations,
published by IEEE Press, edited by Shashi Phoha, Thomas F. La Porta and
Christopher Griffin , 2004 (in press). Edited volume resulting from overflow
to special issue on Sensor Networks in IEEE Transactions on Mobile
Computing.
15
P.
Baldi, G. Wesley Hatfield, and Li M. Fu. Clustering Algorithms for Gene
Expression Analysis. Handbook of Computational Molecular Biology. S.
Aluru Editor, CRC Press, (2004).
14
S.
Kremer and P. Baldi. Hidden Markov Models and Neural Networks.
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.
Wiley, (2004).
13
P.
Baldi. Surprise: A Shortcut for Attention? In: Neurobiology of Attention.
L. Itti, G. Rees, and J. Tsotsos Editors, Academic Press, (2004).
12 . S.
P. Hung, G. Wesley Hatfield, S. Sundaresh, and P. Baldi. Understanding DNA
Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data
Sets. In: Genomics, Proteomics, and Vaccines. G. Grandi Editor, John Wiley
and Sons, (2003).
11 . P. Baldi. A
Computational Theory of Surprise, in Information, Coding, and Mathematics.
M. Blaum Editor, Kluwer, 1-25, (2002).
10.
P. Baldi, G. Pollastri, P. Frasconi, and A. Vullo. New Machine Learning
Methods for the Prediction of Protein Topologies, in Artificial
Intelligence and Heuristic Methods in Bioinformatics. P. Frasconi and R.
Shamir Editors, IOS Press, (2002).
9·
P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, and G. Soda.
Bidirectional Dynamics for Protein Secondary Structure Prediction.
Sequence Learning: Paradigms,
Algorithms, and Applications. R. Sun and L. Giles Editors, Springer Verlag, 99-120, (2000).
8·
P. Baldi, S. Brunak, P. Frasconi, G. Pollastri.
Bidirectional IOHMMs and Recurrent Neural Networks for Protein Secondary Structure Prediction.
Protein Sequence Analysis in the Genomic Era,
. R. Casadio and L. Masotti Editors, CLUEB, Bologna, Italy, (2000).
7·
P. Baldi,
Y. Chauvin, and V. Mittal Henkle. Software Foundation Libraries for the Design
of Intelligent Systems. Neural Nets WIRN
Vietri 98. Proceedings of the 10-th Italian Workshop on Neural Nets. M.
Marinaro and R. Tagliaferri Editors. Springer Verlag Series on Perspectives on
Neural Computing Series, J. Taylor Series Editor, (1998).
Chapter
6·
P. Baldi.
Probabilistic Models of Neuronal Spike Trains, in Adaptive Processing of Temporal Information. C.L. Giles and M. Gori
Editors, Lecture Notes in Computer Science, Springer Verlag, New York, 198-228,
(1998).
5·
P. Baldi,
Y. Chauvin, and K. Hornik. Back-propagation and unsupervised learning in linear
networks, in Back-Propagation: Theory,
Architectures and Applications. Y. Chauvin and D.E. Rumelhart Editors,
Lawrence Erlbaum Associates, Hillsdale, New Jersey, 389-432, (1995).
4·
P. Baldi.
Gradient Descent Learning Algorithms: A Unified Perspective, in Back-Propagation:
Theory, Architectures and Applications. Y. Chauvin and D.E. Rumelhart
Editors, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 509-541, (1995).
3·
P. Baldi
and Y. Chauvin. When Neural Networks Play Sherlock Holmes, in Back-Propagation:
Theory, Architectures and Applications. Y. Chauvin and D.E. Rumelhart
Editors, Lawrence Erlbaum Associates, Hillsdale, New Jersey, 487-507, (1995).
2·
P. Baldi
and Y. Chauvin. Statistical Models of Proteins: an Application to the
G-Protein-Coupled Receptor Family, in Modern
Approaches in Molecular Bioinformatics. S. Schulze-Kremer Editor, IOS Press,
Amsterdam/New York, 53-102 (1994).
1·
P. Baldi,
Y. Rinott, and C. Stein. A Normal Approximation for the Number of Local Maxima
of a Random Function on a Graph, in
Probability, Statistics and Mathematics: Papers in Honor of Samuel Karlin,
T.W. Anderson, K.B. Athreya and D.L. Iglehart, Editors, Academic Press (1989).
refereed
journals - book chapters
Refereed
Conference Proceedings
44. L. Itti and P. Baldi. “Bayesian Surprise
Attracts Human Attention”, Advances in Neural Information Processing
Systems 18, NIPS 2005, in press, (2005).
43. R. Jurdak, P. Baldi, C. V. Lopes.
"Energy-Aware Adaptive Low Power Listening for Sensor Networks", To appear
in proceedings of the 2nd International Workshop on Networked Sensing
Systems (INSS). San Diego, CA. June, 2005.
42. R. Jurdak, C. V. Lopes, and P. Baldi.
“Programming Model for Supporting Complex Optimizations in Sensor Networks,”
Proceedings of the Fourth International IEEE/ACM Conference on Information
Processing in Sensor Networks (IPSN’05).
Los Angeles, CA. April, 2005.
41. R. Jurdak, C. V. Lopes, P. Baldi. Emergy-aware
Adaptive Low Power Listening for Sensor Networks. Second International
Workshop on Networked Sensing Systems, San Diego, June 2005.
40. R. Jurdak, C. V. Lopes, P. Baldi.
Programming Model for Supporting Complex Optimizations in Sensor Networks.
The Fourth International Conference on Information Processing in Sensor
Networks.
39. J. Cheng and P. Baldi. Three-Stage
Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph
Algorithms. Proceedings of the 2005 Conference on Intelligent Systems for
Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).
38. L. Ralaivola, J. Chen, P. Phung, J. Bruand,
S. J. Swamidass, and P. Baldi. Kernels for Small Molecules and the
Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity. Proceedings
of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB
05. Bioinformatics, in press, (2005).
37. S. Danziger, S. J. Swamidass, J. Zeng, L.
Dearth, Q. Lu, J. H. Chen, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, R. K.
Brachmann, and R. H. Lathrop. Functional census of mutation sequence spaces:
The example of p53 cancer rescue mutants.
36. J. Cheng and P. Baldi. Three-Stage
Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph
Algorithms. Proceedings of the 2005 Conference on Intelligent Systems for
Molecular Biology, ISMB 05. Bioinformatics, in press, (2005).
35. L. Ralaivola, J. Chen, P. Phung, J. Bruand,
S. J. Swamidass, and P. Baldi. Kernels for Small Molecules and the
Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity. Proceedings
of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB
05. Bioinformatics, in press, (2005).
34. R. Jurdak, C. V. Lopes, P. Baldi. Adaptive
Low Power Listening for Sensor Networks. 11th Annual International
Conference on Mobile Computing and Networking.
33
L. Itti, P. Baldi. A Principled Approach to Detecting Surprising Events in
Video. In: Proc. IEEE Conference on Computer Vision and Pattern
Recognition (CVPR), Jun 2005.
32. L.
Ralaivola, L. Wu, and P. Baldi. SVM and Pattern-Enriched Common Fate Graphs
for the Game of GO. European Symposium on Artificial Neural Networks (ESANN),
Bruges, Belgium, April 2005. Accepted for Oral Persentation.
31
A. Mandal, C. V. Lopes, T. Givargis, A.
Haghighat, R. Jurdak, and P. Baldi. Beep: 3D Indoor Positioning Using
Audible Sound. Proceedings of the 2004 IEEE Consumer Communications and
Networking Conference, in press, (2004).
30 P.
Baldi, J. Cheng, and A. Vullo. Large-Scale Prediction of Disulphide Bond
Connectivity. Advances in Neural Information Processing Systems 17,
NIPS 2004, in press, (2004).
29 R. Jurdak, C. Videira Lopes, and P.
Baldi. An Identfication Scheme for Location Systems Using Robust Acoustic
Signals. Proceeding of the ACS/IEEE International Conference on Pervasive
Services, Beirut, Lebanon. IEEE Computer Society Press, (2004).
28 G. Pollastri, P.
Baldi, A. Vullo, and P. Frasconi. Prediction of Protein Topologies Using
GIOHMMs and GRNNs. Advances in Neural Information Processing Systems 15,
S. Becker, S. Thrun, and K. Obermayer Editors, MIT Press, Cambridge, MA,
(2003).
27 G. Pollastri and P. Baldi.
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using
Lateral Propagation From All Four Cardinal Corners. Proceedings of the 2002
Conference on Intelligent Systems for Molecular Biology, ISMB 02.
Bioinformatics, 18, Supplement 1, S62-S70, (2002). Nominated for Best Paper
Award.
26·
G. Pollasti, P. Baldi, P.
Fariselli, R. Casadio. Improved Prediction of the Number of Residue Contacts in
Proteins by Recurrent Neural Networks. Proceedings of the 2001 Conference on
Intelligent Systems for Molecular Biology, (ISMB01), Copenhagen, Denmark, AAAI
Press (2001).
25·
M. G. Di Benedetto and P. Baldi. A Model for
Self-Organizing Large Scale Wireless Networks. International Symposium on 3G
Infrastructure and Services. Athens, Greece, July 2001.
24·
P. Baldi, G. Pollastri, C. A. F. Andersen, and S. Brunak.
Matching Protein Beta-Sheet Partners by Feedforward and Recurrent Neural Networks.
Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology, (ISMB00),
La Jolla, CA, 25-36, AAAI Press (2000). Article
23·
S. Hampson, P. Baldi, D. Kibler, and S. Sandmeyer. Analysis of Yeast’s ORFs Upstream Regions
by Parallel Processing, Microarrays, and Computational Methods.
Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology, (ISMB00),
La Jolla, CA, 190-201, AAAI Press (2000). Article
22·
P. Baldi, G. Pollastri, C. A. F. Andersen, and S. Brunak.
Protein Beta-Sheet Partner Prediction by Neural Networks.
Artifical Neural Networks in Medicine and Biology. Proceedings of the ANNIMAB-1 Conference,
Göteborg, Sweden, H. Malmgren, M. Borga and L. Niklasson Editors, Springer Verlag, (2000).
21·
P. Baldi,
S. Brunak, P. Frasconi, G. Pollastri, and G. Soda. Bidirectional Dynamics for
Protein Secondary Structure Prediction, Proceedings of the Sixteenth International Joint Conference on
Artificial Intelligence (IJCAI99), Stockholm, Sweden (1999), in press.
20·
P. Baldi,
S. Brunak, Y. Chauvin, and A. Gorm Pedersen. Computational Applications of DNA
Structural Scales, Proceedings of the 1998
Conference on Intelligent Systems for Molecular Biology, (ISMB98), Montreal,
Canada, 35-42, AAAI Press (1998).
19·
P. Baldi,
A. Gorm Pedersen, S. Brunak, and Y. Chauvin. Characterization of Prokaryotic and
Eukaryotic Promoters Using Hidden Markov Models, Proceedings
of the 1996 Conference on Intelligent Systems for Molecular Biology (ISMB96),
Washington University, Saint Louis, 182-191, AAAI Press, (1996).
18·
P. Baldi,
S. Brunak, Y. Chauvin, and A. Krogh. Hidden Markov Models for Human Genes:
Periodic Patterns in Exon Sequences, Theoretical
and Computational Methods in Genome Research, S.Suhai Editor, Plenum, NY,
(1996).
17·
P. Baldi
and K. Hornik. Universal Approximation and Learning of Trajectories Using
Oscillators, Advances in Neural
Information Processing Systems 8, D. S. Touretzky, M. C. Mozer, and M. E.
Hasselmo Editors, MIT Press, Cambridge MA,
451-457, (1996).
16·
P. Baldi
and Y. Chauvin. Protein Modeling with Hybrid Hidden Markov Model/Neural Network
Architectures, Proceedings of the 1995
Conference on Intelligent Systems for Molecular Biology (ISMB95), Cambridge
(UK), 39-47, (1995).
15·
P. Baldi,
Y. Chauvin, S. Brunak, J. Engelbrecht, and A. Krogh.
Periodic Sequence Patterns in Human Exons,
Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology
(ISMB95), Cambridge (UK), 30-38, (1995).
14·
P. Smyth,
U. Fayadd, P. Perona, M. Burl, and P. Baldi. Inferring Ground Truth from
Subjective Labelling of Venus Images, Advances
in Neural Information Processing Systems, G. Tesauro, D. S. Touretzky and T.
K. Leen Editors, MIT Press, Cambridge MA, 1085-1092, (1995).
13·
P. Baldi
and Y. Chauvin. Trading Decision Learning: from Theory to Personal Traders, Proceedings
of the Second International Conference on Neural Networks in the Capital Markets,
Pasadena, CA (1994).
12·
P. Baldi,
S. Brunak, Y. Chauvin, J. Engelbrecht, and A. Krogh. Hidden Markov Models of
Human Genes, Advances in Neural
Information Processing Systems, J. D. Cowan, G. Tesauro and J. Alspector
Editors, Morgan Kauffmann Publishers, 761-768, (1994).
11·
P. Baldi
and Y. Chauvin. Discrimination of Tyrosine and Serine/Threonine Kinase
Sub-Families by Hidden Markov Models, Proceedings
of The Third International Conference on Bioinformatics and Genome Research,
World Scientific Publishing Co., New Jersey, (1994).
10·
P. Baldi
and Y. Chauvin. Modeling Protein Families and Human Genes: Hidden Markov Models
and a Little Beyond, Proceedings of the
1994 Fifth Generation Computing Symposium, Workshop on Fusion of Molecular
Biology and Knowledge Processing, (Tokyo, Japan), (1994).
9·
P. Baldi,
Y. Chauvin, T. Hunkapiller, and M. A. McClure. Hidden Markov Models in Molecular
Biology: New Algorithms and Applications, Advances in Neural Information Processing Systems, S. J. Hanson, J.
D. Cowan and C. Lee Giles Editors, Morgan Kauffmann Publishers, 747-754, (1993).
8·
P. Baldi
and Nikzad Toomarian. Learning Trajectories with a Hierarchy of Oscillatory
Modules, Proceedings of the 1993 IEEE
International Conference on Neural Networks, San Francisco, CA, Volume III,
1172-1176, and also, in similar form, in Proceedings of the 1993 European Symposium on Artificial Neural Networks
(ESANN93), Brussels, 183-188.
7·
P. Baldi
and Y. Chauvin. Trading Decision Learning, Neural Networks for Computing Conference (abstract), Snowbird, UT,
(1992).
6·
P. Baldi.
A Modular Hierarchical Approach to Learning, Proceedings of the 2nd International Conference on Fuzzy Logic and
Neural Networks, (Iizuka, Japan), Vol. 2, 985-988, (1992).
5·
P. Baldi.
Computing with Arrays of Bell-Shaped and Sigmoid Functions. Bernstein
Polynomials, the Heat Equation and Universal Approximation Properties, Proceedings
of the 1990 Conference on Neural Information Processing Systems, Denver, CO,
Morgan Kauffman Publishers, 735-742, (1991).
4·
P. Baldi,
Y. Rinott, and C. Stein. On the Distribution of the Number of Local Minima of a
Random Function on a Graph, Proceedings of
the 1989 Conference on Neural Information Processing Systems, Denver, CO,
Morgan Kauffman Publishers, 727-732, (1990).
3·
P. Baldi.
Neural Networks and Principal Component Analysis: Landscapes and Algorithms,
Proceedings of the 1988 Conference on Neural Information Processing,
Denver, CO, Morgan Kauffman Publishers, 65-72, (1989).
2·
P. Baldi
and S.S. Venkatesh. On Properties of Networks of Neuron-Like Elements:
Complexity and Capacity, Proceedings of
the IEEE Conference on Neural Information Processing Systems (Denver 1987),
published by the American Institute of Physics, (D.Z. Anderson, Editor).
1·
P. Baldi
and E.B. Baum. Caging and Exhibiting Ultrametric Structures, Proceedings
of the Conference on Neural Networks for Computing, Snowbird, Utah, April
1986, published by the American Institute of Physics, 35-40, (1986), (John S.
Denker, Editor).
