| * | 2009 |
|---|
| 102 | EE | Joel Ossher,
Sushil Krishna Bajracharya,
Erik Linstead,
Pierre Baldi,
Cristina Videira Lopes:
SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects.
MSR 2009: 183-186 |
| 101 | EE | Erik Linstead,
Pierre Baldi:
Mining the coherence of GNOME bug reports with statistical topic models.
MSR 2009: 99-102 |
| 100 | EE | Raja Jurdak,
Pierre Baldi,
Cristina Videira Lopes:
Software-driven sensor networks for short-range shallow water applications.
Ad Hoc Networks 7(5): 837-848 (2009) |
| 99 | EE | Marty C. Brandon,
Douglas C. Wallace,
Pierre Baldi:
Data structures and compression algorithms for genomic sequence data.
Bioinformatics 25(14): 1731-1738 (2009) |
| 98 | EE | Christophe N. Magnan,
Arlo Z. Randall,
Pierre Baldi:
SOLpro: accurate sequence-based prediction of protein solubility.
Bioinformatics 25(17): 2200-2207 (2009) |
| 97 | EE | Xiaohui Xie,
Paul Rigor,
Pierre Baldi:
MotifMap: a human genome-wide map of candidate regulatory motif sites.
Bioinformatics 25(2): 167-174 (2009) |
| 96 | EE | Erik Linstead,
Sushil Krishna Bajracharya,
Trung Chi Ngo,
Paul Rigor,
Cristina Videira Lopes,
Pierre Baldi:
Sourcerer: mining and searching internet-scale software repositories.
Data Min. Knowl. Discov. 18(2): 300-336 (2009) |
| 2008 |
|---|
| 95 | EE | Daniel S. Hirschberg,
Pierre Baldi:
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers.
DCC 2008: 520 |
| 94 | EE | Pierre Baldi,
Ryan W. Benz:
BLASTing small molecules - statistics and extreme statistics of chemical similarity scores.
ISMB 2008: 357-365 |
| 93 | EE | Pierre Baldi,
Cristina Videira Lopes,
Erik Linstead,
Sushil Krishna Bajracharya:
A theory of aspects as latent topics.
OOPSLA 2008: 543-562 |
| 92 | EE | Michael J. Sweredoski,
Pierre Baldi:
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure.
Bioinformatics 24(12): 1459-1460 (2008) |
| 91 | EE | Arlo Z. Randall,
Jianlin Cheng,
Michael J. Sweredoski,
Pierre Baldi:
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins.
Bioinformatics 24(4): 513-520 (2008) |
| 90 | EE | Lin Wu,
Pierre Baldi:
Learning to play Go using recursive neural networks.
Neural Networks 21(9): 1392-1400 (2008) |
| 2007 |
|---|
| 89 | EE | Erik Linstead,
Paul Rigor,
Sushil Krishna Bajracharya,
Cristina Videira Lopes,
Pierre Baldi:
Mining concepts from code with probabilistic topic models.
ASE 2007: 461-464 |
| 88 | EE | Otávio Augusto Lazzarini Lemos,
Sushil Krishna Bajracharya,
Joel Ossher,
Ricardo Santos Morla,
Paulo Cesar Masiero,
Pierre Baldi,
Cristina Videira Lopes:
CodeGenie: using test-cases to search and reuse source code.
ASE 2007: 525-526 |
| 87 | EE | Suman Sundaresh,
Arlo Z. Randall,
Berkay Unal,
Jeannine M. Petersen,
John T. Belisle,
M. Gill Hartley,
Melanie Duffield,
Richard W. Titball,
D. Huw Davies,
Philip L. Felgner,
Pierre Baldi:
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.
ISMB/ECCB (Supplement of Bioinformatics) 2007: 508-518 |
| 86 | EE | Pierre Baldi:
Learning and Charting Chemical Space with Strings and Graphs: Challenges and Opportunities for AI and Machine Learning.
MLG 2007 |
| 85 | EE | Erik Linstead,
Paul Rigor,
Sushil Krishna Bajracharya,
Cristina Videira Lopes,
Pierre Baldi:
Mining Eclipse Developer Contributions via Author-Topic Models.
MSR 2007: 30 |
| 84 | EE | Erik Linstead,
Paul Rigor,
Sushil Krishna Bajracharya,
Cristina Videira Lopes,
Pierre Baldi:
Mining Internet-Scale Software Repositories.
NIPS 2007 |
| 83 | EE | Jianlin Cheng,
Pierre Baldi:
Improved residue contact prediction using support vector machines and a large feature set.
BMC Bioinformatics 8: (2007) |
| 82 | EE | Jonathan H. Chen,
Erik Linstead,
Sanjay Joshua Swamidass,
Dennis Wang,
Pierre Baldi:
ChemDB update - full-text search and virtual chemical space.
Bioinformatics 23(17): 2348-2351 (2007) |
| 81 | EE | Michael J. Sweredoski,
Kevin J. Donovan,
Bao D. Nguyen,
A. J. Shaka,
Pierre Baldi:
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling.
Bioinformatics 23(21): 2829-2835 (2007) |
| 80 | EE | Raja Jurdak,
Pierre Baldi,
Cristina Videira Lopes:
Adaptive Low Power Listening for Wireless Sensor Networks.
IEEE Trans. Mob. Comput. 6(8): 988-1004 (2007) |
| 79 | EE | Eduardo Ruiz-Pesini,
Marie T. Lott,
Vincent Procaccio,
Jason C. Poole,
Marty C. Brandon,
Dan Mishmar,
Christina Yi,
James Kreuziger,
Pierre Baldi,
Douglas C. Wallace:
An enhanced MITOMAP with a global mtDNA mutational phylogeny.
Nucleic Acids Research 35(Database-Issue): 823-828 (2007) |
| 2006 |
|---|
| 78 | EE | Lin Wu,
Pierre Baldi:
A Scalable Machine Learning Approach to Go.
NIPS 2006: 1521-1528 |
| 77 | EE | Sushil Krishna Bajracharya,
Trung Chi Ngo,
Erik Linstead,
Yimeng Dou,
Paul Rigor,
Pierre Baldi,
Cristina Videira Lopes:
Sourcerer: a search engine for open source code supporting structure-based search.
OOPSLA Companion 2006: 681-682 |
| 76 | EE | Jianlin Cheng,
Pierre Baldi:
A machine learning information retrieval approach to protein fold recognition.
Bioinformatics 22(12): 1456-1463 (2006) |
| 75 | EE | Suman Sundaresh,
Denise L. Doolan,
Siddiqua Hirst,
Yunxiang Mu,
Berkay Unal,
D. Huw Davies,
Philip L. Felgner,
Pierre Baldi:
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques.
Bioinformatics 22(14): 1760-1766 (2006) |
| 74 | EE | Jianlin Cheng,
Michael J. Sweredoski,
Pierre Baldi:
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Data Min. Knowl. Discov. 13(1): 1-10 (2006) |
| 73 | EE | Samuel A. Danziger,
Sanjay Joshua Swamidass,
Jue Zeng,
Lawrence R. Dearth,
Qiang Lu,
Jonathan H. Chen,
Jianlin Cheng,
Vinh P. Hoang,
Hiroto Saigo,
Ray Luo,
Pierre Baldi,
Rainer K. Brachmann,
Richard H. Lathrop:
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.
IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 114-125 (2006) |
| 72 | EE | Gianluca Pollastri,
Alessandro Vullo,
Paolo Frasconi,
Pierre Baldi:
Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.
Journal of Computational Biology 13(3): 631-650 (2006) |
| 71 | EE | Cristina Videira Lopes,
Amir Haghighat,
Atri Mandal,
Tony Givargis,
Pierre Baldi:
Localization of off-the-shelf mobile devices using audible sound: architectures, protocols and performance assessment.
Mobile Computing and Communications Review 10(2): 38-50 (2006) |
| 2005 |
|---|
| 70 | EE | Laurent Itti,
Pierre Baldi:
A Principled Approach to Detecting Surprising Events in Video.
CVPR (1) 2005: 631-637 |
| 69 | EE | Liva Ralaivola,
Lin Wu,
Pierre Baldi:
SVM and pattern-enriched common fate graphs for the game of go.
ESANN 2005: 485-490 |
| 68 | EE | Raja Jurdak,
Pierre Baldi,
Cristina Videira Lopes:
State-Driven Energy Optimization in Wireless Sensor Networks.
ICW/ICHSN/ICMCS/SENET 2005: 356-363 |
| 67 | EE | Sanjay Joshua Swamidass,
Jonathan H. Chen,
Jocelyne Bruand,
Peter Phung,
Liva Ralaivola,
Pierre Baldi:
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.
ISMB (Supplement of Bioinformatics) 2005: 359-368 |
| 66 | EE | Jianlin Cheng,
Pierre Baldi:
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms.
ISMB (Supplement of Bioinformatics) 2005: 75-84 |
| 65 | EE | Laurent Itti,
Pierre Baldi:
Bayesian Surprise Attracts Human Attention.
NIPS 2005 |
| 64 | EE | Sanjay Joshua Swamidass,
Pierre Baldi:
Statistical Distribution of Chemical Fingerprints.
WILF 2005: 11-18 |
| 63 | EE | Jonathan H. Chen,
Sanjay Joshua Swamidass,
Yimeng Dou,
Jocelyne Bruand,
Pierre Baldi:
ChemDB: a public database of small molecules and related chemoinformatics resources.
Bioinformatics 21(22): 4133-4139 (2005) |
| 62 | EE | Steven E. Hampson,
B. S. Gaut,
Pierre Baldi:
Statistical detection of chromosomal homology using shared-gene density alone.
Bioinformatics 21(8): 1339-1348 (2005) |
| 61 | EE | Jianlin Cheng,
Michael J. Sweredoski,
Pierre Baldi:
Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.
Data Min. Knowl. Discov. 11(3): 213-222 (2005) |
| 60 | EE | Jianlin Cheng,
Lucas Scharenbroich,
Pierre Baldi,
Eric Mjolsness:
Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology.
IEEE Intelligent Systems 20(3): 68-75 (2005) |
| 59 | EE | Suman Sundaresh,
She-pin Hung,
G. Wesley Hatfield,
Pierre Baldi:
How noisy and replicable are DNA microarray data?
IJBRA 1(1): 31-50 (2005) |
| 58 | EE | Pierre Baldi,
Michal Rosen-Zvi:
On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks.
Neural Networks 18(8): 1080-1086 (2005) |
| 57 | EE | Liva Ralaivola,
Sanjay Joshua Swamidass,
Hiroto Saigo,
Pierre Baldi:
Graph kernels for chemical informatics.
Neural Networks 18(8): 1093-1110 (2005) |
| 56 | EE | Marty C. Brandon,
Marie T. Lott,
Kevin Cuong Nguyen,
Syawal Spolim,
Shamkant B. Navathe,
Pierre Baldi,
Douglas C. Wallace:
MITOMAP: a human mitochondrial genome database - 2004 update.
Nucleic Acids Research 33(Database-Issue): 611-613 (2005) |
| 55 | EE | Jianlin Cheng,
Arlo Z. Randall,
Michael J. Sweredoski,
Pierre Baldi:
SCRATCH: a protein structure and structural feature prediction server.
Nucleic Acids Research 33(Web-Server-Issue): 72-76 (2005) |
| 54 | EE | Raja Jurdak,
Pierre Baldi,
Cristina Videira Lopes:
U-MAC: a proactive and adaptive UWB medium access control protocol.
Wireless Communications and Mobile Computing 5(5): 551-566 (2005) |
| 2004 |
|---|
| 53 | EE | Raja Jurdak,
Cristina Videira Lopes,
Pierre Baldi:
An Acoustic Identification Scheme for Location Systems.
ICPS 2004: 61-70 |
| 52 | EE | Pierre Baldi,
Jianlin Cheng,
Alessandro Vullo:
Large-Scale Prediction of Disulphide Bond Connectivity.
NIPS 2004 |
| 51 | EE | Arlo Z. Randall,
Pierre Baldi,
Luis P. Villarreal:
Structural proteomics of the poxvirus family.
Artificial Intelligence in Medicine 31(2): 105-115 (2004) |
| 50 | EE | Yimeng Dou,
Pierre-François Baisnée,
Gianluca Pollastri,
Yann Pécout,
James Nowick,
Pierre Baldi:
ICBS: a database of interactions between protein chains mediated by ?-sheet formation.
Bioinformatics 20(16): 2767-2777 (2004) |
| 49 | EE | Raja Jurdak,
Cristina Videira Lopes,
Pierre Baldi:
A survey, classification and comparative analysis of medium access control protocols for ad hoc networks.
IEEE Communications Surveys and Tutorials 6(1-4): 2-16 (2004) |
| 48 | EE | Yann Guermeur,
Gianluca Pollastri,
André Elisseeff,
Dominique Zelus,
Hélène Paugam-Moisy,
Pierre Baldi:
Combining protein secondary structure prediction models with ensemble methods of optimal complexity.
Neurocomputing 56: 305-327 (2004) |
| 2003 |
|---|
| 47 | | Pierre Baldi,
Paolo Frasconi,
Padhraic Smyth:
Modeling the Internet and the Web: Probabilistic Method and Algorithms
John Wiley 2003 |
| 46 | EE | Pierre Baldi:
Machine Learning Methods for Computational Proteomics and Beyond.
Canadian Conference on AI 2003: 8 |
| 45 | EE | Pierre Baldi,
Gianluca 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) |
| 2002 |
|---|
| 44 | | Gianluca Pollastri,
Pierre Baldi:
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners.
ISMB 2002: 62-70 |
| 43 | EE | Gianluca Pollastri,
Pierre Baldi,
Alessandro Vullo,
Paolo Frasconi:
Prediction of Protein Topologies Using Generalized IOHMMS and RNNs.
NIPS 2002: 1449-1456 |
| 42 | | Steven Hampson,
Dennis F. Kibler,
Pierre Baldi:
Distribution patterns of over-represented k-mers in non-coding yeast DNA.
Bioinformatics 18(4): 513-528 (2002) |
| 41 | | Pierre-François Baisnée,
Steven Hampson,
Pierre Baldi:
Why are complementary DNA strands symmetric?
Bioinformatics 18(8): 1021-1033 (2002) |
| 40 | EE | Pierre Baldi,
Gianluca Pollastri:
A Machine-Learning Strategy for Protein Analysis.
IEEE Intelligent Systems 17(2): 28-35 (2002) |
| 2001 |
|---|
| 39 | | Gianluca Pollastri,
Pierre Baldi,
Piero Fariselli,
Rita Casadio:
Improved prediction of the number of residue contacts in proteins by recurrent neural networks.
ISMB (Supplement of Bioinformatics) 2001: 234-242 |
| 38 | | Pierre Baldi,
Søren Brunak:
Bioethics, Fiction Science, and the Future of Mankind - Session Introduction.
Pacific Symposium on Biocomputing 2001 |
| 37 | EE | Pierre Baldi,
Søren Brunak,
Paolo Frasconi,
Gianluca Pollastri,
Giovanni Soda:
Bidirectional Dynamics for Protein Secondary Structure Prediction.
Sequence Learning 2001: 80-104 |
| 36 | | Pierre-François Baisnée,
Pierre Baldi,
Søren Brunak,
Anders Gorm Pedersen:
Flexibility of the genetic code with respect to DNA structure.
Bioinformatics 17(3): 237-248 (2001) |
| 35 | | Pierre Baldi,
Anthony 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) |
| 2000 |
|---|
| 34 | | Steven Hampson,
Pierre Baldi,
Dennis F. Kibler,
Suzanne B. Sandmeyer:
Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods.
ISMB 2000: 190-201 |
| 33 | | Pierre Baldi,
Gianluca Pollastri,
Claus A. F. Andersen,
Søren Brunak:
Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks.
ISMB 2000: 25-36 |
| 32 | | Pierre Baldi,
Pierre-François Baisnée:
Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths.
Bioinformatics 16(10): 865-889 (2000) |
| 31 | | Pierre Baldi:
On the convergence of a clustering algorithm for protein-coding regions in microbial genomes.
Bioinformatics 16(4): 367-371 (2000) |
| 30 | | Pierre Baldi,
Søren Brunak,
Yves Chauvin,
Claus A. F. Andersen,
Henrik Nielsen:
Assessing the accuracy of prediction algorithms for classification: an overview.
Bioinformatics 16(5): 412-424 (2000) |
| 1999 |
|---|
| 29 | | Pierre Baldi,
Søren Brunak,
Yves Chauvin,
Anders Gorm Pedersen:
Structural basis for triplet repeat disorders: a computational analysis.
Bioinformatics 15(11): 918-929 (1999) |
| 28 | | Pierre Baldi,
Søren Brunak,
Paolo Frasconi,
Giovanni Soda,
Gianluca Pollastri:
Exploiting the past and the future in protein secondary structure prediction.
Bioinformatics 15(11): 937-946 (1999) |
| 27 | EE | Anders Gorm Pedersen,
Pierre Baldi,
Yves Chauvin,
Søren Brunak:
The Biology of Eukaryotic Promoter Prediction - A Review.
Computers & Chemistry 23(3-4): 191-207 (1999) |
| 1998 |
|---|
| 26 | | Pierre Baldi,
Søren Brunak,
Yves Chauvin,
Anders Gorm Pedersen:
Computational Applications of DNA Structural Scales.
ISMB 1998: 35-42 |
| 25 | | Pierre Baldi,
Michael C. Vanier,
James M. Bower:
On the Use of Bayesian Methods for Evaluating Compartmental Neural Models.
Journal of Computational Neuroscience 5(3): 285-314 (1998) |
| 1997 |
|---|
| 24 | EE | Pierre Baldi:
Probabilistic Models of Neuronal Spike Trains.
Summer School on Neural Networks 1997: 198-228 |
| 1996 |
|---|
| 23 | | Anders Gorm Pedersen,
Pierre Baldi,
Søren Brunak,
Yves Chauvin:
Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models.
ISMB 1996: 182-191 |
| 1995 |
|---|
| 22 | | Pierre Baldi,
Søren Brunak,
Yves Chauvin,
Jacob Engelbrecht,
Anders Krogh:
Periodic Sequence Patterns in Human Exons.
ISMB 1995: 30-38 |
| 21 | | Pierre Baldi,
Yves Chauvin:
Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures.
ISMB 1995: 39-47 |
| 20 | EE | Pierre Baldi,
Kurt Hornik:
Universal Approximnation and Learning of Trajectories Using Oscillators.
NIPS 1995: 451-457 |
| 19 | | Pierre Baldi:
Substitution Matrices and Hidden Markov Models.
Journal of Computational Biology 2(3): 487-491 (1995) |
| 1994 |
|---|
| 18 | EE | Padhraic Smyth,
Usama M. Fayyad,
Michael C. Burl,
Pietro Perona,
Pierre Baldi:
Inferring Ground Truth from Subjective Labelling of Venus Images.
NIPS 1994: 1085-1092 |
| 17 | | Pierre Baldi,
Yves Chauvin:
Hidden Markov Models of the G-Protein-Coupled Receptor Family.
Journal of Computational Biology 1(4): 311-336 (1994) |
| 16 | EE | Pierre Baldi,
Yves Chauvin:
Smooth On-Line Learning Algorithms for Hidden Markov Models.
Neural Computation 6(2): 307-318 (1994) |
| 1993 |
|---|
| 15 | EE | Pierre Baldi,
Søren Brunak,
Yves Chauvin,
Jacob Engelbrecht,
Anders Krogh:
Hidden Markov Models for Human Genes.
NIPS 1993: 761-768 |
| 14 | | Pierre Baldi,
Santosh S. Venkatesh:
Random interactions in higher order neural networks.
IEEE Transactions on Information Theory 39(1): 274- (1993) |
| 13 | EE | Pierre Baldi,
Yves Chauvin:
Neural Networks for Fingerprint Recognition.
Neural Computation 5(3): 402-418 (1993) |
| 1992 |
|---|
| 12 | EE | Pierre Baldi,
Yves Chauvin,
Tim Hunkapiller,
Marcella A. McClure:
Hidden Markov Models in Molecular Biology: New Algorithms and Applications.
NIPS 1992: 747-754 |
| 1991 |
|---|
| 11 | EE | Santosh S. Venkatesh,
Pierre Baldi:
Programmed interactions in higher-order neural networks: Maximal capacity.
J. Complexity 7(3): 316-337 (1991) |
| 10 | EE | Santosh S. Venkatesh,
Pierre Baldi:
Programmed interactions in higher-order neural networks: The outer-product algorithm.
J. Complexity 7(4): 443-479 (1991) |
| 1990 |
|---|
| 9 | EE | Pierre Baldi:
Computing with Arrays of Bell-Shaped and Sigmoid Functions.
NIPS 1990: 735-742 |
| 1989 |
|---|
| 8 | EE | Pierre Baldi,
Yosef Rinott,
Charles Stein:
On the Distribution of the Number of Local Minima of a Random Function on a Graph.
NIPS 1989: 727-732 |
| 7 | EE | Amir F. Atiya,
Pierre Baldi:
Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis.
Int. J. Neural Syst. 1(2): 103-124 (1989) |
| 6 | EE | Pierre Baldi,
Kurt Hornik:
Neural networks and principal component analysis: Learning from examples without local minima.
Neural Networks 2(1): 53-58 (1989) |
| 1988 |
|---|
| 5 | EE | Pierre Baldi:
Linear Learning: Landscapes and Algorithms.
NIPS 1988: 65-72 |
| 4 | | Pierre Baldi:
Neural networks, orientations of the hypercube, and algebraic threshold functions.
IEEE Transactions on Information Theory 34(3): 523-530 (1988) |
| 3 | | Pierre Baldi:
Group Actions and Learning for a Family of Automata.
J. Comput. Syst. Sci. 36(1): 1-15 (1988) |
| 2 | | Pierre Baldi:
Neural Networks, Acyclic Orientations of the Hypercube, and Sets of Orthogonal Vectors.
SIAM J. Discrete Math. 1(1): 1-13 (1988) |
| 1987 |
|---|
| 1 | EE | Pierre Baldi,
Santosh S. Venkatesh:
On Properties of Networks of Neuron-Like Elements.
NIPS 1987: 41-51 |
