Bruce A. Shapiro

According to our database1, Bruce A. Shapiro authored at least 39 papers between 1984 and 2015.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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PhD thesis 
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Links

On csauthors.net:

Bibliography

2015
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.
BMC Bioinformatics, 2015

2014
High Performance Computing Studies of RNA Nanotubes.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2012
A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection.
J. Bioinformatics and Computational Biology, 2012

Pre-miRNA classification via combinatorial feature mining and boosting.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
Data mining of functional RNA structures in genomic sequences.
Wiley Interdisc. Rew.: Data Mining and Knowledge Discovery, 2011

2010
CyloFold: secondary structure prediction including pseudoknots.
Nucleic Acids Research, 2010

Characterization of structural features for small regulatory RNAs in Escherichia coli genomes.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2008
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.
Nucleic Acids Research, 2008

2007
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Research, 2007

Toward an Integrated RNA Motif Database.
Proceedings of the Data Integration in the Life Sciences, 4th International Workshop, 2007

2006
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Research, 2006

2003
A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2003

Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm.
Computational Biology and Genome Informatics, 2003

2002
Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining.
IEEE Trans. Knowl. Data Eng., 2002

2001
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation.
Bioinformatics, 2001

Determination of RNA folding pathway functional intermediates using a massively parallel genetic algorithm (abstract of invited talk).
BIOKDD, 2001

2000
An Index Structure for Data Mining and Clustering.
Knowl. Inf. Syst., 2000

An Approximate Search Engine for Structural Databases.
Proceedings of the 2000 ACM SIGMOD International Conference on Management of Data, 2000

1999
New Techniques for DNA Sequence Classification.
Journal of Computational Biology, 1999

Stem Trace: an interactive visual tool for comparative RNA structure analysis.
Bioinformatics, 1999

Sisyphus and Ulysses.
Proceedings of the 26th Annual Conference on Computer Graphics and Interactive Techniques, 1999

Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering.
Proceedings of the Fifth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 1999

RNA Structure Analysis: A Multifaceted Approach.
Pattern Discovery in Biomolecular Data, 1999

1998
Optimization of an RNA Folding Algorithm for Parallel Architectures.
Parallel Computing, 1998

An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees.
IEEE Trans. Pattern Anal. Mach. Intell., 1998

1997
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
Computer Applications in the Biosciences, 1997

Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
Computer Applications in the Biosciences, 1997

Automated Discovery of Active Motifs in Three Dimensional Molecules.
Proceedings of the Third International Conference on Knowledge Discovery and Data Mining (KDD-97), 1997

1996
An annealing mutation operator in the genetic algorithms for RNA folding.
Computer Applications in the Biosciences, 1996

Automated Discovery of Active Motifs in Multiple RNA Secondary Structures.
Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96), 1996

1995
Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction.
IJHPCA, 1995

1994
A massively parallel genetic algorithm for RNA secondary structure prediction.
The Journal of Supercomputing, 1994

Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results.
Proceedings of the 1994 ACM SIGMOD International Conference on Management of Data, 1994

1990
Comparing multiple RNA secondary structures using tree comparisons.
Computer Applications in the Biosciences, 1990

A computational procedure for assessing the significance of RNA secondary structure.
Computer Applications in the Biosciences, 1990

1989
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.
Computer Applications in the Biosciences, 1989

1988
An algorithm for comparing multiple RNA secondary structures.
Computer Applications in the Biosciences, 1988

1986
A sequence analysis system encompassing rules for DNA helical distortion.
Nucleic Acids Research, 1986

1984
Generating non-overlapping displays of nucleic acid secondary structure.
Nucleic Acids Research, 1984


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