Bruce A. Shapiro

According to our database, Bruce A. Shapiro authored at least 40 papers between 1984 and 2018.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2018

RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.

Jacob S. Lu, Eckart Bindewald, Wojciech Kasprzak, Bruce A. Shapiro

Bioinform., 2018

2015

Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.

Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang

BMC Bioinform., 2015

2014

High Performance Computing Studies of RNA Nanotubes.

Shyam R. Badu, Roderik Melnik, Maxim V. Paliy, Sanjay Prabhakar, Ali Sebetci, Bruce A. Shapiro

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.

Lei Hua, Jason T. L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro, Kaizhong Zhang

J. Bioinform. Comput. Biol., 2012

Pre-miRNA classification via combinatorial feature mining and boosting.

Ling Zhong, Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011

Data mining of functional RNA structures in genomic sequences.

Shu-Yun Le, Bruce A. Shapiro

WIREs Data Mining Knowl. Discov., 2011

2010

CyloFold: secondary structure prediction including pseudoknots.

Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro

Nucleic Acids Res., 2010

Characterization of structural features for small regulatory RNAs in Escherichia coli genomes.

Shu-Yun Le, Bruce A. Shapiro

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.

Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro

Nucleic Acids Res., 2008

2007

RADAR: a web server for RNA data analysis and research.

Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian, Bruce A. Shapiro

Nucleic Acids Res., 2007

Toward an Integrated RNA Motif Database.

Jason Tsong-Li Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li, Kaushik Ghosh

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.

Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro

Nucleic Acids Res., 2006

2003

A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method.

Moon K. Kim, Robert L. Jernigan, Bruce A. Shapiro, Gregory S. Chirikjian

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.

Bruce A. Shapiro, David Bengali, Wojciech Kasprzak, Jin Chu Wu

Proceedings of the Computational Biology and Genome Informatics, 2003

2002

Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining.

Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Isidore Rigoutsos, Kaizhong Zhang

IEEE Trans. Knowl. Data Eng., 2002

2001

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

Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts

Bioinform., 2001

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

Bruce A. Shapiro, David Bengali, Wojciech Kasprzak

Proceedings of the ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2001), 2001

2000

An Index Structure for Data Mining and Clustering.

Xiong Wang, Jason Tsong-Li Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang

Knowl. Inf. Syst., 2000

An Approximate Search Engine for Structural Databases.

Jason Tsong-Li Wang, Xiong Wang, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang, Xinhuan Zheng, Qicheng Ma, Zasha Weinberg

Proceedings of the 2000 ACM SIGMOD International Conference on Management of Data, 2000

1999

New Techniques for DNA Sequence Classification.

Jason Tsong-Li Wang, Steve Rozen, Bruce A. Shapiro, Dennis E. Shasha, Zhiyuan Wang, Maisheng Yin

J. Comput. Biol., 1999

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

Wojciech Kasprzak, Bruce A. Shapiro

Bioinform., 1999

Sisyphus and Ulysses.

Jean-Pierre Hébert, Bruce A. Shapiro, Denny Bollay, David Bothman, Scott Masch

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.

Jason Tsong-Li Wang, Xiong Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang

Proceedings of the Fifth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 1999

RNA Structure Analysis: A Multifaceted Approach.

Bruce A. Shapiro, Wojciech Kasprzak, Jin Chu Wu, Kathleen M. Currey

Proceedings of the Pattern Discovery in Biomolecular Data: Tools, 1999

1998

Optimization of an RNA Folding Algorithm for Parallel Architectures.

Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Jacob V. Maizel

Parallel Comput., 1998

An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees.

Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Kathleen M. Currey

IEEE Trans. Pattern Anal. Mach. Intell., 1998

1997

Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.

Bruce A. Shapiro, Jin Chu Wu

Comput. Appl. Biosci., 1997

Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.

Kathleen M. Currey, Bruce A. Shapiro

Comput. Appl. Biosci., 1997

Automated Discovery of Active Motifs in Three Dimensional Molecules.

Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang

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.

Bruce A. Shapiro, Jin Chu Wu

Comput. Appl. Biosci., 1996

Automated Discovery of Active Motifs in Multiple RNA Secondary Structures.

Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Chia-Yo Chang

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.

Bruce A. Shapiro, Jih-Hsiang Chen, Tim Busse, Joseph Navetta, Wojciech Kasprzak, Jacob V. Maizel Jr.

Int. J. High Perform. Comput. Appl., 1995

1994

A massively parallel genetic algorithm for RNA secondary structure prediction.

Bruce A. Shapiro, Joseph Navetta

J. Supercomput., 1994

Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results.

Jason Tsong-Li Wang, Gung-Wei Chirn, Thomas G. Marr, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang

Proceedings of the 1994 ACM SIGMOD International Conference on Management of Data, 1994

1990

Comparing multiple RNA secondary structures using tree comparisons.

Bruce A. Shapiro, Kaizhong Zhang

Comput. Appl. Biosci., 1990

A computational procedure for assessing the significance of RNA secondary structure.

Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Kathleen M. Currey, Jacob V. Maizel

Comput. Appl. Biosci., 1990

1989

RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.

Shu-Yun Le, John Owens, Ruth Nussinov, Jih-Hsiang Chen, Bruce A. Shapiro, Jacob V. Maizel

Comput. Appl. Biosci., 1989

1988

An algorithm for comparing multiple RNA secondary structures.

Bruce A. Shapiro

Comput. Appl. Biosci., 1988

1986

A sequence analysis system encompassing rules for DNA helical distortion.

Bruce A. Shapiro, Ruth Nussinov, Lewis E. Lipkin, Jacob V. Maizel

Nucleic Acids Res., 1986

1984

Generating non-overlapping displays of nucleic acid secondary structure.

Bruce A. Shapiro, Jacob V. Maizel, Lewis E. Lipkin, Kathleen M. Currey, Colin G. Whitney

Nucleic Acids Res., 1984