Bruce A. Shapiro

Publication Activity (10 Years)

Years Active: 1984-2018
Publications (10 Years): 2

Top Topics

Weak Classifiers

Computational Methods

Solvent Accessibility

Top Venues

Publications

Jacob S. Lu, Eckart Bindewald, Wojciech Kasprzak, Bruce A. Shapiro
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinform. 34 (24) (2018)
Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. BMC Bioinform. 16 (2015)
Shyam R. Badu, Roderik Melnik, Maxim V. Paliy, Sanjay Prabhakar, Ali Sebetci, Bruce A. Shapiro
High Performance Computing Studies of RNA Nanotubes. IWBBIO (2014)
Ling Zhong, Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro
Pre-miRNA classification via combinatorial feature mining and boosting. BIBM (2012)
Lei Hua, Jason T. L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro, Kaizhong Zhang
A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection. J. Bioinform. Comput. Biol. 10 (4) (2012)
Shu-Yun Le, Bruce A. Shapiro
Data mining of functional RNA structures in genomic sequences. WIREs Data Mining Knowl. Discov. 1 (1) (2011)
Shu-Yun Le, Bruce A. Shapiro
Characterization of structural features for small regulatory RNAs in Escherichia coli genomes. BIBM (2010)
Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro
CyloFold: secondary structure prediction including pseudoknots. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res. 36 (Database-Issue) (2008)
Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian, Bruce A. Shapiro
RADAR: a web server for RNA data analysis and research. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Jason Tsong-Li Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li, Kaushik Ghosh
Toward an Integrated RNA Motif Database. DILS (2007)
Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Moon K. Kim, Robert L. Jernigan, Bruce A. Shapiro, Gregory S. Chirikjian
A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method. METMBS (2003)
Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Isidore Rigoutsos, Kaizhong Zhang
Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining. IEEE Trans. Knowl. Data Eng. 14 (4) (2002)
Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. Bioinform. 17 (1) (2001)
Bruce A. Shapiro, David Bengali, Wojciech Kasprzak
Determination of RNA folding pathway functional intermediates using a massively parallel genetic algorithm (abstract of invited talk). BIOKDD (2001)
Xiong Wang, Jason Tsong-Li Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang
An Index Structure for Data Mining and Clustering. Knowl. Inf. Syst. 2 (2) (2000)
Jason Tsong-Li Wang, Xiong Wang, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang, Xinhuan Zheng, Qicheng Ma, Zasha Weinberg
An Approximate Search Engine for Structural Databases. SIGMOD Conference (2000)
Jason Tsong-Li Wang, Xiong Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang
Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering. KDD (1999)
Wojciech Kasprzak, Bruce A. Shapiro
Stem Trace: an interactive visual tool for comparative RNA structure analysis. Bioinform. 15 (1) (1999)
Jason Tsong-Li Wang, Steve Rozen, Bruce A. Shapiro, Dennis E. Shasha, Zhiyuan Wang, Maisheng Yin
New Techniques for DNA Sequence Classification. J. Comput. Biol. 6 (2) (1999)
Jean-Pierre Hébert, Bruce A. Shapiro, Denny Bollay, David Bothman, Scott Masch
Sisyphus and Ulysses. SIGGRAPH Electronic Art and Animation Catalog (1999)
Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Kathleen M. Currey
An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees. IEEE Trans. Pattern Anal. Mach. Intell. 20 (8) (1998)
Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Jacob V. Maizel
Optimization of an RNA Folding Algorithm for Parallel Architectures. Parallel Comput. 24 (11) (1998)
Bruce A. Shapiro, Jin Chu Wu
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. Comput. Appl. Biosci. 13 (4) (1997)
Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang
Automated Discovery of Active Motifs in Three Dimensional Molecules. KDD (1997)
Kathleen M. Currey, Bruce A. Shapiro
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm. Comput. Appl. Biosci. 13 (1) (1997)
Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Chia-Yo Chang
Automated Discovery of Active Motifs in Multiple RNA Secondary Structures. KDD (1996)
Bruce A. Shapiro, Jin Chu Wu
An annealing mutation operator in the genetic algorithms for RNA folding. Comput. Appl. Biosci. 12 (3) (1996)
Bruce A. Shapiro, Jih-Hsiang Chen, Tim Busse, Joseph Navetta, Wojciech Kasprzak, Jacob V. Maizel Jr.
Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction. Int. J. High Perform. Comput. Appl. 9 (1) (1995)
Jason Tsong-Li Wang, Gung-Wei Chirn, Thomas G. Marr, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang
Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results. SIGMOD Conference (1994)
Bruce A. Shapiro, Joseph Navetta
A massively parallel genetic algorithm for RNA secondary structure prediction. J. Supercomput. 8 (3) (1994)
Bruce A. Shapiro, Kaizhong Zhang
Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6 (4) (1990)
Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Kathleen M. Currey, Jacob V. Maizel
A computational procedure for assessing the significance of RNA secondary structure. Comput. Appl. Biosci. 6 (1) (1990)
Shu-Yun Le, John Owens, Ruth Nussinov, Jih-Hsiang Chen, Bruce A. Shapiro, Jacob V. Maizel
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus. Comput. Appl. Biosci. 5 (3) (1989)
Bruce A. Shapiro
An algorithm for comparing multiple RNA secondary structures. Comput. Appl. Biosci. 4 (3) (1988)
Bruce A. Shapiro, Ruth Nussinov, Lewis E. Lipkin, Jacob V. Maizel
A sequence analysis system encompassing rules for DNA helical distortion. Nucleic Acids Res. 14 (1) (1986)
Bruce A. Shapiro, Jacob V. Maizel, Lewis E. Lipkin, Kathleen M. Currey, Colin G. Whitney
Generating non-overlapping displays of nucleic acid secondary structure. Nucleic Acids Res. 12 (1) (1984)