Bruce A. Shapiro

41 papers A* 3Journal 26Unranked 9
YearRankTypeTitle / Venue / Authors
2018 J jnl
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.
Bioinform.
Jacob S. Lu, Eckart Bindewald, Wojciech Kasprzak, Bruce A. Shapiro
2015 J jnl
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.
BMC Bioinform.
Yang Song, Lei Hua, Bruce A. Shapiro, Jason Tsong-Li Wang
2014 — conf
High Performance Computing Studies of RNA Nanotubes.
IWBBIO
Shyam R. Badu, Roderik Melnik, Maxim V. Paliy, Sanjay Prabhakar, Ali Sebetci, Bruce A. Shapiro
2012 J jnl
A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection.
J. Bioinform. Comput. Biol.
Lei Hua, Jason T. L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro, Kaizhong Zhang
2012 — conf
Pre-miRNA classification via combinatorial feature mining and boosting.
BIBM
Ling Zhong, Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro
2011 J jnl
Data mining of functional RNA structures in genomic sequences.
WIREs Data Mining Knowl. Discov.
Shu-Yun Le, Bruce A. Shapiro
2010 — conf
Characterization of structural features for small regulatory RNAs in Escherichia coli genomes.
BIBM
Shu-Yun Le, Bruce A. Shapiro
2010 J jnl
CyloFold: secondary structure prediction including pseudoknots.
Nucleic Acids Res.
Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro
2008 J jnl
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.
Nucleic Acids Res.
Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, Bruce A. Shapiro
2007 J jnl
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res.
Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian, Bruce A. Shapiro
2007 — conf
Toward an Integrated RNA Motif Database.
DILS
Jason Tsong-Li Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li, Kaushik Ghosh
2006 J jnl
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Res.
Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro
2003 — conf
A Study of Conformational Changes in Macromolecules: The Coarse-Grained Elastic Network Interpolation Method.
METMBS
Moon K. Kim, Robert L. Jernigan, Bruce A. Shapiro, Gregory S. Chirikjian
2003 — ch.
Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm.
Computational Biology and Genome Informatics
Bruce A. Shapiro, David Bengali, Wojciech Kasprzak, Jin Chu Wu
2002 J jnl
Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining.
IEEE Trans. Knowl. Data Eng.
Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Isidore Rigoutsos, Kaizhong Zhang
2001 — conf
Determination of RNA folding pathway functional intermediates using a massively parallel genetic algorithm (abstract of invited talk).
BIOKDD
Bruce A. Shapiro, David Bengali, Wojciech Kasprzak
2001 J jnl
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation.
Bioinform.
Bruce A. Shapiro, Jin Chu Wu, David Bengali, Mark J. Potts
2000 — conf
An Approximate Search Engine for Structural Databases.
SIGMOD Conference
Jason Tsong-Li Wang, Xiong Wang, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang, Xinhuan Zheng, Qicheng Ma, Zasha Weinberg
2000 J jnl
An Index Structure for Data Mining and Clustering.
Knowl. Inf. Syst.
Xiong Wang, Jason Tsong-Li Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang
1999 A* conf
Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering.
KDD
Jason Tsong-Li Wang, Xiong Wang, King-Ip (David) Lin, Dennis E. Shasha, Bruce A. Shapiro, Kaizhong Zhang
1999 J jnl
New Techniques for DNA Sequence Classification.
J. Comput. Biol.
Jason Tsong-Li Wang, Steve Rozen, Bruce A. Shapiro, Dennis E. Shasha, Zhiyuan Wang, Maisheng Yin
1999 — book
Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications
Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha
1999 — ch.
RNA Structure Analysis: A Multifaceted Approach.
Pattern Discovery in Biomolecular Data
Bruce A. Shapiro, Wojciech Kasprzak, Jin Chu Wu, Kathleen M. Currey
1999 — conf
Sisyphus and Ulysses.
SIGGRAPH Electronic Art and Animation Catalog
Jean-Pierre Hébert, Bruce A. Shapiro, Denny Bollay, David Bothman, Scott Masch
1999 J jnl
Stem Trace: an interactive visual tool for comparative RNA structure analysis.
Bioinform.
Wojciech Kasprzak, Bruce A. Shapiro
1998 J jnl
An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees.
IEEE Trans. Pattern Anal. Mach. Intell.
Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Kathleen M. Currey
1998 J jnl
Optimization of an RNA Folding Algorithm for Parallel Architectures.
Parallel Comput.
Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Jacob V. Maizel
1997 A* conf
Automated Discovery of Active Motifs in Three Dimensional Molecules.
KDD
Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang
1997 J jnl
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
Comput. Appl. Biosci.
Bruce A. Shapiro, Jin Chu Wu
1997 J jnl
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
Comput. Appl. Biosci.
Kathleen M. Currey, Bruce A. Shapiro
1996 J jnl
An annealing mutation operator in the genetic algorithms for RNA folding.
Comput. Appl. Biosci.
Bruce A. Shapiro, Jin Chu Wu
1996 A* conf
Automated Discovery of Active Motifs in Multiple RNA Secondary Structures.
KDD
Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang, Chia-Yo Chang
1995 J jnl
Optimization and Performance Analysis of a Massively Parallel Dynamic Programming Algorithm for Rna Secondary Structure Prediction.
Int. J. High Perform. Comput. Appl.
Bruce A. Shapiro, Jih-Hsiang Chen, Tim Busse, Joseph Navetta, Wojciech Kasprzak, Jacob V. Maizel Jr.
1994 J jnl
A massively parallel genetic algorithm for RNA secondary structure prediction.
J. Supercomput.
Bruce A. Shapiro, Joseph Navetta
1994 — conf
Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results.
SIGMOD Conference
Jason Tsong-Li Wang, Gung-Wei Chirn, Thomas G. Marr, Bruce A. Shapiro, Dennis E. Shasha, Kaizhong Zhang
1990 J jnl
A computational procedure for assessing the significance of RNA secondary structure.
Comput. Appl. Biosci.
Jih-Hsiang Chen, Shu-Yun Le, Bruce A. Shapiro, Kathleen M. Currey, Jacob V. Maizel
1990 J jnl
Comparing multiple RNA secondary structures using tree comparisons.
Comput. Appl. Biosci.
Bruce A. Shapiro, Kaizhong Zhang
1989 J jnl
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.
Comput. Appl. Biosci.
Shu-Yun Le, John Owens, Ruth Nussinov, Jih-Hsiang Chen, Bruce A. Shapiro, Jacob V. Maizel
1988 J jnl
An algorithm for comparing multiple RNA secondary structures.
Comput. Appl. Biosci.
Bruce A. Shapiro
1986 J jnl
A sequence analysis system encompassing rules for DNA helical distortion.
Nucleic Acids Res.
Bruce A. Shapiro, Ruth Nussinov, Lewis E. Lipkin, Jacob V. Maizel
1984 J jnl
Generating non-overlapping displays of nucleic acid secondary structure.
Nucleic Acids Res.
Bruce A. Shapiro, Jacob V. Maizel, Lewis E. Lipkin, Kathleen M. Currey, Colin G. Whitney