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)

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)

An algorithm for comparing multiple RNA secondary structures. - Bruce A. Shapiro (Comput. Appl. Biosci., 1988)

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)

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)

Comparing multiple RNA secondary structures using tree comparisons. - Bruce A. Shapiro; Kaizhong Zhang (Comput. Appl. Biosci., 1990)

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 (SIGMOD Conference, 1994)

A massively parallel genetic algorithm for RNA secondary structure prediction. - Bruce A. Shapiro; Joseph Navetta (J. Supercomput., 1994)

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)

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 (KDD, 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 Three Dimensional Molecules. - Xiong Wang; Jason Tsong-Li Wang; Dennis E. Shasha; Bruce A. Shapiro; Sitaram Dikshitulu; Isidore Rigoutsos; Kaizhong Zhang (KDD, 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)

Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. - Bruce A. Shapiro; Jin Chu Wu (Comput. Appl. Biosci., 1997)

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)

Optimization of an RNA Folding Algorithm for Parallel Architectures. - Jih-Hsiang Chen; Shu-Yun Le; Bruce A. Shapiro; Jacob V. Maizel (Parallel Comput., 1998)

RNA Structure Analysis: A Multifaceted Approach. - Bruce A. Shapiro; Wojciech Kasprzak; Jin Chu Wu; Kathleen M. Currey (Pattern Discovery in Biomolecular Data, 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 (KDD, 1999)

Sisyphus and Ulysses. - Jean-Pierre Hébert; Bruce A. Shapiro; Denny Bollay; David Bothman; Scott Masch (SIGGRAPH Electronic Art and Animation Catalog, 1999)

Stem Trace: an interactive visual tool for comparative RNA structure analysis. - Wojciech Kasprzak; Bruce A. Shapiro (Bioinform., 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)

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 (SIGMOD Conference, 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)

Determination of RNA folding pathway functional intermediates using a massively parallel genetic algorithm (abstract of invited talk). - Bruce A. Shapiro; David Bengali; Wojciech Kasprzak (BIOKDD, 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)

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)

Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm. - Bruce A. Shapiro; David Bengali; Wojciech Kasprzak; Jin Chu Wu (Computational Biology and Genome Informatics, 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 (METMBS, 2003)

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)

Toward an Integrated RNA Motif Database. - Jason Tsong-Li Wang; Dongrong Wen; Bruce A. Shapiro; Katherine G. Herbert; Jing Li; Kaushik Ghosh (DILS, 2007)

RADAR: a web server for RNA data analysis and research. - Mugdha Khaladkar; Vivian Bellofatto; Jason Tsong-Li Wang; Bin Tian 002; Bruce A. Shapiro (Nucleic Acids Res., 2007)

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)

Characterization of structural features for small regulatory RNAs in Escherichia coli genomes. - Shu-Yun Le; Bruce A. Shapiro (BIBM, 2010)

CyloFold: secondary structure prediction including pseudoknots. - Eckart Bindewald; Tanner Kluth; Bruce A. Shapiro (Nucleic Acids Res., 2010)

Data mining of functional RNA structures in genomic sequences. - Shu-Yun Le; Bruce A. Shapiro (WIREs Data Mining Knowl. Discov., 2011)

Pre-miRNA classification via combinatorial feature mining and boosting. - Ling Zhong; Jason T. L. Wang; Dongrong Wen; Bruce A. Shapiro (BIBM, 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)

High Performance Computing Studies of RNA Nanotubes. - Shyam R. Badu; Roderik Melnik; Maxim V. Paliy; Sanjay Prabhakar; Ali Sebetci; Bruce A. Shapiro (IWBBIO, 2014)

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)

RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. - Jacob S. Lu; Eckart Bindewald; Wojciech Kasprzak; Bruce A. Shapiro (Bioinform., 2018)