Bruce A. Shapiro

发表

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

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 2002, IEEE Trans. Knowl. Data Eng..

Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization

Kaizhong Zhang, Bruce A. Shapiro, Junilda Spirollari, 2009, Bioinformatics and biology insights.

An approximate search engine for structural databases

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 2000, SIGMOD '00.

High Performance Computing Studies of RNA Nanotubes

Bruce A. Shapiro, Shyam R. Badu, Roderik Melnik, 2014, IWBBIO.

An algorithm for comparing multiple RNA secondary structures

Bruce A. Shapiro, B. Shapiro, 1988, Comput. Appl. Biosci..

New Techniques for DNA Sequence Classification

Dennis Shasha, Steve Rozen, Jason Tsong-Li Wang, 1999, J. Comput. Biol..

Evaluating a class of distance-mapping algorithms for data mining and clustering

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 1999, KDD '99.

RNA Structure Analysis: A Multifaceted Approach

Jin Chu Wu, Bruce A. Shapiro, Wojciech Kasprzak, 1999, Pattern Discovery in Biomolecular Data.

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

Jin Chu Wu, Bruce A. Shapiro, 1997, Comput. Appl. Biosci..

A massively parallel genetic algorithm for RNA secondary structure prediction

Bruce A. Shapiro, Joseph Navetta, B. Shapiro, 1994, The Journal of Supercomputing.

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

Eckart Bindewald, Bruce A. Shapiro, Wojciech Kasprzak, 2018, Bioinform..

A computational procedure for assessing the significance of RNA secondary structure

Bruce A. Shapiro, Jih-Hsiang Chen, Shu-Yun Le, 1990, Comput. Appl. Biosci..

Pre-miRNA classification via combinatorial feature mining and boosting

Jason Tsong-Li Wang, Ling Zhong, Bruce A. Shapiro, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.

RADAR: a web server for RNA data analysis and research

Bin Tian, Bruce A. Shapiro, Vivian Bellofatto, 2007, Nucleic Acids Res..

Optimization of an RNA Folding Algorithm for Parallel Architectures

Bruce A. Shapiro, Jacob V. Maizel, Jih-H. Chen, 1998, Parallel Comput..

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

Ruth Nussinov, Bruce A. Shapiro, Jih-Hsiang Chen, 1989, Comput. Appl. Biosci..

Automated Discovery of Active Motifs in Three Dimensional Molecules

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 1997, KDD.

Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus

Bruce A. Shapiro, Wojciech K. Kasprzak, B. Shapiro, 2012 .

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

Bruce A. Shapiro, Wojciech Kasprzak, David Bengali, 2001, BIOKDD.

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

Bruce A. Shapiro, Kathleen M. Currey, B. Shapiro, 1997, Comput. Appl. Biosci..

Automated Discovery of Active Motifs in Multiple RNA Secondary Structures

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 1996, KDD.

Combinatorial pattern discovery for scientific data: some preliminary results

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 1994, SIGMOD '94.

IMPLEMENTATION A REAL TIME PICTURE PROCESSOR FOR USE IN BIOLOGIC CELL IDENTIFICATION II. HARDWARE

Peter Kaiser, Bruce A. Shapiro, Lewis E. Lipkin, 2011 .

Data mining of functional RNA structures in genomic sequences

Bruce A. Shapiro, Shu-Yun Le, S. Le, 2011, WIREs Data Mining Knowl. Discov..

CyloFold: secondary structure prediction including pseudoknots

Eckart Bindewald, Bruce A. Shapiro, Tanner Kluth, 2010, Nucleic Acids Res..

An approximate search engine for structural databases

Kaizhong Zhang, Dennis Shasha, Bruce A. Shapiro, 2000, SIGMOD 2000.

Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications

Dennis Shasha, Bruce A. Shapiro, Jason T. L. Wang, 1999 .

Comparing multiple RNA secondary structures using tree comparisons

Kaizhong Zhang, Bruce A. Shapiro, Kaizhong Zhang, 1990, Comput. Appl. Biosci..

Toward an Integrated RNA Motif Database

Jing Li, Katherine G. Herbert, Jason Tsong-Li Wang, 2007, DILS.

Sisyphus and Ulysses

Bruce A. Shapiro, Jean-Pierre Hébert, Denny Bollay, 1999, SIGGRAPH '99.

Evaluation of Selected Kissing-Loops as Building Blocks in RNA Nano Design

Bruce A. Shapiro, Taejin Kim, Robert J. Fisher, 2010 .

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

Bruce A. Shapiro, Wojciech Kasprzak, B. Shapiro, 1999, Bioinform..

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

Bruce A. Shapiro, Shu-Yun Le, S. Le, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

An Index Structure for Data Mining and Clustering

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 2000, Knowledge and Information Systems.

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

Kaizhong Zhang, Dennis Shasha, Jason Tsong-Li Wang, 1998, IEEE Trans. Pattern Anal. Mach. Intell..

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign

Eckart Bindewald, Robert Hayes, Bruce A. Shapiro, 2007, Nucleic Acids Res..

A Method for Discovering Common Patterns from Two RNA Secondary Structures and its Application to Structural Repeat Detection

Kaizhong Zhang, Xiang Ji, Lei Hua, 2012, J. Bioinform. Comput. Biol..

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

Gregory S. Chirikjian, Robert L. Jernigan, Moon K. Kim, 2003, METMBS.

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

Yang Song, Lei Hua, Jason Tsong-Li Wang, 2015, BMC Bioinformatics.

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

Bruce A. Shapiro, Jih-Hsiang Chen, Jacob V. Maizel, 1995, Int. J. High Perform. Comput. Appl..

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments

Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro, 2006, Nucleic Acids Res..

An annealing mutation operator in the genetic algorithms for RNA folding

Jin Chu Wu, Bruce A. Shapiro, B. Shapiro, 1996, Comput. Appl. Biosci..

Coarse-Grained Computational Characterization of RNA Nanocube Flexibility Correlates with Experiments

Robert L. Jernigan, Michael T. Zimmermann, Bruce A. Shapiro, 2013 .

A sequence analysis system encompassing rules for DNA helical distortion

Ruth Nussinov, Bruce A. Shapiro, Jacob V. Maizel, 1986, Nucleic Acids Res..

Generating non-overlapping displays of nucleic acid secondary structure

Bruce A. Shapiro, Jacob V. Maizel, Lewis E. Lipkin, 1984, Nucleic Acids Res..

Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm

Jin Chu Wu, Bruce A. Shapiro, Wojciech Kasprzak, 2003, Computational Biology and Genome Informatics.

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

Jin Chu Wu, Bruce A. Shapiro, David Bengali, 2001, Bioinform..

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

Bruce A. Shapiro, Wojciech K. Kasprzak, Jonathan D. Dinman, 2014, Nature.

Molecular Dynamics Simulations of the Denaturation and Refolding of an RNA Tetraloop

Bruce A. Shapiro, Buyong Ma, Wen Li, 2001, Journal of biomolecular structure & dynamics.

Bruce A. Shapiro, Christine Vogel, Daijin Ko, 2009 .

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

Bruce A. Shapiro, Wojciech Kasprzak, Yaroslava G. Yingling, 2008, Journal of Virology.

A Pseudoknot in a Preactive Form of a Viral RNA Is Part of a Structural Switch Activating Minus-Strand Synthesis

Bruce A. Shapiro, Guohua Zhang, Jiuchun Zhang, 2006, Journal of Virology.

Structural polymorphism of the HIV-1 leader region explored by computational methods

Bruce A. Shapiro, Wojciech Kasprzak, Eckart Bindewald, 2005, Nucleic acids research.

Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches.

Bruce A. Shapiro, Taejin Kim, Eckart Bindewald, 2016, Nano letters.