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ORCIDBruce A. Shapiro
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2010 – 2019
- 2018
[j26]Jacob S. Lu, Eckart Bindewald, Wojciech Kasprzak, Bruce A. Shapiro:
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinform. 34(24): 4297-4299 (2018)- 2015
- [j25]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: 39:1-39:15 (2015) - 2014
- [c12]Shyam R. Badu, Roderik Melnik, Maxim V. Paliy, Sanjay Prabhakar, Ali Sebetci, Bruce A. Shapiro:
High Performance Computing Studies of RNA Nanotubes. IWBBIO 2014: 601-607 - 2012
- [j24]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) - [c11]Ling Zhong, Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro:
Pre-miRNA classification via combinatorial feature mining and boosting. BIBM 2012: 1-4 - 2011
- [j23]Shu-Yun Le, Bruce A. Shapiro:
Data mining of functional RNA structures in genomic sequences. WIREs Data Mining Knowl. Discov. 1(1): 88-95 (2011) - 2010
- [j22]Eckart Bindewald, Tanner Kluth, Bruce A. Shapiro:
CyloFold: secondary structure prediction including pseudoknots. Nucleic Acids Res. 38(Web-Server-Issue): 368-372 (2010) - [c10]Shu-Yun Le, Bruce A. Shapiro:
Characterization of structural features for small regulatory RNAs in Escherichia coli genomes. BIBM 2010: 68-72
2000 – 2009
- 2008
- [j21]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): 392-397 (2008) - 2007
- [j20]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): 300-304 (2007) - [c9]Jason Tsong-Li Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li, Kaushik Ghosh:
Toward an Integrated RNA Motif Database. DILS 2007: 27-36 - 2006
- [j19]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): 405-411 (2006) - 2003
- [c8]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: 140-145 - [p2]Bruce A. Shapiro, David Bengali, Wojciech Kasprzak, Jin Chu Wu:
Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm. Computational Biology and Genome Informatics 2003: 1-33 - 2002
- [j18]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): 731-749 (2002) - 2001
- [j17]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): 137-148 (2001) - [c7]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: 1 - 2000
- [j16]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): 161-184 (2000) - [c6]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: 584
1990 – 1999
- 1999
- [j15]Wojciech Kasprzak, Bruce A. Shapiro:
Stem Trace: an interactive visual tool for comparative RNA structure analysis. Bioinform. 15(1): 16-31 (1999) - [j14]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): 209-218 (1999) - [c5]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: 307-311 - [c4]Jean-Pierre Hébert, Bruce A. Shapiro, Denny Bollay, David Bothman, Scott Masch:
Sisyphus and Ulysses. SIGGRAPH Electronic Art and Animation Catalog 1999: 8-9 - [p1]Bruce A. Shapiro, Wojciech Kasprzak, Jin Chu Wu, Kathleen M. Currey:
RNA Structure Analysis: A Multifaceted Approach. Pattern Discovery in Biomolecular Data 1999: 183-215 - [e1]Jason Tsong-Li Wang, Bruce A. Shapiro, Dennis E. Shasha:
Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications. Oxford University Press 1999, ISBN 0-19-511940-1 [contents] - 1998
- [j13]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): 889-895 (1998) - [j12]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): 1617-1634 (1998) - 1997
- [j11]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): 1-12 (1997) - [j10]Bruce A. Shapiro, Jin Chu Wu:
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. Comput. Appl. Biosci. 13(4): 459-471 (1997) - [c3]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: 89-95 - 1996
- [j9]Bruce A. Shapiro, Jin Chu Wu:
An annealing mutation operator in the genetic algorithms for RNA folding. Comput. Appl. Biosci. 12(3): 171-180 (1996) - [c2]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: 70-75 - 1995
- [j8]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): 29-39 (1995) - 1994
- [j7]Bruce A. Shapiro, Joseph Navetta:
A massively parallel genetic algorithm for RNA secondary structure prediction. J. Supercomput. 8(3): 195-207 (1994) - [c1]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: 115-125 - 1990
- [j6]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): 7-18 (1990) - [j5]Bruce A. Shapiro, Kaizhong Zhang:
Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci. 6(4): 309-318 (1990)
1980 – 1989
- 1989
- [j4]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): 205-210 (1989) - 1988
- [j3]Bruce A. Shapiro:
An algorithm for comparing multiple RNA secondary structures. Comput. Appl. Biosci. 4(3): 387-393 (1988) - 1986
- [j2]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): 75-86 (1986) - 1984
- [j1]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): 75-88 (1984)
Coauthor Index
aka: Jason T. L. Wang
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