2008 |
30 | EE | 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 Research 36(Database-Issue): 392-397 (2008) |
2007 |
29 | EE | 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 |
28 | EE | 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 Research 35(Web-Server-Issue): 300-304 (2007) |
2006 |
27 | EE | Eckart Bindewald,
Thomas D. Schneider,
Bruce A. Shapiro:
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Research 34(Web-Server-Issue): 405-411 (2006) |
2003 |
26 | | 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 |
25 | | 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 |
24 | EE | Xiong Wang,
Jason Tsong-Li Wang,
Dennis 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 |
23 | EE | 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 |
22 | | Bruce A. Shapiro,
Jin Chu Wu,
David Bengali,
Mark J. Potts:
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation.
Bioinformatics 17(1): 137-148 (2001) |
2000 |
21 | EE | Jason Tsong-Li Wang,
Xiong Wang,
Dennis Shasha,
Bruce A. Shapiro,
Kaizhong Zhang,
Xinhuan Zheng,
Qicheng Ma,
Zasha Weinberg:
An Approximate Search Engine for Structural Databases.
SIGMOD Conference 2000: 584 |
20 | EE | Xiong Wang,
Jason Tsong-Li Wang,
King-Ip Lin,
Dennis Shasha,
Bruce A. Shapiro,
Kaizhong Zhang:
An Index Structure for Data Mining and Clustering.
Knowl. Inf. Syst. 2(2): 161-184 (2000) |
1999 |
19 | | Jason Tsong-Li Wang,
Bruce A. Shapiro,
Dennis Shasha:
Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications
Oxford University Press 1999 |
18 | EE | Jason Tsong-Li Wang,
Xiong Wang,
King-Ip Lin,
Dennis Shasha,
Bruce A. Shapiro,
Kaizhong Zhang:
Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering.
KDD 1999: 307-311 |
17 | | 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 |
16 | | Wojciech Kasprzak,
Bruce A. Shapiro:
Stem Trace: an interactive visual tool for comparative RNA structure analysis.
Bioinformatics 15(1): 16-31 (1999) |
15 | | Jason Tsong-Li Wang,
Steve Rozen,
Bruce A. Shapiro,
Dennis Shasha,
Zhiyuan Wang,
Maisheng Yin:
New Techniques for DNA Sequence Classification.
Journal of Computational Biology 6(2): 209-218 (1999) |
1998 |
14 | EE | Jason Tsong-Li Wang,
Bruce A. Shapiro,
Dennis 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) |
13 | | Jih-H. Chen,
Shu-Yun Le,
Bruce A. Shapiro,
Jacob V. Maizel:
Optimization of an RNA Folding Algorithm for Parallel Architectures.
Parallel Computing 24(11): 1617-1634 (1998) |
1997 |
12 | | Xiong Wang,
Jason Tsong-Li Wang,
Dennis Shasha,
Bruce A. Shapiro,
Sitaram Dikshitulu,
Isidore Rigoutsos,
Kaizhong Zhang:
Automated Discovery of Active Motifs in Three Dimensional Molecules.
KDD 1997: 89-95 |
11 | | Kathleen M. Currey,
Bruce A. Shapiro:
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
Computer Applications in the Biosciences 13(1): 1-12 (1997) |
10 | | Bruce A. Shapiro,
Jin Chu Wu:
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
Computer Applications in the Biosciences 13(4): 459-471 (1997) |
1996 |
9 | | Jason Tsong-Li Wang,
Bruce A. Shapiro,
Dennis Shasha,
Kaizhong Zhang,
Chia-Yo Chang:
Automated Discovery of Active Motifs in Multiple RNA Secondary Structures.
KDD 1996: 70-75 |
8 | | Bruce A. Shapiro,
Jin Chu Wu:
An annealing mutation operator in the genetic algorithms for RNA folding.
Computer Applications in the Biosciences 12(3): 171-180 (1996) |
1994 |
7 | EE | Jason Tsong-Li Wang,
Gung-Wei Chirn,
Thomas G. Marr,
Bruce A. Shapiro,
Dennis Shasha,
Kaizhong Zhang:
Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results.
SIGMOD Conference 1994: 115-125 |
1990 |
6 | | Jih-H. Chen,
Shu-Yun Le,
Bruce A. Shapiro,
Kathleen M. Currey,
Jacob V. Maizel:
A computational procedure for assessing the significance of RNA secondary structure.
Computer Applications in the Biosciences 6(1): 7-18 (1990) |
5 | | Bruce A. Shapiro,
Kaizhong Zhang:
Comparing multiple RNA secondary structures using tree comparisons.
Computer Applications in the Biosciences 6(4): 309-318 (1990) |
1989 |
4 | | Shu-Yun Le,
J. Owens,
Ruth Nussinov,
Jih-H. Chen,
Bruce A. Shapiro,
Jacob V. Maizel:
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.
Computer Applications in the Biosciences 5(3): 205-210 (1989) |
1988 |
3 | | Bruce A. Shapiro:
An algorithm for comparing multiple RNA secondary structures.
Computer Applications in the Biosciences 4(3): 387-393 (1988) |
1986 |
2 | | Bruce A. Shapiro,
Ruth Nussinov,
L. E. Lipkin,
Jacob V. Maizel:
A sequence analysis system encompassing rules for DNA helical distortion.
Nucleic Acids Research 14(1): 75-86 (1986) |
1984 |
1 | | Bruce A. Shapiro,
Jacob V. Maizel,
L. E. Lipkin,
Kathleen M. Currey,
Colin G. Whitney:
Generating non-overlapping displays of nucleic acid secondary structure.
Nucleic Acids Research 12(1): 75-88 (1984) |