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Our Science – Shapiro Website

Bruce A. Shapiro, Ph.D.

Selected Publications
1)  Bindewald E, Grunewald C, Boyle B, O'Connor M, Shapiro BA.
Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.
J. Mol. Graph. Model. 27(3): 299-308, 2008. [Journal]
2)  Shapiro BA, Bindewald E, Kasprzak W, Yingling Y.
Protocols for the in silico design of RNA nanostructures.
Methods Mol. Biol. 474: 93-115, 2008. [Journal]
3)  Stupina VA, Meskauskas A, McCormack JC, Yingling YG, Shapiro BA, Dinman JD, Simon AE.
The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits.
RNA. 14(11): 2379-93, 2008. [Journal]
4)  Shapiro B, Bindewald E, Kasprzak W, Yingling Y. Gazit E, Nussinov R, eds.
Protocols for the In silico Design of RNA Nanostructures. In: Nanostructure Design Methods and Protocols. Volume .
Totowa, NJ: Humana Press; 2008. p. 93-115 [Book Chapter]
5)  Martinez HM, Maizel JV, Shapiro BA.
RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA.
J. Biomol. Struct. Dyn. 25: 669-83, 2008. [Journal]
6)  Severcan I, Geary C, Jaeger L, Bindewald E, Kasprzak W, Shapiro B. Alterovitz G, Ramoni M, Benson R, eds.
Computational and Experimental RNA Nanoparticle Design. In: Automation in Genomics and Proteomics: An Engineering Case-Based Approach. Volume .
Hoboken: Wiley Publishing; 2008. In Press. [Book Chapter]
7)  Bindewald E, Hayes R, Yingling YG, Kasprzak W, Shapiro BA.
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.
Nucleic Acids Res. 36: D392-7, 2008. [Journal]
8)  McCormack JC, Yuan X, Yingling YG, Kasprzak W, Zamora RE, Shapiro BA, Simon AE.
Structural domains within the 3' untranslated region of Turnip crinkle virus.
J. Virol. 82: 8706-20, 2008. [Journal]
9)  Wang J, Wen D, Shapiro B, Herbert K, Li J, Ghosh K. Cohen-Boulakia S, Tannen V, eds.
Toward an Integrated RNA Motif Database. In: Data Integration in the Life Sciences/Lecture Notes in Bioinformatics. Volume 4544.
Berlin: Springer; 2007. p. 27-36 [Book Chapter]
10)  Shapiro BA, Yingling YG, Kasprzak W, Bindewald E.
Bridging the gap in RNA structure prediction.
Curr. Opin. Struct. Biol. 17: 157-65, 2007. [Journal]
11)  Yingling YG, Shapiro BA.
Computational Design of an RNA Hexagonal Nanoring and an RNA Nanotube.
Nano Lett. 7(8): 2328-2334, 2007. Full Text Article. [Journal]
12)  Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res. W300-4, 2007. [Journal]
13)  Yingling YG, Shapiro BA.
The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain.
J. Biomol. Struct. Dyn. 24: 303-20, 2007. [Journal]
14)  Zhang J, Zhang G, Guo R, Shapiro BA, Simon AE.
A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis.
J. Virol. 80(18): 9181-91, 2006. [Journal]
15)  Bindewald E, Schneider TD, Shapiro BA.
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Nucleic Acids Res. 34: W405-11, 2006. [Journal]
16)  Shapiro BA, Kasprzak W, Grunewald C, Aman J.
Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.
J. Mol. Graph. Model. 25: 514-531, 2006. [Journal]
17)  Bindewald E, Shapiro BA.
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers.
RNA. 12: 342-52, 2006. [Journal]
18)  Hastings W, Yingling YG, Chirikijian GS, Shapiro BA.
Structural and dynamical classification of RNA single-base bulges for nanostructure design.
J. Comp. Theor. Nanoscience. 3: 63-77, 2006. [Journal]
19)  Gee AH, Kasprzak W, Shapiro BA.
Structural Differentiation of the HIV-1 Poly(A) Signals.
J Biomol Struct Dyn. 23: 417-28, 2006. [Journal]
20)  Yingling YG, Shapiro BA.
The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation.
J Mol Graph Model. 25: 261-274, 2006. [Journal]
21)  Linnstaedt SD, Kasprzak WK, Shapiro BA, Casey JL.
The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing.
RNA. 12(8): 1521-1533, 2006. [Journal]
22)  Seko Y, Cole S, Kasprzak W, Shapiro B, Ragheb J.
The role of cytokine mRNA stability in pathogenesis in autoimmune disease.
Autoimmun. Rev. 5(5): 299-305, 2006. [Journal]
23)  Tortorici MA, Shapiro BA, Patton JT.
A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments.
RNA. 12(1): 133-46, 2005. [Journal]
24)  Yingling YG, Shapiro BA.
Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita.
J Mol Biol. 348: 27-42, 2005. [Journal]
25)  Kasprzak W, Bindewald E, Shapiro BA.
Structural polymorphism of the HIV-1 leader region explored by computational methods.
Nucleic Acids Res. 33: 7151-7163, 2005. [Journal]
26)  Shapiro BA, Kasprzak W.
Visual Data Mining of RNA Secondary Structure and Folding Pathways as Determined by the Massively Parallel Genetic Alogorithm.
Conference Proceedings of the 36th Symposium on the Interface 2004: Computational Biology and Bioinformatics. CDROM: Baltimore, MD, 2004. [Journal]
27)  Kim MK, Li W, Shapiro BA, Chirikjian GS.
A Comparison Between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA.
J Biomol Struct Dyn. 21: 395-406, 2003. [Journal]
28)  Kim MK, Jernigan RL, Shapiro BA, Chirikjian GS.
A study of conformational changes in macromolecules: The coarse-grained elastic network interpolation method.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'03. CSREA Press: Las Vegas, Nevada, 2003. [Journal]
29)  Li W, Ma B, Shapiro BA.
Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations.
Nucleic Acids Res. 31: 629-38, 2003. [Journal]
30)  Shapiro BA, Bengali D, Kasprzak W, Wu JC.
Exploring RNA intermediate conformations with the massively parallel genetic algorithm.
. In Wang, J. T. L., Wu C. H. and Wang, P. P (Eds.): Computational Biology and Genome Informatics. New Jersey, World Scientific Pub. Co. .: 1-33, 2003. [Journal]
31)  Wang X, Wang JTL, Shasha D, Shapiro BA, Rigoustsos I, Zhang K.
Finding patterns in three-dimensional graphs: Algorithms and applicaitons to scientific data mining.
IEEE Transactions on Knowledge and Data Engineering. 14(4): 731-49, 2002. [Journal]
32)  Pattabiraman N, Martinez HM, Shapiro BA.
Molecular Modeling and Dynamics Studies of HIV-1 Kissing Loop Structures.
J Biomol Struct Dyn. 20: 397-412, 2002. [Journal]
33)  Kasprzak W, Shapiro BA.
Structural dependencies of the HIV-1 dimer initiation site as determined by the massively parallel genetic algorithm.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. CSREA Press: 48-54, 2002. [Journal]
34)  Chen JH, Shapiro BA, Maizel JV.
Theoretical approach for determining energy rules for tRNA.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. CSREA Press: 69-74, 2002. [Journal]
35)  Shapiro BA, Bengali D, Kasprzak W, Wu JC.
Computational insights into RNA folding pathways: Getting from here to there.
The Proceedings of the Atlantic Symposium on Computational Biology. Genome Information Systems and Technology: 10-13, 2001. [Journal]
36)  Li W, Ma B, Shapiro BA.
Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop.
J. Biomol. Struct. Dyn. 19(3): 381-96, 2001. [Journal]
37)  Atha DH, Kasprzak W, O'Connell CD, Shapiro BA.
Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling.
Nucleic Acids Res. 29: 4643-53, 2001. [Journal]
38)  Shapiro BA, Bengali D, Kasprzak W, Wu JC.
RNA folding pathway functional intermediates: their prediction and analysis.
J Mol Biol. 312: 27-44, 2001. [Journal]
39)  Shapiro BA, Wu JC, Bengali D, Potts MJ.
The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation.
Bioinformatics. 17: 137-48, 2001. [Journal]
40)  Wang X, Wang JTL, Lin KI, Shasha D, Shapiro BA, Zhang K.
An index structure for data mining and clustering.
Knowledge and Information Systems. 2: 161-84, 2000. [Journal]
41)  Willian S, Tracy S, Chapman N, Leser S, Romero J, Shapiro B, Currey K.
Mutations in a conserved enteroviral RNA oligonucleotide sequence affect positive strand viral RNA synthesis.
Archives of Virology. 145: 2061-86, 2000. [Journal]
42)  Wu JC, Shapiro BA.
A Boltzmann filter improves the prediction of RNA folding pathways in a massively parallel genetic algorithm.
J Biomol Struct Dyn. 17: 581-95, 1999. [Journal]
43)  Wang JTL, Wang X, Lin KI, Shasha D, Shapiro BA, Zhang K.
Evaluating a class of distrance-mapping algorithms for data mining and clustering.
Proceedings of International Conference on Knowledge discovery and Data Mining. 307-311, 1999. [Journal]
44)  Wang JT, Rozen S, Shapiro BA, Shasha D, Wang Z, Yin M.
New techniques for DNA sequence classification.
J Comput Biol. 6: 209-18, 1999. [Journal]
45)  Wang JTL, Marr TG, Rozen S, Shasha D, Shapiro BA, Chirn GW, Wang Z, Zhang K.
Pattern discovery and classification in biosequences.
Book: Pattern Discovery in Biomolecular Data. In: Wang J, Shapiro BA, Shasha D, Eds: 55-74, 1999. [Journal]
46)  Apostolico A, Comin M, Parida L.
Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications.
. New York, Oxford Univ. Press, 1999. [Journal]
47)  Shapiro BA, Kasprzak W, Wu JC, Currey K.
RNA structure analysis: A multifaceted approach.
Book: Pattern discovery in Biomolecular Data. In: Wang J, Shapiro BA Shasha D, Eds: 183-215, 1999. [Journal]
48)  Kasprzak W, Shapiro B.
Stem Trace: An interactive visual tool for comparative RNA structure analysis.
Bioinformatics. 15(1): 16-31, 1999. [Journal]
49)  Wang JTL, Shapiro BA, Shasha D, Zhang K, Currey KM.
An algorithm for finding the largest common substructures of two trees.
IEEE Trans. Pattern Anal. Machine Intell. 20: 889-95, 1998. [Journal]
50)  Chen JH, Shapiro BA, Maizel JV.
Optimization of an RNA folding algorithm for parallel architectures.
Parallel Computing. 24: 1617-34, 1998. [Journal]
51)  Wang X, Wang JTL, Shasha D, Shapiro BA, Dikshitulu S, rigoutsos I, Zhang K.
Automated discovery of active motiffs in three-dimensional molecules.
AAAI Press - AIII Proceedings of the 3rd International Conference on Knowledge, Discovery and Data Mining. 89-95, 1997. [Journal]
52)  Tracy S, Chapman N, Ramsingh A, Romero J, Currey K, Shapiro B, Barry WM, Chin T.
Coxsackie virus genetics and the cardiovirulent phenotype.
The Role of Immune Mechanisms in Cardiovascular Diseases. Chapter 8: 169-90, 1997. [Journal]
53)  Currey KM, Shapiro BA.
High order structures of Coxsackie virus B 5' Nontranslated Region RNA.
Coxsackie B Viruses. 223: 169-190, 1997. [Journal]
54)  Currey KM, Shapiro BA.
Higher order structures of coxsackievirus B 5' nontranslated region RNA.
Curr Top Microbiol Immunol. 223: 169-90, 1997. [Journal]
55)  Shapiro BA, Wu JC.
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm.
Comput Appl Biosci. 13: 459-71, 1997. [Journal]
56)  Currey KM, Shapiro BA.
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
Comput Appl Biosci. 13: 1-12, 1997. [Journal]
57)  Shapiro BA, Wu JC.
An annealing mutation operator in the genetic algorithms for RNA folding.
Comput Appl Biosci. 12: 171-80, 1996. [Journal]
58)  Wang JTL, Shapiro BA, Shasha D, Zhang K, Chang CY.
Automated discovery of active motifs in multiple RNA secondary structures.
AAAI Proceedings of the 2nd International Conference on Knowledge Dicovery and Data Mining. Simoudis E, Han J and Fayyad U, Editors: 70-75, 1996. [Journal]
59)  Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW, Lee TY.
Complementary classification approaches for protein sequences.
Protein Eng. 9: 381-6, 1996. [Journal]
60)  Shapiro BA, Kasprzak W.
STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis.
J Mol Graph. 14: 194-205, 222-4, 1996. [Journal]
61)  Shapiro BA, Chen JH, Busse T, Navetta J, Kasprzak W, Maizel JV.
Optimization and performance analysis of a massively parallel dynamic programming algorithm for RNA secondary structure prediction.
The International Journal of Supercomputer Applications. 9(1): 29-39, 1995. [Journal]
62)  Shapiro BA, Kasprzak W.
STRUCTURELAB: A heterogeneous computer system for the anlaysis of RNA structures.
Association of Lisp Users Meeting and Workshop Proceedings. Clarisse O, editor: 1-19, 1995. [Journal]
63)  Chapman NM, Hufnagel G, Tracy S, Barry WH, Zhao L, Currey K, Shapiro B.
The cardiovirulent phenotype of coxsackie virus B3 is determined at a single site in the genomic 5' non-translation region.
J Virol. 69(8): 4607-18, 1995. [Journal]
64)  Shapiro BA, Navetta J.
A massiverly parallel genetic algorithm for RNA secondary structure prediction.
The Journal of Supercomputing. 8: 195-207, 1994. [Journal]
65)  Wang JTL, Chirn GW, Marr TG, Shapiro BA, Shasha D, Zhang K.
Combinatorial pattern discovery for scientific data: Some preliminar results.
Proceedings of the ACM SIGMOD International Conference on Management of Data. Snodgrass RT and Winslett M, Eds.: 115-25, 1994. [Journal]
66)  Wang TJL, Chirn GW, Marr TG, Shapiro BA, Shasha D, Zhang K.
Combinatorial pattern discovery for scientific data: Some preliminary results.
ACM SIGMOD Record. 23(2): 115-25, 1994. [Journal]
67)  Wang JT, Marr TG, Shasha D, Shapiro BA, Chirn GW.
Discovering active motifs in sets of related protein sequences and using them for classification.
Nucleic Acids Res. 22: 2769-75, 1994. [Journal]
68)  Sakaguchi K, Zambrano N, Baldwin ET, Shapiro BA, Erickson JW, Omichinski JG, Clore GM, Gronenborn AM, Appella E.
Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein.
Proc Natl Acad Sci U S A. 90: 5219-23, 1993. [Journal]
69)  Dayton ET, Konings DA, Powell DM, Shapiro BA, Butini L, Maizel JV, Dayton AI.
Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein.
J Virol. 66: 1139-51, 1992. [Journal]
70)  Cheng SW, Lynch EC, Leason KR, Court DL, Shapiro BA, Friedman DI.
Functional importance of sequence in the stem-loop of a transcription terminator.
Science. 254: 1205-7, 1991. [Journal]
71)  Le SY, Shapiro BA, Chen JH, Nussinov R, Maizel JV.
RNA pseudoknots downstream of the frameshift sites of retroviruses.
Genet Anal Tech Appl. 8: 191-205, 1991. [Journal]
72)  Chen JH, Shapiro B, Currey KM, Maizel JV.
A computaitonal procedure for assessing the significance of RNA secondary structure.
Comput. Appl. Biosci. 6: 7-18, 1990. [Journal]
73)  Shapiro BA, Zhang KZ.
Comparing multiple RNA secondary structures using tree comparisons.
Comput Appl Biosci. 6: 309-18, 1990. [Journal]
74)  Nussinov R, Shapiro B, Le SY, Maizel JV.
Speeding up the dynamic folding algorithm for planar RNA folding.
Math. Biosci. 100: 33-47, 1990. [Journal]
75)  Margalit H, Shapiro BA, Oppenheim AB, Maizel JV.
Detection of common motifs in RNA secondary structures.
Nucleic Acids Res. 17: 4829-45, 1989. [Journal]
76)  Le SY, Owens J, Nussinov R, Chen JH, Shapiro B, Maizel JV.
RNA secondary structure: Comparison and determination of frequently recurring substructures.
Comput. Appl. Biosci. 5: 205-10, 1989. [Journal]
77)  Shapiro BA.
An algorithm for comparing multiple RNA secondary structures.
Comput Appl Biosci. 4: 387-93, 1988. [Journal]
78)  Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL.
Helix stability in prokaryotic promoter regions.
Biochemistry. 27: 5179-88, 1988. [Journal]
79)  Shapiro BA, Nussinov R, Lipkin LE, Maizel JV.
An interactive dot matrix system for locating potentially significant features in nucleic acid molecules.
J Biomol Struct Dyn. 4: 697-706, 1987. [Journal]
80)  Jernigan RL, Sarai A, Shapiro B, Nussinov R.
Relationship between curved DNA conformations and slow gel migration.
J. Biomol. Struct. Dyn. 4(4): 561-67, 1987. [Journal]
81)  Shapiro BA, Nussinov R, Lipkin LE, Maizel JV.
A sequence analysis system encompassing rules for DNA helical distortion.
Nucleic Acids Res. 14: 75-86, 1986. [Journal]
82)  Nussinov R, Shapiro B, Lipkin LE, Maizel JV.
DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation.
J. Mol. Biol. 177: 591-607, 1984. [Journal]
83)  Nussinov R, Shapiro B, Lipkin LE, Maizel JV.
Enhancer elements share local homologous twist-angle variations with helical periodicity.
Biochimica et Biophysica Acta. 783: 246-57, 1984. [Journal]
84)  Shapiro BA, Maizel J, Lipkin LE, Currey K, Whitney C.
Generating non-overlapping displays of nucleic acid secondary structure.
Nucleic Acids Res. 12: 75-88, 1984. [Journal]
85)  Shapiro BA, LIpkin LE.
Nucleic acid morphology: Analysis and synthesis.
Computing in Biological Science. Geison, MJ and Barrett AN, Editors: 233-71, 1983. [Journal]
86)  Shapiro BA, Lipkin LE, Maizel J.
An interactive technique for the display of nucleic acid secondary structure.
Nucleic Acids Res. 10: 7041-52, 1982. [Journal]
87)  Dhar R, Ellis RW, Shih TY, Oroszlan S, Shapiro B, Maizel J, Lowy D, Scolnick E.
Nucleotide sequence of p21 transforming protein of harvey murine sarcoma virus.
Science. 217(3): 934-36, 1982. [Journal]
88)  Shapiro B, Pisa J, Sklansky J.
Skeleton generation from boundary sequences of biological objects.
Computer Graphics and Image Processing. 136053, 1981. [Journal]
89)  Shapiro B, Lipkin L, Maizel J.
Computerized generation of secondary structure maps for nucleic acids.
Comput. Biomed. Res. 12: 545-68, 1979. [Journal]
90)  Lipkin L, Lemkin P, Wade M, Shapiro B.
Digital analysis of living cell image sequences in support of cytotoxicity-carcinogenesis research.
Proc. IEEE Workshop Analysis of Time-Varying Imagery. IEEE, 1979. [Journal]
91)  Lipkin L, Lemkin P, Shapiro B, Sklansky J.
Preprocessing of electron micrographs of nucleic acid molecules for automatic analysis by computer.
Comput Biomed Res. 12: 279-89, 1979. [Journal]
92)  Lemkin P, Shapiro B, Lipkin L, Maizel J, Sklansky J, Schultz M.
Preprocessing of electron micrographs of nucleic acid molecules for automatic analysis by computer. II. Noise removal and gap filling.
Comput Biomed Res. 12: 615-30, 1979. [Journal]
93)  Shapiro B, Pisa J, Sklansky J.
Skeletons from sequential boundary data.
Proc. IEEE Pattern Recognition and Image Processing. IEEE: 265-70, 1979. [Journal]
94)  Lemkin P, Merril C, Lipkin L, Van Keuren M, Oertel W, Shapiro B, Wade M, Schultz M, Smith E.
Software aids for the analysis of 2D gel electrophoresis images.
Comput Biomed Res. 12: 517-44, 1979. [Journal]
95)  Shapiro B.
Language processor generation with BNF inputs: Methods and implementation.
Comput. Programs Biomed. 7: 85-98, 1977. [Journal]
96)  Shapiro B, Lipkin L.
The circle transform, an articulable shape descriptor.
Proceedings of the Seventh Annual Symposium on Automatic Imagery Pattern Recognition. Washington, DC, Electronic Industries Association: 88-90, 1977. [Journal]
97)  Shapiro B, Lipkin L.
The circle transform, an articulable shape descriptor.
Comput. Biomed. Res. 10: 511-28, 1977. [Journal]
98)  Lemkin P, Carman G, Lipkin L, Shapiro B, Schultz M, Kaiser P.
A real time picture processor for use in biologic cell identification. I. System design.
J Histochem Cytochem. 22: 725-31, 1974. [Journal]
99)  Carman G, Lemkin P, Lipkin L, Shapiro B, Schultz M, Kaiser P.
A real time picture processor for use in biologic cell identification. II. Hardware implementation.
J Histochem Cytochem. 22: 732-40, 1974. [Journal]
100)  Shapiro B, Lemkin P, Lipkin L.
The application of artificial intelligence techniques to biologic cell identification.
J Histochem Cytochem. 22: 741-50, 1974. [Journal]

This page was last updated on 12/1/2008.