Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization (2009)
Junilda Spirollari, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park, Bruce A. Shapiro
Thermodynamic processes with free energy parameters are often used in algorithms that solve the free energy minimization problem to predict secondary structures of single RNA sequences. While results...
Linnstaedt, Sarah D., Kasprzak, Wojciech K., Shapiro, Bruce A., Casey, John L.
RNA editing by the host RNA adenosine deaminase ADAR1 at the amber/W site of hepatitis delta virus RNA plays a central role in the viral replication cycle by affecting the balance between viral RNA...
BA: CorreLogo: an online server for 3D sequence logos (2008)
Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Abstract Evaluating A Class of Distance-Mapping Algorithms for Data Mining and Clustering* (2008)
Jason Tsong-li, Wang+ Xiong Wang, Dennis Shasha, Bruce A. Shapiro
A distance-mapping algorithm takes a set of objects and a distance metric and then maps those objects to a Euclidean or pseudoEuclidean space in such a way that the distances among objects are...
Bindewald, Eckart, Hayes, Robert, Yingling, Yaroslava G., Kasprzak, Wojciech, Shapiro, Bruce A.
We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions....
Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang, Maisheng Yin
Key words: algorithms, consensus sequence, pattern matching, tools for computational biology, DNA sequence recognition
Xiong Wang, King-ip Lin, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang
Abstract. In this paper we present an index structure, called MetricMap, that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such a way that the...
Ffl Xiong Wang, Xiong Wang, Xiong Wang, King-ip Lin, ...
ditor, Combinatorial Pattern Matching, pages 104 -- 117, Lecture Notes in Computer Science, SpringerVerlag, 1998. ffl Xiong Wang, Jason T.L. Wang, Dennis Shasha, Bruce Shapiro, Sitaram Dikshitulu,...
Bruce A. Shapiro, Wojciech Kasprzak
RNA folding pathways are proving to be quite important in the determination of RNA function. Studies indicate that RNA may enter intermediate conformational states that are key to its functionality....
RADAR: a web server for RNA data analysis and research (2007)
Khaladkar, Mugdha, Bellofatto, Vivian, Wang, Jason T. L., Tian, Bin, Shapiro, Bruce A.
RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are...
Linnstaedt, Sarah D., Kasprzak, Wojciech K., Shapiro, Bruce A., Casey, John L.
RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments (2006)
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
TORTORICI, M. ALEJANDRA, SHAPIRO, BRUCE A., PATTON, JOHN T.
Replication of the segmented double-stranded (ds)RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) to use 11 different (+)RNAs as templates for (−) strand synthesis....
Linnstaedt, Sarah D., Kasprzak, Wojciech K., Shapiro, Bruce A., Casey, John L.
RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the...
BINDEWALD, ECKART, SHAPIRO, BRUCE A.
We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input...
Linnstaedt, Sarah D., Kasprzak, Wojciech K., Shapiro, Bruce A., Casey, John L.
RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the...
TORTORICI, M. ALEJANDRA, SHAPIRO, BRUCE A., PATTON, JOHN T.
Replication of the segmented double-stranded (ds)RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) to use 11 different (+)RNAs as templates for (−) strand synthesis....
Structural polymorphism of the HIV-1 leader region explored by computational methods (2005)
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
Xiong Wang, Dennis Shasha, Bruce A. Shapiro, Isidore Rigoutsos, Kaizhong Zhang
This paper presents a method for finding patterns in three dimensional (3D) graphs. Each node in a graph is an undecomposable or atomic unit and has a label. Edges are links between the atomic units....
Atha, Donald H., Kasprzak, Wojciech, OConnell, Catherine D., Shapiro, Bruce A.
We have analyzed previously three representative p53 single-point mutations by capillary-electrophoresis single-strand conformation polymorphism (CE-SSCP). In the current study, we compared our...
Shapiro, Bruce A., Wu, Jin Chu, Bengali, David, Potts, Mark J.
A massively parallel Genetic Algorithm (GA) has been applied to RNA sequence folding on three different computer architectures. The GA, an evolution-like algorithm that is applied to a large...
An index structure for data mining and clustering (2000)
Xiong Wang, King-ip Lin, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang
Abstract. In this paper we present an index structure, called Metric-Map, that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such away that the...
An index structure for data mining and clustering (2000)
Xiong Wang, King-ip Lin, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang
Abstract. In this paper we present an index structure, called Metric-Map, that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such a way that the...
Evaluating A Class of Distance-Mapping Algorithms for Data Mining and Clustering (1999)
Xiong Wang, King-ip Lin, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang
A distance-mapping algorithm takes a set of objects and a distance metric and then maps those objects to a Euclidean or pseudo-Euclidean space in such a way that the distances among objects are...
New techniques for DNA sequence classification (1999)
Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang, Maisheng Yin
DNA sequence classification is the activity of determining whether or not an unlabeled sequence S belongs to an existing class C. This paper proposes two new techniques for DNA sequence...
An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees (1998)
Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang, Kathleen M. Currey
Ordered, labeled trees are trees in which each node has a label and the left-to-right order of its children (if it has any) is fixed. Such trees have many applications in vision, pattern recognition,...
An algorithm for finding the largest approximately common substructures of two trees (1998)
Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang, Kathleen M. Currey
Abstract | Ordered, labeled trees are trees in which each node has a label and the left-to-right order of its children (if it has any) is xed. Such trees have many applications in vision, pattern...
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm (1997)
Shapiro, Bruce A., Wu, Jin Chu
Motivation Using the genetic algorithm (GA) for RNA folding on a massively parallel supercomputer, MasPar MP-2 with 16384 processors, we successfully predicted the existence of H-type pseudoknots in...
Currey, Kathleen M., Shapiro, Bruce A.
Comparison of the secondary structure of the 5' non-coding region of poliovirus 3 RNA derived from the genetic algorithm with the model of Skinner et al. (J. Mol. Biol., 207, 379–392, 1989)...
An annealing mutation operator in the genetic algorithms for RNA folding (1996)
Shapiro, Bruce A., Wu, Jin Chu
An annealing mutation operator in the genetic algorithms (GA) for RNA folding on a MasPar MP-2 has been designed. The mutation probability descends along a hyperbola with respect to the size of the...
Complementary classification approaches for protein sequences (1996)
Wang, Jason T.L., Marr, Thomas G., Shasha, Dennis, Shapiro, Bruce A., Chirn, Gung-Wei, Lee, T.Y.
We have studied five methods of protein classification and have applied them to the 768 groups of related proteins in the PROSITE catalog. Four of these methods are based on searching a database of...
Wang, Jason T.L., Marr, Thomas G., Shasha, Dennis, Shapiro, Bruce A., Chirn, Gung-Wei
We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences;...
Comparing multiple RNA secondary structures using tree comparisons (1990)
Shapiro, Bruce A., Zhang, Kaizhong
In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the...
Detection of common motifs in RNA secondary structures (1989)
Margalit, Hanah, Shapiro, Bruce A., Oppenheim, Amos B., Maizel, Jacob V.
We describe a novel computerized system for comparison of RNA secondary structures and demonstrate its use for experimental studies. The system is able to screen a very large number of structures, to...
An algorithm for comparing multiple RNA secondary structures (1988)
A new distributed computational procedure is presented for rapidly determining the similarity of multiple conformations of RNA secondary structures. A data abstraction scheme is utilized to reduce...
A sequence analysis system encompassing rules for DNA helical distortion (1986)
Shapiro, Bruce A, Nussinov, Ruth, Lipkin, Lewis E., Maizel, Jacob V.
Recently, it has been shown by Calladine (1982) and Dickerson (1983) that DNA distortions due to steric clashes between opposing purines and pyrimidines can be quantitated based upon four sum...
An interactive technique for the display of nucleic acid secondary structure (1982)
Shapiro, Bruce A., Lipkin, Lewis E., Maizel, Jacob
The ability to visualize nucleic acid secondary structure has become qyite important since the advent of computer prediction and biochemical techniques that depict such structures. Manually drawing...
Atha, Donald H., Kasprzak, Wojciech, O’Connell, Catherine D., Shapiro, Bruce A.
We have analyzed previously three representative p53 single-point mutations by capillary-electrophoresis single-strand conformation polymorphism (CE-SSCP). In the current study, we compared our...
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
Structural polymorphism of the HIV-1 leader region explored by computational methods
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
TORTORICI, M. ALEJANDRA, SHAPIRO, BRUCE A., PATTON, JOHN T.
Replication of the segmented double-stranded (ds)RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) to use 11 different (+)RNAs as templates for (−) strand synthesis....
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
BINDEWALD, ECKART, SHAPIRO, BRUCE A.
We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input...
Atha, Donald H., Kasprzak, Wojciech, O’Connell, Catherine D., Shapiro, Bruce A.
We have analyzed previously three representative p53 single-point mutations by capillary-electrophoresis single-strand conformation polymorphism (CE-SSCP). In the current study, we compared our...
Li, Wen, Ma, Buyong, Shapiro, Bruce A.
The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding...
Structural polymorphism of the HIV-1 leader region explored by computational methods
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
TORTORICI, M. ALEJANDRA, SHAPIRO, BRUCE A., PATTON, JOHN T.
Replication of the segmented double-stranded (ds)RNA genome of rotavirus requires the viral RNA-dependent RNA polymerase (RdRP) to use 11 different (+)RNAs as templates for (−) strand synthesis....
BINDEWALD, ECKART, SHAPIRO, BRUCE A.
We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Zhang, Jiuchun, Zhang, Guohua, Guo, Rong, Shapiro, Bruce A., Simon, Anne E.
RNA can adopt different conformations in response to changes in the metabolic status of cells, which can regulate processes such as transcription, translation, and RNA cleavage. We previously...
The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing
Linnstaedt, Sarah D., Kasprzak, Wojciech K., Shapiro, Bruce A., Casey, John L.
RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the...
RADAR: a web server for RNA data analysis and research
Khaladkar, Mugdha, Bellofatto, Vivian, Wang, Jason T. L., Tian, Bin, Shapiro, Bruce A.
RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are...
Bindewald, Eckart, Hayes, Robert, Yingling, Yaroslava G., Kasprzak, Wojciech, Shapiro, Bruce A.
We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions....
Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus▿
McCormack, John C., Yuan, Xuefeng, Yingling, Yaroslava G., Kasprzak, Wojciech, Zamora, Rodolfo E., Shapiro, Bruce A., ...
The genomes of positive-strand RNA viruses undergo conformational shifts that complicate efforts to equate structures with function. We have initiated a detailed analysis of secondary and tertiary...
Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference
Santhanam, Arti N., Bindewald, Eckart, Rajasekhar, Vinagolu K., Larsson, Ola, Sonenberg, Nahum, Colburn, Nancy H., ...
Eukaryotic cap-dependent mRNA translation is mediated by the initiation factor eIF4E, which binds mRNAs and stimulates efficient translation initiation. eIF4E is often overexpressed in human cancers....
Santhanam, Arti N., Bindewald, Eckart, Rajasekhar, Vinagolu K., Larsson, Ola, Sonenberg, Nahum, Colburn, Nancy H., ...
The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits
Stupina, Vera A., Meskauskas, Arturas, McCormack, John C., Yingling, Yaroslava G., Shapiro, Bruce A., Dinman, Jonathan D., ...
During cap-dependent translation of eukaryotic mRNAs, initiation factors interact with the 5′ cap to attract ribosomes. When animal viruses translate in a cap-independent fashion, ribosomes...