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...
FOOTPRINT: A New Algorithm for Charge State Deconvolution of Complex ESI Mass Spectra (2008)
Hailing Zhang, Kaizhong Zhang, Bin Ma, Cunjie Zhang, A Doherty-kirby, Gilles Lajoie
Complex protein mixtures are often difficult to separate due to similar physico-chemical properties of the proteins in mixture. Mass spectrometry has the potential to resolve such mixture and give...
Deploying Wireless Sensor Networks under Limited Mobility Constraints (2008)
Wenjun Gu, Xiaole Bai, Dong Xuan, Bin Ma, Kaizhong Zhang
In this paper, we study the issue of sensor networks deployment using limited mobility sensors. By limited mobility, we mean that the maximum distance that sensors are capable of moving to is...
Deploying Wireless Sensor Networks under Limited Mobility Constraints (2008)
Student Member, Wenjun Gu, Xiaole Bai, Dong Xuan, Bin Ma, Kaizhong Zhang
Abstract—In this paper, we study the issue of sensor network deployment using limited mobility sensors. By limited mobility, we mean that the maximum distance that sensors are capable of moving to...
COMPLEXITIES AND ALGORITHMS FOR GLYCAN STRUCTURE SEQUENCING USING TANDEM MASS SPECTROMETRY ∗ (2008)
Baozhen Shan, Bin Ma, Kaizhong Zhang, Gilles Lajoie
Determining glycan structures is vital to comprehend cell-matrix, cell-cell, and even intracellular biological events. Glycan structure sequencing, which is to determine the primary structure of a...
Abstract An algorithm for detecting homologues of known structured RNAs in genomes (2008)
Shu-yun Le, Jacob V. Maizel, Kaizhong Zhang
Distinct RNA structures are frequently involved in a widerange of functions in various biological mechanisms. The three dimensional RNA structures solved by X-ray crystallography and various...
Exact and Approximate Algorithms for Unordered 'he Matching (2008)
Dennis Shasha, Kaizhong Zhang, Frank Y. Shih
Abstract-We consider the problem of comparison between unordered trees, i.e., trees for which the order among siblings is unimportant. The criterion for comparison is the distance as measured by a...
MetricMap: An embedding technique for processing distance-based queries in metric spaces (2008)
Xiong Wang, Dennis Shasha, Kaizhong Zhang
Abstract—In this paper, we present an embedding technique, called MetricMap, which is capable of estimating distances in a pseudometric space. Given a database of objects and a distance function...
WORD COMPLEXITY AND REPETITIONS IN WORDS 1 (2008)
Lucian Ilie, Sheng Yu, Kaizhong Zhang
With ideas from data compression and combinatorics on words, we introduce a complexity measure for words, called repetition complexity, which quantifies the amount of repetition in a word. The...
Li, Lei, Wu, Chenggang, Huang, Haiming, Zhang, Kaizhong, Gan, Jacob, Li, Shawn S.-C.
Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have...
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...
TREEDIFF: A System for Document Comparison by Structure (2007)
Girish Patel, Liam Relihan, Dennis Shasha, Kaizhong Zhang, ...
rstructure comparison(A, B): to determine whether or not A contains B as an approximate subtree; it returns the closest matching subtree of A and the distance between that subtree and B. 3 Query...
sequencing by tandem mass spectrometry (2007)
Bin Ma, Kaizhong Zhang, Christopher Hendrie, Chengzhi Liang, Ming Li, A Doherty-kirby, ...
PEAKS: powerful software for peptide de novo
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set...
Kaizhong Zhang, Dennis Shasha, Communicated T. Jiang
We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with nodes being Labeled). This problem is motivated by the study of information retrieval for bio-chemical and...
Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang
x We study the computational complexity and approximation of several problems arising in the comparison of evolutionary trees. It is shown that the maximum agreement subtree (MAST) problem for three...
RNA secondary structure prediction via energy density minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alex, Kaizhong Zhang, ...
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety...
RNA Secondary Structure Prediction via Energy Density Minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alexander Ebhardt, H. Alex, ...
There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety of...
SPIDER: Software for Protein identification from Sequence Tags with De Novo Sequencing Error (2004)
Yonghua Han, Bin Ma, Kaizhong Zhang
For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are...
Peaks: Powerful software for peptide de novo sequencing by tandem mass spectrometry (2003)
Bin Ma, Kaizhong Zhang, Christopher Hendrie, Chengzhi Liang, Ming Li, A Doherty-kirby, ...
A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental...
Finding approximate patterns in undirected acyclic graphs (2002)
Kaizhong Zhang, George Chang, Dennis Shasha
We consider an approximate pattern matching problem for undirected acyclic graphs. Specifically, let P be a pattern graph, D a data graph and t an integer. We present an algorithm to locate a...
ATreeGrep: Approximate Searching in Unordered Trees (2002)
Dennis Shasha, Huiyuan Shan, Kaizhong Zhang
An unordered labeled tree is a tree in which each node has a string label and the parent-child relationship is significant, but the order among siblings is unimportant. This paper presents an...
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....
A general edit distance between RNA structures (2002)
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set...
RNA molecules with structure dependent functions are uniquely folded (2002)
Le, Shu-Yun, Zhang, Kaizhong, Maizel, Jacob V.
Cis‐acting elements in post‐transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure. These structures are expected to be significantly...
Edit distance between two RNA structures (2001)
Guo-hui Lin, Bin Ma, Kaizhong Zhang
Arc-annotated sequences are useful in representing the structural information of RNA sequences. Typically, RNA secondary and tertiary structures could be represented by a set of nested arcs and a set...
The longest common subsequence problem for arc-annotated sequences (2000)
Tao Jiang, Bin Ma, Kaizhong Zhang
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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...
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...
Structural matching and discovery in document databases (1997)
Dennis Shasha, Liam Relihan, Kaizhong Zhang, Girish Patel
Structural matching and discovery in documents such as SGML and HTML is important for data warehousing [6], version management [7, 11], hypertext authoring, digital libraries [4] and Internet...
Automated Discovery of Active Motifs in Three Dimensional Molecules (1997)
Xiong Wang, Dennis Shasha, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in three dimensional (3D) molecules. Each node in a molecule is represented by a 3D point...
Approximate Tree Matching in the Presence of Variable Length Don't Cares (1993)
Ordered labeled trees are trees in which the sibling order matters. This paper presents algorithms for three problems having to do with approximate matching for such trees with variable-length...
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...
The editing distance between trees :--algorithms and applications /--by KaiZhong Zhang. (1989)
Thesis (Ph. D.)--New York University, 1989.
RNA molecules with structure dependent functions are uniquely folded
Le, Shu-Yun, Zhang, Kaizhong, Maizel, Jacob V.
Cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure. These structures are expected to be significantly more...
RNA molecules with structure dependent functions are uniquely folded
Le, Shu-Yun, Zhang, Kaizhong, Maizel, Jacob V.
Cis-acting elements in post-transcriptional regulation of gene expression are often correlated with distinct local RNA secondary structure. These structures are expected to be significantly more...
Li, Lei, Wu, Chenggang, Huang, Haiming, Zhang, Kaizhong, Gan, Jacob, Li, Shawn S.-C.
Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have...