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Displaying 1-18 out of 18 total
Compressed Index for Dynamic Text
Found in: Data Compression Conference
By Wing-Kai Hon, Tak-Wah Lam, Kunihiko Sadakane, Wing-Kin Sung, Siu-Ming Yiu
Issue Date:March 2004
pp. 102
This paper investigates how to index a text which is subject to updates. The best solution in the literature is based on suffix tree using O(n log n) bits of storage, where n is the length of the text. It supports finding all occurrences of a pattern P in ...
 
Breaking a Time-and-Space Barrier in Constructing Full-Text Indices
Found in: Foundations of Computer Science, Annual IEEE Symposium on
By Wing-Kai Hon, Kunihiko Sadakane, Wing-Kin Sung
Issue Date:October 2003
pp. 251
<p>Suffix trees and suffix arrays are the most prominent full-text indices, and their construction algorithms are well studied. It has been open for a long time whether these indices can be constructed in both 0(n log n) time and 0(n log n)-bit worki...
 
Variable Number of Tandem Repeats (VNTR) Stands
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Xiaoan Dong, Sam Yuan Sung, Wing-Kin Sung, Chew Lim Tan
Issue Date:May 2004
pp. 483
This paper introduces a novel motif discovery algorithm based on the use of constraint mechanism and constraint rules. The key idea is to convert sets of similar substrings of the DNA sequences into patterns, as early as possible, using constraint mechanis...
 
Bioinformatics Applications in Genomics
Found in: Computer
By Wing-Kin Sung
Issue Date:June 2012
pp. 57-63
Instead of analyzing one gene at a time, researchers are using computational pipelines to evaluate genome-wide data consisting of hundreds of billions of bits of raw data to assist in pan-Asian data analysis.
 
Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Sylvain Guillemot, Jesper Jansson, Wing-Kin Sung
Issue Date:July 2011
pp. 1141-1147
HASH(0x295bbbc)
 
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By C. Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung, Louxin Zhang
Issue Date:July 2007
pp. 394-402
The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proved NP-hard even for galled recombination networ...
 
CPS-tree: A Compact Partitioned Suffix Tree for Disk-based Indexing on Large Genome Sequences
Found in: Data Engineering, International Conference on
By Swee-Seong Wong, Wing-Kin Sung, Limsoon Wong
Issue Date:April 2007
pp. 1350-1354
Suffix tree is an important data structure for indexing a long sequence (like a genome sequence) or a concatenation of sequences. It finds many applications in practice, especially in the domain of bioinformatics. Suffix tree allows for efficient pattern s...
 
LocalMotif - An In-Silico Tool for Detecting Localized Motifs in Regulatory Sequences
Found in: Tools with Artificial Intelligence, IEEE International Conference on
By Vipin Narang, Wing-Kin Sung, Ankush Mittal
Issue Date:November 2006
pp. 791-799
In silico motif finding algorithms are often used for discovering protein-DNA binding sites in a set of regulatory sequences. Current algorithms mainly address motif discovery in short sequences. Analyzing long sequences can be quite challenging not only d...
 
ConstrainedMotif: A Periodicity Constraint Based Algorithm to Predict Cell-Cycle Associated Promoter Motifs Using Time-Course Gene Expression Data
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Yingren Liu, Karuturi R. Krishna Murthy, Wing-Kin Sung
Issue Date:October 2005
pp. 250-257
Motivation: Cell-cycle associated promoter motif prediction is very important to understand the cell-cycle control and process. Modeling genome-wide gene expression as a function of the promoter sequence motif features has drawn great attention recently. T...
 
Multimodality as a Criterion for Feature Selection in Unsupervised Analysis of Gene Expression Data
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Yi Li, Wing-Kin Sung, Lance D. Miller
Issue Date:October 2005
pp. 276-280
One important way that gene expression data are often analysed in an unsupervised way is to cluster the samples without reference to any annotations about them. Before clustering, the data are often subjected to a feature selection preprocessing step, in w...
 
Learning Multi-Time Delay Gene Network Using Bayesian Network Framework
Found in: Tools with Artificial Intelligence, IEEE International Conference on
By Tie-Fei Liu, Wing-Kin Sung, Ankush Mittal
Issue Date:November 2004
pp. 640-645
Exact determination of gene network is required to discover the higher-order structures of an organism and to interpret its behavior. Most research work in learning gene networks either assumes that there is no time delay in gene expression or that there i...
 
Fast and Accurate Probe Selection Algorithm for Large Genomes
Found in: Computational Systems Bioinformatics Conference, International IEEE Computer Society
By Wing-Kin Sung, Wah-Heng Lee
Issue Date:August 2003
pp. 65
The oligo microarray (DNA chip) technology in recent years has a significant impact on genomic study. Many fields such as gene discovery, drug discovery, toxicological research and disease diagnosis, will certainly benefit from its use. A microarray is an ...
 
Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Samuel Ieong, Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung, Siu-Ming Yiu
Issue Date:March 2001
pp. 183
In this paper we investigate the computational problem of predicting RNA secondary structures that allow any kinds of pseudoknots. The general belief is that allowing pseudoknots makes the problem very difficult. Existing polynomial-time algorithms, which ...
 
Guest Editorial for the International Conference on Genome Informatics (GIW 2013)
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Frank Eisenhaber,Wing-Kin Sung,Limsoon Wong
Issue Date:January 2014
pp. 5-6
The nine papers in this special section were presented at the 2013 International Conference on Genome Informatics.
   
Learning Gene Network Using Conditional Dependence
Found in: Tools with Artificial Intelligence, IEEE International Conference on
By Tie-Fei Liu, Wing-Kin Sung
Issue Date:November 2006
pp. 800-804
Gene network, conventionally, is learned by studying the pairwise correlation of the microarray expression profiles of different genes. This approach, however, is reported to be effective only for learning a small portion of the regulatory pairs due to the...
 
Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Jesper Jansson, Sylvain Guillemot, Wing-Kin Sung
Issue Date:July 2011
pp. 1141-1147
HASH(0x295bbbc)
     
General techniques for comparing unrooted evolutionary trees
Found in: Proceedings of the twenty-ninth annual ACM symposium on Theory of computing (STOC '97)
By Hing-Fung Ting, Ming-Yang Kao, Tak-Wah Lam, Teresa M. Przytycka, Wing-Kin Sung
Issue Date:May 1997
pp. 54-65
We present efficient new randomized and deterministic methods for transforming optimal solutions for a type of relaxed integer linear program into provably good solutions for the corresponding NP-hard discrete optimization problem. Without any constraint v...
     
Construction of Online Catalog Topologies Using Decision Trees
Found in: Advanced Issues of E-Commerce and Web-Based Information Systems, International Workshop on
By David Yang, Wing-kin Sung, Siu-Ming Yiu, David Cheung, Wai-Shing Ho, Tak-Wah Lam, Sau-Dan Lee
Issue Date:June 2000
pp. 223
Organization of a web site is important to help users get the most out of the site. A good web site should help visitor's _nd the information they want easily. Visitors typically find information by searching for selected terms of interest or by following ...
 
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