Yip, Kevin Y, Kim, Philip M, McDermott, Drew, Gerstein, Mark
Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy:...
Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While...
Application Note An Integrated System for Studying Residue Coevolution in Proteins (2008)
Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew Mcdermott
Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not...
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz, Mark Gerstein
Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks...
Identifying projected clusters from gene expression profiles (2008)
Kevin Y. Yip, David W. Cheung, Michael K. Ng, Kei-hoi Cheung
In microarray gene expression data, clusters may hide in certain subspaces. For example, a set of co-regulated genes may have similar expression patterns in only a subset of the samples in which...
In microarray gene expression data, clusters may hide in subspaces. Traditional clustering algorithms that make use of similarity measurements in the full input space may fail to detect the clusters....
An integrated system for studying residue coevolution in proteins (2008)
Yip, Kevin Y., Patel, Prianka, Kim, Philip M., Engelman, Donald M., McDermott, Drew, Gerstein, Mark
Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not...
Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology (2007)
Lu, Long J., Sboner, Andrea, Huang, Yuanpeng J., Lu, Hao Xin, Gianoulis, Tara A., Yip, Kevin Y., ...
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation...
Smith, Andrew K, Cheung, Kei-Hoi, Yip, Kevin Y, Schultz, Martin, Gerstein, Mark B
Abstract Background A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among...
SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services (2006)
Kevin Y. Yip, Peishen Qi, Martin Schultz, David W. Cheung, Kei-hoi Cheung
Clustering is a popular method for analyzing microarray data. Given the large number of clustering algorithms being available, it is difficult to identify the most suitable ones for a particular...
On mining micro-array data by order-preserving submatrix (2006)
Lin Cheung, Kevin Y. Yip, David W. Cheung, Ben Kao, Michael K. Ng
We study the problem of pattern-based subspace clustering. Unlike traditional clustering methods that focus on grouping objects with similar values on a set of dimensions, clustering by pattern...
SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services (2006)
Kevin Y. Yip, Kevin Y. Yip, Peishen Qi, Peishen Qi, Martin Schultz, Martin Schultz, ...
Clustering is a popular method for analyzing microarray data. Given the large number of clustering algorithms being available, it is difficult to identify the most suitable ones for a particular...
Yip, Kevin Y., Yu, Haiyuan, Kim, Philip M., Schultz, Martin, Gerstein, Mark
Summary: Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular...
Mining periodic patterns with gap requirement from sequences (2005)
Minghua Zhang, Ben Kao, David W. Cheung, Kevin Y. Yip
We study a problem of mining frequently occurring periodic patterns with a gap requirement from sequences. Given a character sequence S of length L and a pattern P of length l, we consider P a...
Mining periodic patterns with gap requirement from sequences (2005)
Minghua Zhang, Ben Kao, David W. Cheung, Kevin Y. Yip
We study a problem of mining frequently occurring periodic patterns with a gap requirement from sequences. Given a character sequence S of length L and a pattern P of length l, weconsiderP a...
On discovery of extremely low-dimensional clusters using semi-supervised projected clustering (2005)
Recent studies suggest that projected clusters with extremely low dimensionality exist in many real datasets. A number of projected clustering algorithms have been proposed in the past several years,...
YeastHub: a semantic web use case for integrating data in the life sciences domain (2005)
Cheung, Kei-Hoi, Yip, Kevin Y., Smith, Andrew, DeKnikker, Remko, Masiar, Andy, Gerstein, Mark
Motivation: As the semantic web technology is maturing and the need for life sciences data integration over the web is growing, it is important to explore how data integration needs can be addressed...
A web services choreography scenario for interoperating bioinformatics applications (2004)
De Knikker, Remko, Guo, Youjun, Li, Jin-long, Kwan, Albert KH, Yip, Kevin Y, Cheung, David W, ...
Abstract Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are...
On Discovery of Extremely Low-Dimensional Clusters Using Semi-Supervised Projected Clustering (2004)
Kevin Y. Yip, David W. Cheung, Michael K. Ng
Recent studies suggest that projected clusters with extremely low dimensionality exist in many real datasets. A number of projected clustering algorithms have been proposed in the past several years,...
HARP: A practical projected clustering algorithm (2004)
Kevin Y. Yip, David W. Cheung, Ieee Computer Society, Michael K. Ng
Abstract—In high-dimensional data, clusters can exist in subspaces that hide themselves from traditional clustering methods. A number of algorithms have been proposed to identify such projected...
A Highly-usable Projected Clustering Algorithm for Gene Expression Profiles (2003)
Kevin Y. Yip, David W. Cheung, Michael K. Ng
Projected clustering has become a hot research topic due to its ability to cluster high-dimensional data. However, most existing projected clustering algorithms depend on some critical user...
A web services choreography scenario for interoperating bioinformatics applications
De Knikker, Remko, Guo, Youjun, Li, Jin-long, Kwan, Albert KH, Yip, Kevin Y, Cheung, David W, ...
A web services choreography scenario for interoperating bioinformatics applications
De Knikker, Remko, Guo, Youjun, Li, Jin-long, Kwan, Albert KH, Yip, Kevin Y, Cheung, David W, ...
Development of Grid-like Applications for Public Health Using Web 2.0 Mashup Techniques
Scotch, Matthew, Yip, Kevin Y., Cheung, Kei-Hoi
Development of public health informatics applications often requires the integration of multiple data sources. This process can be challenging due to issues such as different file formats, schemas,...
Motivation: An important problem in systems biology is reconstructing complete networks of interactions between biological objects by extrapolating from a few known interactions as examples. While...