DOI: 10.1093/bioinformatics/bth065 (2009)
A metric model of amino acid substitution
Errata for “A Metric Model of Amino Acid Substitution” (2008)
Weijia Xu, Weijia Xu, Daniel P. Miranker
Due to a programming error, two substitution values in the derived distance metric must be changed in order to form a metric rather than just one as stated in the paper. As a result, the value of the...
Abstract Indexing Protein Sequences in Metric Space (2008)
Weijia Xu, Daniel P. Miranker, Rui Mao, Shu Wang
The hyper-exponential growth of biological sequence data and complex queries demand new approaches of managing sequence databases where sequence data is preprocessed off-line and organized in data...
Willard S. Willard, Rui Mao, Wenguo Liu, Weijia Xu, Shulin Ni, Daniel P. Miranker
mSQL is an extended SQL query language targeting the expanding area of biological sequence databases and sequence analysis methods. The core aspects include first-class data types for biological...
Daniel P. Miranker, Willard J. Briggs, Rui Mao, Shulin Ni, Weijia Xu, Arthur Kaufmann, ...
The Bulletin of the Technical Committee on Data Engineering is published quarterly and is distributed to all TC members. Its scope includes the design, implementation, modelling, theory and...
Abstract MoBIoS: A Metric-Space DBMS to Support Biological Discovery 1 (2008)
Daniel Miranker, Weijia Xu, Rui Mao
MoBIoS is a specialized database management system whose storage manager is based on metric-space indexing, and whose query language entails biological data types. When relational database management...
On Metric-Space Indexing and Real Workloads (2008)
Rui Mao, Ving I. Lei, Smriti Ramakrishnan, Weijia Xu, Daniel P. Miranker
Contemporary technology is fostering new demands to manage large collections of complex data, including the contents of multimedia and biological databases. In many cases the similarity of the data...
Abstract Metric-Space Search of Protein Sequence Databases (2008)
Weijia Xu, Rui Mao, Shu Wang, Daniel P. Miranker
Motivation: Growing sequence databases are instigating sequence retrieval systems that construct k-mer (hot-spot) indexes off-line to speed up the on-line query execution. For fixed k, the content of...
Abstract MoBIoS: A Metric-Space DBMS to Support Biological Discovery 1 (2008)
Daniel Miranker, Weijia Xu, Rui Mao
MoBIoS is a specialized database management system whose storage manager is based on metric-space indexing, and whose query language entails biological data types. When relational database management...
BIOINFORMATICS ORIGINAL PAPER Data and Text mining (2006)
Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, ...
doi:10.1093/bioinformatics/btl118 A fast coarse filtering method for peptide identification by mass spectrometry
A fast coarse filtering method for peptide identification by mass spectrometry (2006)
Ramakrishnan, Smriti R., Mao, Rui, Nakorchevskiy, Aleksey A., Prince, John T., Willard, Willard S., Xu, Weijia, ...
Motivation: We reformulate the problem of comparing mass-spectra by mapping spectra to a vector space model. Our search method leverages a metric space indexing algorithm to produce an initial...
On Optimizing Distance-Based Similarity Search for Biological Databases (2005)
Rui Mao, Weijia Xu, Smriti Ramakrishnan, Glen Nuckolls, Daniel P. Miranker
Similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. We consider distance-based indexing for three...
DOI: 10.1093/bioinformatics/bth929 (2004)
Weijia Xu, Willard J. Briggs, Joanna Padolina, Ruth E. Timme, Wenguo Liu, Al Linder, ...
Vol. 20 Suppl. 1 2004, pages i355–i362
Biosequence use cases in mobios sql (2004)
Daniel P. Miranker, Willard J Briggs, Rui Mao, Shulin Ni, Weijia Xu
The sequencing and annotation of entire genomes has enriched the content of biological sequence databases such that new methods of sequence analysis, comparison and retrieval are being invented and...
A metric model of amino acid substitution (2004)
Xu, Weijia, Miranker, Daniel P.
Motivation: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed...
Xu, Weijia, Briggs, Willard J., Padolina, Joanna, Timme, Ruth E., Liu, Wenguo, Linder, C. Randal, ...
Motivation: For the purpose of identifying evolutionary reticulation events in flowering plants, we determine a large number of paired, conserved DNA oligomers that may be used as primers to amplify...
A metric model of amino acid substitution (2004)
Xu, Weijia, Miranker, Daniel P.
Motivation: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed...
A metric model of amino acid substitution (2004)
Xu, Weijia, Miranker, Daniel P.
Motivation: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed...
Motivation: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed...
An Assessment of a Metric Space Database Index to Support Sequence Homology (2003)
Rui Mao, Weijia Xu, Neha Singh, Daniel P. Miranker
Hierarchical metric-space clustering methods have been commonly used to organize proteomes into taxonomies. Consequently, it is often anticipated that hierarchical clustering can be leveraged as a...
SQL extensions and database mechanisms for managing biosequences (2003)
Willard J Briggs, Wenguo Liu, Rui Mao, Weijia Xu, Daniel P. Miranker
Biologically effective retrieval and analysis of sequences entails much more than finding matching strings. While identification and storage of biological sequences usually comprises long functional...
Evaluation of Lateral Strength and Deflection for Cracked Unreinforced Masonry Walls. (1998)
An analytical model for lateral strength and deflection of cracked unreinforced masonry walls is developed. Post cracked behavior is considered by neglecting shear transfer across cracked masonry....
Analysis of the effects of confinement on bond behavior /--by Weijia Xu. (1988)
Thesis (M.S.C.E.)--University of Washington, 1988.