with repeated and shuffled elements (2008)
Benjamin Raphael, Degui Zhi, Haixu Tang, Pavel Pevzner
A novel method for multiple alignment of sequences
Local Structural Comparison with Global Structural Descriptors (2008)
Degui Zhi, Maxim Shatsky, Steven E. Brenner
Protein sequence and structure are fundamental objects in computational biology. The sequence comparison problem has been widely addressed, resulting in a spectrum of algorithms ranging from the...
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly (2008)
Degui Zhi, Uri Keich, Pavel Pevzner, Steffen Heber, Haixu Tang
Abstract—Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the...
Benjamin Raphael, Degui Zhi, Haixu Tang, Pavel Pevzner, Email Alerting, Benjamin Raphael, ...
A novel method for multiple alignment of sequences with repeated
Benjamin Raphael, Degui Zhi, Haixu Tang, Pavel Pevzner, Email Alerting, Benjamin Raphael, ...
A novel method for multiple alignment of sequences with repeated
Representing and comparing protein structures as paths in three-dimensional space (2006)
Zhi, Degui, Krishna, S Sri, Cao, Haibo, Pevzner, Pavel, Godzik, Adam
Abstract Background Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a...
Identifying repeat domains in large genomes (2006)
Zhi, Degui, Raphael, Benjamin J, Price, Alkes L, Tang, Haixu, Pevzner, Pavel A
Abstract We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short...
Roepcke, Stefan, Zhi, Degui, Vingron, Martin, Arndt, Peter F.
For ribosomal protein (RP) genes the start of transcription is rigidly controlled to maintain the 5′-TOP signal on the messenger RNA. The responsible regulatory mechanism is not yet fully...
Biological molecules are composed of discrete units, called domains. The study of the identity and organization of these domains can reveal the correspondence between individual units in different...
Discovery and analysis of mosaic arrangements in biological sequences and structures (2006)
Thesis (Ph. D.)--University of California, San Diego, 2006.
Bmc Bioinformatics, Degui Zhi, S Sri Krishna, Haibo Cao, Pavel Pevzner, Adam Godzik
Research article Representing and comparing protein structures as paths in three-dimensional space
AliWABA: alignment on the web through an A-Bruijn approach (2006)
Jones, Neil C., Zhi, Degui, Raphael, Benjamin J.
Multiple sequence alignment programs are an invaluable tool in computational biology. A-Bruijn Alignment (ABA) is a method for multiple sequence alignment that represents an alignment as a directed...
A novel method for multiple alignment of sequences with repeated and shuffled elements (2004)
Raphael, Benjamin, Zhi, Degui, Tang, Haixu, Pevzner, Pavel
We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an...
A novel method for multiple alignment of sequences with repeated and shuffled elements
Raphael, Benjamin, Zhi, Degui, Tang, Haixu, Pevzner, Pavel
We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an...
Identifying repeat domains in large genomes
Zhi, Degui, Raphael, Benjamin J, Price, Alkes L, Tang, Haixu, Pevzner, Pavel A
A graph-based method for the analysis of repeat families in a repeat library is presented that helps elucidating the evolutionary history of repeats.
AliWABA: alignment on the web through an A-Bruijn approach
Jones, Neil C., Zhi, Degui, Raphael, Benjamin J.
Multiple sequence alignment programs are an invaluable tool in computational biology. A-Bruijn Alignment (ABA) is a method for multiple sequence alignment that represents an alignment as a directed...
Representing and comparing protein structures as paths in three-dimensional space
Zhi, Degui, Krishna, S Sri, Cao, Haibo, Pevzner, Pavel, Godzik, Adam
A novel method for multiple alignment of sequences with repeated and shuffled elements
Raphael, Benjamin, Zhi, Degui, Tang, Haixu, Pevzner, Pavel
We describe ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences. The major difference between ABA and existing multiple alignment methods is that ABA represents an...
Identifying repeat domains in large genomes
Zhi, Degui, Raphael, Benjamin J, Price, Alkes L, Tang, Haixu, Pevzner, Pavel A
A graph-based method for the analysis of repeat families in a repeat library is presented that helps elucidating the evolutionary history of repeats.
AliWABA: alignment on the web through an A-Bruijn approach
Jones, Neil C., Zhi, Degui, Raphael, Benjamin J.
Multiple sequence alignment programs are an invaluable tool in computational biology. A-Bruijn Alignment (ABA) is a method for multiple sequence alignment that represents an alignment as a directed...