BMC Bioinformatics BioMed Central (2009)
Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif
Research article Phylogenetic detection of conserved gene clusters in microbial genomes
Using shotgun sequence data to find active restriction enzyme genes (2009)
Zheng, Yu, Posfai, Janos, Morgan, Richard D., Vincze, Tamas, Roberts, Richard J.
Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological...
DISTRIBUTED ARCHITECTURE FOR LARGE SCALE IMAGE-BASED SEARCH (2008)
Yu Zheng, Xing Xie, Wei-ying Ma
In recent years, some computer vision algorithms such as SIFT (Scale Invariant Feature Transform) have been employed in image similarity match to perform image-based search applications. However,...
Trusted Computing-Based Security Architecture For 4G Mobile Networks (2008)
Yu Zheng, Dake He, Weichi Yu, Xiaohu Tang
In this paper security requirements and security architecture for 4G systems are presented with the consideration of Trusted Computing (TC) for mobile equipment (ME). The security framework based on...
Juhong Ha, Yu Zheng, Gary Geunbae Lee
One of the most significant problems in POS (Part-of-Speech) tagging of Chinese texts is an identification of words in a sentence, since there is no blank to delimit the words. Because it is...
AKA and Authorization Scheme For 4G Mobile Networks Based on Trusted Mobile Platform (2008)
Yu Zheng, Dake He, Xiaohu Tang, Hongxia Wang
Abstract―Future 4G mobile communication networks are expected to provide all IP-based services for heterogeneous wireless access technologies. Security service for mobile user as a major challenge...
Yu Zheng, Wen-han Qian, Yu Zheng, Wen-han Qian
Friction uncertainty and contact position uncertainty may have a disastrous effect on the closure properties of grasps. This paper reflects our approach to handling these uncertainties in...
Letter Computational Identification of Operons in Microbial Genomes (2007)
Yu Zheng, Joseph D. Szustakowski, Lance Fortnow, Richard J. Roberts, Simon Kasif
By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes...
Selection of restriction endonucleases using artificial cells (2007)
Zheng, Yu, Roberts, Richard J.
We describe in this article an in vitro system for the selection of restriction endonucleases using artificial cells. The artificial cells are generated in the form of a water-in-oil emulsion by in...
Some stochastic models and analysis for purchasing duration and brand switching (2007)
Dunn, Reader and Wrigley (1983) first observed in their UK diary data that, when the frequencies of inter-purchase times are plotted, the histograms are dominated by intervals of seven days and...
Some stochastic models and analysis for purchasing duration and brand switching (2007)
Department: Statistics.
Yu Zheng, Beer Christiane, Koester Mario, Wirth Manfred
Abstract Background Retroviral Gag determines virus assembly at the plasma membrane and the formation of virus-like particles in intracellular multivesicular bodies. Thereby, retroviruses exploit by...
Phylogenetic detection of conserved gene clusters in microbial genomes (2005)
Zheng, Yu, Anton, Brian P, Roberts, Richard J, Kasif, Simon
Abstract Background Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as...
Secure DRM scheme for future mobile networks based on trusted mobile platform (2005)
Yu Zheng, Dake He, Hongxia Wang, Xiaohu Tang
Abstract—With the emergence of wide bandwidth wireless networks, mobile Internet is set to provide a significant channel for multimedia content distribution. The need for mobile digital right...
Yu Zheng, Kejie Lu, Dapeng Wu, Yuguang Fang
How to provide high throughput performance is a major challenge in the design of MAC protocol for next generation wireless local area networks (WLANs) and wireless personal area networks (WPANs). To...
Performance Analysis of IEEE 802.11 DCF in Binary Symmetric Channels (2005)
Yu Zheng, Kejie Lu, Dapeng Wu, Yuguang Fang
IEEE 802.11 is the most important standard for wireless local area networks (WLANs). In IEEE 802.11, the fundamental medium access control (MAC) scheme is distributed coordination function (DCF),...
Summary: A graphics package has been developed for performing statistics on interatomic distances and torsion angles in protein secondary structures (STARS) from a protein crystal structure database....
Summary: A graphics package has been developed for performing statistics on inter-atomic distances and torsion angles in protein secondary structures (STARS) from a protein crystal structure...
Segmentally Variable Genes: A New Perspective on Adaptation (2004)
Yu Zheng, Richard J. Roberts, Simon Kasif
Segmentally variable genes show a mosaic pattern of one or more rapidly evolving, variable regions. Discerning their function may provide new insights into the forces that shape genome diversity and...
Segmentally Variable Genes: A New Perspective on Adaptation (2004)
Yu Zheng, Richard J. Roberts, Simon Kasif
Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes...
Identification of genes with fast-evolving regions in microbial genomes (2004)
Zheng, Yu, Roberts, Richard J., Kasif, Simon
Complete sequences of multiple strains of the same microbial species provide an invaluable source for studying the evolutionary dynamics between orthologous genes over a relatively short time scale....
High-frequency on-chip interconnect characterization and measurement (2003)
With technology scaling, interconnect analysis becomes critical in timing and noise analysis. As slew times are being driven below 50 psec and on-chip frequency content is approaching 10 GHz,...
High-frequency on-chip interconnect characterization and measurement (2003)
Department: Electrical Engineering.
Genomic functional annotation using co-evolution profiles of gene clusters (2002)
Zheng, Yu, Roberts, Richard J, Kasif, Simon
Abstract Background The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains...
Computational Identification of Operons in Microbial Genomes (2002)
Zheng, Yu, Szustakowski, Joseph D., Fortnow, Lance, Roberts, Richard J., Kasif, Simon
On-chip oscilloscopes for noninvasive time-domain measurement of waveforms (2001)
Yu Zheng, Student Member, Kenneth L. Shepard
Abstract—High-speed digital design is becoming increasingly analog. In particular, interconnect response at high frequencies can be nonmonotonic with “porch steps ” and ringing. Crosstalk (both...
three-dimensional, shapes-based RLC extraction (2000)
K. L. Shepard, D. Sitaram, Yu Zheng
In this paper, we report the developmentof the first commercial fullchip, three-dimensional, shapes-based, RLCK extraction tool, developed as part of a university-industry collaboration. The...
Genomic functional annotation using co-evolution profiles of gene clusters
Zheng, Yu, Roberts, Richard J, Kasif, Simon
The current speed of sequencing already exceeds the capability of annotation. A new method for functional annotation is proposed using the conservation patterns of gene clusters and has been applied...
Computational Identification of Operons in Microbial Genomes
Zheng, Yu, Szustakowski, Joseph D., Fortnow, Lance, Roberts, Richard J., Kasif, Simon
By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes...
Whole-genome annotation by using evidence integration in functional-linkage networks
Karaoz, Ulas, Murali, T. M., Letovsky, Stan, Zheng, Yu, Ding, Chunming, Cantor, Charles R., ...
The advent of high-throughput biology has catalyzed a remarkable improvement in our ability to identify new genes. A large fraction of newly discovered genes have an unknown functional role,...
Segmentally Variable Genes:A New Perspective on Adaptation
Zheng, Yu, Roberts, Richard J, Kasif, Simon
Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes...
Identification of genes with fast-evolving regions in microbial genomes
Zheng, Yu, Roberts, Richard J., Kasif, Simon
Complete sequences of multiple strains of the same microbial species provide an invaluable source for studying the evolutionary dynamics between orthologous genes over a relatively short time scale....
Characterization of Two New Aminopeptidases in Escherichia coli
Zheng, Yu, Roberts, Richard J., Kasif, Simon, Guan, Chudi
Two genes in the Escherichia coli genome, ypdE and ypdF, have been cloned and expressed, and their products have been purified. YpdF is shown to be a metalloenzyme with Xaa-Pro aminopeptidase...
Genomic functional annotation using co-evolution profiles of gene clusters
Zheng, Yu, Roberts, Richard J, Kasif, Simon
The current speed of sequencing already exceeds the capability of annotation. A new method for functional annotation is proposed using the conservation patterns of gene clusters and has been applied...
Computational Identification of Operons in Microbial Genomes
Zheng, Yu, Szustakowski, Joseph D., Fortnow, Lance, Roberts, Richard J., Kasif, Simon
By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes...
Whole-genome annotation by using evidence integration in functional-linkage networks
Karaoz, Ulas, Murali, T. M., Letovsky, Stan, Zheng, Yu, Ding, Chunming, Cantor, Charles R., ...
The advent of high-throughput biology has catalyzed a remarkable improvement in our ability to identify new genes. A large fraction of newly discovered genes have an unknown functional role,...
Segmentally Variable Genes:A New Perspective on Adaptation
Zheng, Yu, Roberts, Richard J, Kasif, Simon
Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes...
Identification of genes with fast-evolving regions in microbial genomes
Zheng, Yu, Roberts, Richard J., Kasif, Simon
Complete sequences of multiple strains of the same microbial species provide an invaluable source for studying the evolutionary dynamics between orthologous genes over a relatively short time scale....
Characterization of Two New Aminopeptidases in Escherichia coli
Zheng, Yu, Roberts, Richard J., Kasif, Simon, Guan, Chudi
Two genes in the Escherichia coli genome, ypdE and ypdF, have been cloned and expressed, and their products have been purified. YpdF is shown to be a metalloenzyme with Xaa-Pro aminopeptidase...
Selection of restriction endonucleases using artificial cells
Zheng, Yu, Roberts, Richard J.
We describe in this article an in vitro system for the selection of restriction endonucleases using artificial cells. The artificial cells are generated in the form of a water-in-oil emulsion by in...
Using shotgun sequence data to find active restriction enzyme genes
Zheng, Yu, Posfai, Janos, Morgan, Richard D., Vincze, Tamas, Roberts, Richard J.
Whole genome shotgun sequence analysis has become the standard method for beginning to determine a genome sequence. The preparation of the shotgun sequence clones is, in fact, a biological...