Liu, Yuen-Jong, Zheng, Deyou, Balasubramanian, Suganthi, Carriero, Nicholas, Khurana, Ekta, Robilotto, Rebecca, ...
Abstract Background Pseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes...
Profiling RE1/REST-mediated histone modifications in the human genome (2009)
Zheng, Deyou, Zhao, Keji, Mehler, Mark F
Abstract Background The transcriptional repressor REST (RE1 silencing transcription factor, also called NRSF for neuron-restrictive silencing factor) binds to a conserved RE1 motif and represses many...
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes (2009)
Balasubramanian, Suganthi, Zheng, Deyou, Liu, Yuen-Jong, Fang, Gang, Frankish, Adam, Carriero, Nicholas, ...
Abstract Background The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a...
Abstract Background Sequencing and annotation of several mammalian genomes have revealed that segmental duplications are a common architectural feature of primate genomes; in fact, about 5% of the...
PseudoPipe: an automated pseudogene identification pipeline (2008)
Genome Analysis, Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John Karro, Paul M. Harrison, ...
doi:10.1093/bioinformatics/btl116
What is a gene, post-ENCODE? History and updated definition (2007)
Gerstein, Mark B., Bruce, Can, Rozowsky, Joel S., Zheng, Deyou, Du, Jiang, Korbel, Jan O., ...
While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of...
Trinklein, Nathan D., Karaöz, Ulas, Wu, Jiaqian, Halees, Anason, Force Aldred, Shelley, Collins, Patrick J., ...
The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to...
Rozowsky, Joel S., Newburger, Daniel, Sayward, Fred, Wu, Jiaqian, Jordan, Greg, Korbel, Jan O., ...
For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we...
Zheng, Deyou, Frankish, Adam, Baertsch, Robert, Kapranov, Philipp, Reymond, Alexandre, Choo, Siew Woh, ...
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes....
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation (2007)
Karro, John E., Yan, Yangpan, Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Cayting, Philip, ...
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different...
A computational approach for identifying pseudogenes in the ENCODE regions (2006)
Zheng, Deyou, Gerstein, Mark B
Abstract Background Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying...
m-Berezin transform and compact operators (2006)
Zheng, Deyou, Nam, Kyesook, Zhong, Changyong
m-Berezin transforms are introduced for bounded operators on the Bergman space of the unit ball. The norm of the m-Berezin transform as a linear operator from the space of bounded operators to L8 is...
PseudoPipe: an automated pseudogene identification pipeline (2006)
Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John Karro, Paul M. Harrison, Mark Gerstein, ...
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
PseudoPipe: an automated pseudogene identification pipeline (2006)
Zhang, Zhaolei, Carriero, Nicholas, Zheng, Deyou, Karro, John, Harrison, Paul M., Gerstein, Mark
Motivation: Mammalian genomes contain many ‘genomic fossils’ i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or...
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Harrison, Paul M., Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Gerstein, Mark
Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete...
Zheng, Deyou, Aramini, James M., Montelione, Gaetano T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
ZHENG, DEYOU, ARAMINI, JAMES M., MONTELIONE, GAETANO T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
Chern-sing Goh, Ning Lan, Nathaniel Echols, Shawn M. Douglas, Duncan Milburn, Paul Bertone, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at
Access the most recent version at doi: 10.1110/ps.0300203 References (2003)
Deyou Zheng, Yuanpeng J. Huang, Rong Xiao, James Aramini, ...
Automated protein fold determination using a minimal NMR
Automated protein fold determination using a minimal NMR constraint strategy (2003)
Zheng, Deyou, Huang, Yuanpeng J., Moseley, Hunter N.B., Xiao, Rong, Aramini, James, Swapna, G.V.T., ...
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold...
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Harrison, Paul M., Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Gerstein, Mark
Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete...
Coric, Tatjana, Zheng, Deyou, Gerstein, Mark, Canessa, Cecilia M
The acid-sensitive ion channel 1 (ASIC1) is a neuronal Na+ channel insensitive to changes in membrane potential but is gated by external protons. Proton sensitivity is believed to be essential for...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Harrison, Paul M., Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Gerstein, Mark
Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete...
Coric, Tatjana, Zheng, Deyou, Gerstein, Mark, Canessa, Cecilia M
The acid-sensitive ion channel 1 (ASIC1) is a neuronal Na+ channel insensitive to changes in membrane potential but is gated by external protons. Proton sensitivity is believed to be essential for...
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
Karro, John E., Yan, Yangpan, Zheng, Deyou, Zhang, Zhaolei, Carriero, Nicholas, Cayting, Philip, ...
The Pseudogene.org knowledgebase serves as a comprehensive repository for pseudogene annotation. The definition of a pseudogene varies within the literature, resulting in significantly different...
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
Trinklein, Nathan D., Karaöz, Ulaş, Wu, Jiaqian, Halees, Anason, Force Aldred, Shelley, Collins, Patrick J., ...
The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to...
Rozowsky, Joel S., Newburger, Daniel, Sayward, Fred, Wu, Jiaqian, Jordan, Greg, Korbel, Jan O., ...
For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we...
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
Zheng, Deyou, Frankish, Adam, Baertsch, Robert, Kapranov, Philipp, Reymond, Alexandre, Choo, Siew Woh, ...
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes....
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Zheng, Deyou, Aramini, James M., Montelione, Gaetano T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
Automated protein fold determination using a minimal NMR constraint strategy
Zheng, Deyou, Huang, Yuanpeng J., Moseley, Hunter N.B., Xiao, Rong, Aramini, James, Swapna, G.V.T., ...
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold...
A systematic analysis of histone modifications between human segmental duplications shows that two seemingly identical genomic copies have distinct epigenomic properties.
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
Balasubramanian, Suganthi, Zheng, Deyou, Liu, Yuen-Jong, Fang, Gang, Frankish, Adam, Carriero, Nicholas, ...
An analysis of ribosomal protein pseudogenes in the four mammalian genomes reveals no correlation between number of pseudogenes and mRNA abundance.
Small RNAs Originated from Pseudogenes: cis- or trans-Acting?
Guo, Xingyi, Zhang, Zhaolei, Gerstein, Mark B., Zheng, Deyou
Pseudogenes are significant components of eukaryotic genomes, and some have acquired novel regulatory roles. To date, no study has characterized rice pseudogenes systematically or addressed their...