Abstract Background Cyclic AMP receptor protein (CRP), also known as catabolite gene activator protein (CAP), is an important transcriptional regulator widely distributed in many bacteria. The...
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes (2009)
Zhang, Shaoqiang, Xu, Minli, Li, Shan, Su, Zhengchang
Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the...
CUBIC: Search for Binding Sites (2008)
Victor Olman, Jizhu Lu, Phuongan Dam, Zhengchang Su, Ying Xu
The regulation of gene transcription is achieved through specific interactions between transcription factors and their binding sites in the upstream region of the gene being regulated. Correct...
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation (2008)
Peng Wang, Zhengchang Su, Juntao Guo, Ying Xu
Receptor tyrokine kinases are critical regulators of signal transduction pathways mediating cellular homeostasis. Enhanced kinase activities via mutation and other genetic alternations have been...
Computational prediction of Pho regulons in cyanobacteria (2007)
Su, Zhengchang, Olman, Victor, Xu, Ying
Abstract Background Phosphorus is an essential element for all life forms. However, it is limiting in most ecological environments where cyanobacteria inhabit. Elucidation of the phosphorus...
Operon prediction in Pyrococcus furiosus (2007)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Operon prediction using both genome-specific and general genomic information (2007)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Thao T. Tran, Phuongan Dam, Zhengchang Su, G. Tong Zhou, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
and general genomic information (2006)
Phuongan Dam, Victor Olman, Kyle Harris, Zhengchang Su, Ying Xu
Operon prediction using both genome-specific
doi:10.1093/nar/gkl974 Operon prediction in Pyrococcus furiosus (2006)
Thao T. Tran, Phuongan Dam, Zhengchang Su, G. Tong Zhou, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
Operon prediction using both genome-specific and general genomic information (2006)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Operon prediction in Pyrococcus furiosus (2006)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Operon prediction using both genome-specific and general genomic information (2006)
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Operon prediction in Pyrococcus furiosus (2006)
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Computational inference and experimental validation (2005)
Zhengchang Su, Fenglou Mao, Phuongan Dam, Hongwei Wu, Victor Olman, Ian T. Paulsen, ...
of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes (2004)
Victor Olman, Hanchuan Peng, Zhengchang Su, Ying Xu
We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a...
Computational Prediction of Operons in Synechococcus sp. WH8102 (2004)
Synechococcus Sp. Wh, Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang
We computationally predict operons in the Synechococcus sp. WH8102 genome based on three types of genomic data: intergenic distances, COG gene functions and phylogenetic profiles. In the proposed...
In silico reconstruction of the carbon fixation pathway in Synechococcus sp. WH8102 (2004)
Phuongan Dam, Zhengchang Su, Victor Olman, Ying Xu
The carbon fixation pathway plays an essential role in the primary production and natural carbon recycling process. In this paper, we present a computational model of the carbon fixation pathway in...
Zhengchang Su, Phuongan Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Palenik, ...
We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through literature search, mining "high-throughput" biological data of various...
Thesis (Ph. D.)--University of Alabama at Birmingham, School of Joint Health Sciences, 2000.
Csutora, Peter, Su, Zhengchang, Kim, Hak Yong, Bugrim, Andrej, Cunningham, Kyle W., Nuccitelli, Richard, ...
Depletion of endoplasmic reticulum Ca2+ stores leads to the entry of extracellular Ca2+ into the cytoplasm, a process termed capacitative or store-operated Ca2+ entry. Partially purified extracts...
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Su, Zhengchang, Shoemaker, Richard L., Marchase, Richard B., Blalock, J. Edwin
The Ca2+ release-activated Ca2+ (CRAC) channel is the most well documented of the store-operated ion channels that are widely expressed and are involved in many important biological processes....
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
Mao, Fenglou, Su, Zhengchang, Olman, Victor, Dam, Phuongan, Liu, Zhijie, Xu, Ying
Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene...
Csutora, Peter, Su, Zhengchang, Kim, Hak Yong, Bugrim, Andrej, Cunningham, Kyle W., Nuccitelli, Richard, ...
Depletion of endoplasmic reticulum Ca2+ stores leads to the entry of extracellular Ca2+ into the cytoplasm, a process termed capacitative or store-operated Ca2+ entry. Partially purified extracts...
Prediction of functional modules based on comparative genome analysis and Gene Ontology application
Wu, Hongwei, Su, Zhengchang, Mao, Fenglou, Olman, Victor, Xu, Ying
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency...
Su, Zhengchang, Olman, Victor, Mao, Fenglou, Xu, Ying
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence...
Su, Zhengchang, Shoemaker, Richard L., Marchase, Richard B., Blalock, J. Edwin
The Ca2+ release-activated Ca2+ (CRAC) channel is the most well documented of the store-operated ion channels that are widely expressed and are involved in many important biological processes....
Mao, Fenglou, Su, Zhengchang, Olman, Victor, Dam, Phuongan, Liu, Zhijie, Xu, Ying
Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene...
Su, Zhengchang, Mao, Fenglou, Dam, Phuongan, Wu, Hongwei, Olman, Victor, Paulsen, Ian T., ...
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem,...
Operon prediction in Pyrococcus furiosus
Tran, Thao T., Dam, Phuongan, Su, Zhengchang, Poole, Farris L., Adams, Michael W. W., Zhou, G. Tong, ...
Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in...
Operon prediction using both genome-specific and general genomic information
Dam, Phuongan, Olman, Victor, Harris, Kyle, Su, Zhengchang, Xu, Ying
We have carried out a systematic analysis of the contribution of a set of selected features that include three new features to the accuracy of operon prediction. Our analyses have led to a number of...
Novel Changes in Discoidal High Density Lipoprotein Morphology: A Molecular Dynamics Study
Catte, Andrea, Patterson, James C., Jones, Martin K., Jerome, W. Gray, Bashtovyy, Denys, Su, Zhengchang, ...
ApoA-I is a uniquely flexible lipid-scavenging protein capable of incorporating phospholipids into stable particles. Here we report molecular dynamics simulations on a series of progressively smaller...
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
Zhang, Shaoqiang, Xu, Minli, Li, Shan, Su, Zhengchang
Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the...