Predictive chromatin signatures in the mammalian genome (2009)
Hon, Gary C., Hawkins, R. David, Ren, Bing
The DNA sequence of an organism is a blueprint of life: it harbors not only the information about proteins and other molecules produced in each cell, but also instructions on when and where such...
Prediction of regulatory elements in mammalian genomes using chromatin signatures (2008)
Won, Kyoung-Jae, Chepelev, Iouri, Ren, Bing, Wang, Wei
Abstract Background Recent genomic scale survey of epigenetic states in the mammalian genomes has shown that promoters and enhancers are correlated with distinct chromatin signatures, providing a...
2306 Genome-Wide Location and Function of DNA Binding Proteins (2008)
Bing Ren, François Robert, John J. Wyrick, Oscar Aparicio, Ezra G. Jennings, Itamar Simon, ...
Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We...
Networks in Saccharomyces cerevisiae (2008)
S. Nicholson, S. Some, B. Kone, J. Clim, Tong Ihn Lee, Nicola J. Rinaldi, ...
transport (32). The model was also used for tracer forecasts during the MINOS campaign. 40. E. Roeckner et al. “The atmospheric general circulation model ECHAM-4: Model description and simulation...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Barrera, Leah O., Li, Zirong, Smith, Andrew D., Arden, Karen C., Cavenee, Webster K., Zhang, Michael Q., ...
By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic...
Bmc Bioinformatics, Kyoung-jae Won, Iouri Chepelev, Bing Ren, Wei Wang, Kyoung-jae Won, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Prediction of regulatory elements in...
Margaret Burnett, Andrei Sheretov, Bing Ren, Gregg Rothermel
Although there has been recent research into ways to design environments that enable end users to create their own programs, little attention has been given to helping these end users systematically...
Hualin Xi, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, ...
The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI...
Hualin Xi, Hennady P Shulha, Jane M Lin, Teresa R Vales, Yutao Fu, David M Bodine, ...
The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type-specific and housekeeping gene expression. Mapping DNaseI...
An all-round view of eukaryotic transcription (2006)
A report of the Keystone Symposium 'Regulation of Eukaryotic Transcription: From Chromatin to mRNA', Taos, USA, 21-26 April 2006.
Genome-wide location analysis: insights on transcriptional regulation (2006)
Gene expression analysis of microarray data can provide a global view of the transcriptome of a cell or specific tissue type, revealing important information about the kinds of signaling pathways,...
ChIP-chip: Data, Model, and Analysis (2005)
Zheng, Ming, Barrera, Leah O., Ren, Bing, Wu, Ying N
ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA binding proteins in living cells. The ChIP-chip data can be obtained over the...
China has been undergoing economic reform and institutional transition from a planned economy to a market economy in the past twenty years. An important product of this is the emergence of...
"August 2005."
Thesis (Ph.D.)--The Chinese University of Hong Kong, 2005.
Direct isolation and identification of promoters in the human genome (2005)
Kim, Tae Hoon, Barrera, Leah O., Qu, Chunxu, Van Calcar, Sara, Trinklein, Nathan D., Cooper, Sara J., ...
Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human...
Direct isolation and identification of promoters in the human genome (2005)
Kim, Tae Hoon, Barrera, Leah O., Qu, Chunxu, Van Calcar, Sara, Trinklein, Nathan D., Cooper, Sara J., ...
Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human...
Thesis (Ph. D.)--University of Alabama at Birmingham, School of Joint Health Sciences, 2003.
E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints (2002)
Ren, Bing, Cam, Hieu, Takahashi, Yasuhiko, Volkert, Thomas, Terragni, Jolyon, Young, Richard A., ...
Visually testing recursive programs in spreadsheet languages (2001)
Margaret Burnett, Bing Ren, Andrew Ko, Curtis Cook, Gregg Rothermel
Although there has been recent research into ways to design visual programming languages and environments, little attention has been given to systematic testing in these languages, and what work has...
Visually Testing Recursive Programs in Spreadsheet Languages (2001)
Margaret Burnett Bing, Bing Ren, Andrew Ko, Curtis Cook, Gregg Rothermel
Although there has been recent research into ways to design visual programming languages and environments, little attention has been given to systematic testing in these languages, and what work has...
Monte-Carlo Simulation Methods for Finite Flat Plate Winding Flows. (1998)
Shi, Yuzhong, Wu, Qifen, Ren, Bing
This article opts for the use of direct simulation Monte-Carlo methods to solve such problems as those associated with winding flows around flat plates of finite length. The methods in question are...
Mechanisms of transcriptional repression /--a thesis presented by Bing Ren. (1998)
Thesis (Ph. D.)--Harvard University, 1998.
Thesis (Ph. D.)--Michigan State University. Dept. of Biochemistry, 1998.
Remodeling of Yeast Genome Expression in Response to Environmental Changes
Causton, Helen C., Ren, Bing, Koh, Sang Seok, Harbison, Christopher T., Kanin, Elenita, Jennings, Ezra G., ...
We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in...
Ren, Bing, Szalai, Alexander J., Thomas, Orlanda, Hollingshead, Susan K., Briles, David E.
Pneumococcal surface protein A (PspA), a virulence factor of Streptococcus pneumoniae, is exceptionally diverse, being classified into two major families which are over 50% divergent by sequence...
Roche, Hazeline, Ren, Bing, McDaniel, Larry S., Håkansson, Anders, Briles, David E.
Pneumococcal surface protein A (PspA) is able to elicit antibodies in mice and humans that can protect mice against fatal infection with Streptococcus pneumoniae. It has been observed that...
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
Li, Zirong, Van Calcar, Sara, Qu, Chunxu, Cavenee, Webster K., Zhang, Michael Q., Ren, Bing
Overexpression of c-Myc is one of the most common alterations in human cancers, yet it is not clear how this transcription factor acts to promote malignant transformation. To understand the molecular...
PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins
Ren, Bing, Chee, Kerlen J., Kim, Tae Hoon, Maniatis, Tom
The PRDI-BF1/Blimp-1 protein is a transcriptional repressor required for normal B-cell differentiation, and it has been implicated in the repression of β-interferon (IFN-β) and c-myc gene...
Ren, Bing, Szalai, Alexander J., Hollingshead, Susan K., Briles, David E.
Streptococcus pneumoniae infection is a frequent cause of pneumonia, otitis media, meningitis, and septicemia. Pneumococcal surface protein A (PspA) is an important virulence factor on the pathogen...
Direct isolation and identification of promoters in the human genome
Kim, Tae Hoon, Barrera, Leah O., Qu, Chunxu, Van Calcar, Sara, Trinklein, Nathan D., Cooper, Sara J., ...
Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human...
E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints
Ren, Bing, Cam, Hieu, Takahashi, Yasuhiko, Volkert, Thomas, Terragni, Jolyon, Young, Richard A., ...
The E2F transcription factor family is known to play a key role in the timely expression of genes required for cell cycle progression and proliferation, but only a few E2F target genes have been...
Remodeling of Yeast Genome Expression in Response to Environmental Changes
Causton, Helen C., Ren, Bing, Koh, Sang Seok, Harbison, Christopher T., Kanin, Elenita, Jennings, Ezra G., ...
We used genome-wide expression analysis to explore how gene expression in Saccharomyces cerevisiae is remodeled in response to various changes in extracellular environment, including changes in...
Ren, Bing, Szalai, Alexander J., Thomas, Orlanda, Hollingshead, Susan K., Briles, David E.
Pneumococcal surface protein A (PspA), a virulence factor of Streptococcus pneumoniae, is exceptionally diverse, being classified into two major families which are over 50% divergent by sequence...
E2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpoints
Ren, Bing, Cam, Hieu, Takahashi, Yasuhiko, Volkert, Thomas, Terragni, Jolyon, Young, Richard A., ...
The E2F transcription factor family is known to play a key role in the timely expression of genes required for cell cycle progression and proliferation, but only a few E2F target genes have been...
Roche, Hazeline, Ren, Bing, McDaniel, Larry S., Håkansson, Anders, Briles, David E.
Pneumococcal surface protein A (PspA) is able to elicit antibodies in mice and humans that can protect mice against fatal infection with Streptococcus pneumoniae. It has been observed that...
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
Li, Zirong, Van Calcar, Sara, Qu, Chunxu, Cavenee, Webster K., Zhang, Michael Q., Ren, Bing
Overexpression of c-Myc is one of the most common alterations in human cancers, yet it is not clear how this transcription factor acts to promote malignant transformation. To understand the molecular...
PRDI-BF1/Blimp-1 repression is mediated by corepressors of the Groucho family of proteins
Ren, Bing, Chee, Kerlen J., Kim, Tae Hoon, Maniatis, Tom
The PRDI-BF1/Blimp-1 protein is a transcriptional repressor required for normal B-cell differentiation, and it has been implicated in the repression of β-interferon (IFN-β) and c-myc gene...
Ren, Bing, Szalai, Alexander J., Hollingshead, Susan K., Briles, David E.
Streptococcus pneumoniae infection is a frequent cause of pneumonia, otitis media, meningitis, and septicemia. Pneumococcal surface protein A (PspA) is an important virulence factor on the pathogen...
Direct isolation and identification of promoters in the human genome
Kim, Tae Hoon, Barrera, Leah O., Qu, Chunxu, Van Calcar, Sara, Trinklein, Nathan D., Cooper, Sara J., ...
Transcriptional regulatory elements play essential roles in gene expression during animal development and cellular response to environmental signals, but our knowledge of these regions in the human...
An all-round view of eukaryotic transcription
A report of the Keystone Symposium 'Regulation of Eukaryotic Transcription: From Chromatin to mRNA', Taos, USA, 21-26 April 2006.
Xi, Hualin, Shulha, Hennady P, Lin, Jane M, Vales, Teresa R, Fu, Yutao, Bodine, David M, ...
The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI...
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
Barrera, Leah O., Li, Zirong, Smith, Andrew D., Arden, Karen C., Cavenee, Webster K., Zhang, Michael Q., ...
By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
Hon, Gary, Ren, Bing, Wang, Wei
Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory...
An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome
Won, Kyoung-Jae, Agarwal, Saurabh, Shen, Li, Shoemaker, Robert, Ren, Bing, Wang, Wei
In eukaryotic genomes, it is challenging to accurately determine target sites of transcription factors (TFs) by only using sequence information. Previous efforts were made to tackle this task by...
China’s business network structure during institutional transitions
Bing Ren, Kevin Au, Thomas Birtch
Business networks, Interlocking directorates, China, Institutional transitions,
Li, Yan, Reddy, Marpadga A., Miao, Feng, Shanmugam, Narkunaraja, Yee, Jiing-Kuan, Hawkins, David, ...
Nuclear factor κ-B (NF-κB)-regulated inflammatory genes, such as TNF-α (tumor necrosis factor-α), play key roles in the pathogenesis of inflammatory diseases, including diabetes and the metabolic...
Discovery and Annotation of Functional Chromatin Signatures in the Human Genome
Hon, Gary, Wang, Wei, Ren, Bing
Transcriptional regulation in human cells is a complex process involving a multitude of regulatory elements encoded by the genome. Recent studies have shown that distinct chromatin signatures mark a...