McKernan, Kevin Judd, Peckham, Heather E., Costa, Gina L., McLaughlin, Stephen F., Fu, Yutao, Tsung, Eric F., ...
We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw...
Zhenjun Hu, Yutao Fu, Anason S. Halees, Szymon M. Kielbasa, Zhiping Weng
Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques...
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...
Nucleosome positioning signals in genomic DNA (2007)
Peckham, Heather E., Thurman, Robert E., Fu, Yutao, Stamatoyannopoulos, John A., Noble, William Stafford, Struhl, Kevin, ...
Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae...
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...
Zhang, Zhengdong D., Paccanaro, Alberto, Fu, Yutao, Weissman, Sherman, Weng, Zhiping, Chang, Joseph, ...
The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of...
Xi, Hualin, Yu, Yong, Fu, Yutao, Foley, Jonathan, Halees, Anason, Weng, Zhiping
A set of 723 high-quality human core promoter sequences were compiled and analyzed for overrepresented motifs. Beside the two well-characterized core promoter motifs (TATA and Inr), several known...
Transcription factor binding and modified histones in human bidirectional promoters (2007)
Lin, Jane M., Collins, Patrick J., Trinklein, Nathan D., Fu, Yutao, Xi, Hualin, Myers, Richard M., ...
Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of...
Letter Nucleosome positioning signals in genomic DNA (2007)
Heather E. Peckham, Robert E. Thurman, Yutao Fu, John A. Stamatoyannopoulos, William Stafford Noble, Kevin Struhl, ...
Access the most recent version at doi: 10.1101/gr.6101007
MotifViz: an analysis and visualization tool for motif discovery (2004)
Yutao Fu, Martin C. Frith, Peter M. Haverty, Zhiping Weng
Detecting overrepresented known transcription factor binding motifs in a set of promoter sequences of co-regulated genes has become an important approach to deciphering transcriptional regulatory...
Gene expression module discovery using gibbs sampling (2004)
Recent advances in high throughput profiling of gene expression have catalyzed an explosive growth in functional genomics aimed at the elucidation of genes that are differentially expressed in...
Hu, Zhenjun, Fu, Yutao, Halees, Anason S., Kielbasa, Szymon M., Weng, Zhiping
Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques...
MotifViz: an analysis and visualization tool for motif discovery (2004)
Fu, Yutao, Frith, Martin C., Haverty, Peter M., Weng, Zhiping
Detecting overrepresented known transcription factor binding motifs in a set of promoter sequences of co-regulated genes has become an important approach to deciphering transcriptional regulatory...
Detection of functional DNA motifs via statistical over-representation (2004)
Frith, Martin C., Fu, Yutao, Yu, Liqun, Chen, Jiang-Fan, Hansen, Ulla, Weng, Zhiping
The interaction of proteins with DNA recognition motifs regulates a number of fundamental biological processes, including transcription. To understand these processes, we need to know which motifs...
Fu, Yutao, O'Kelly, Charles, Sieracki, Michael, Distel, Daniel L.
Selective grazing by protists can profoundly influence bacterial community structure, and yet direct, quantitative observation of grazing selectivity has been difficult to achieve. In this...
Detection of functional DNA motifs via statistical over-representation
Frith, Martin C., Fu, Yutao, Yu, Liqun, Chen, Jiang-Fan, Hansen, Ulla, Weng, Zhiping
The interaction of proteins with DNA recognition motifs regulates a number of fundamental biological processes, including transcription. To understand these processes, we need to know which motifs...
MotifViz: an analysis and visualization tool for motif discovery
Fu, Yutao, Frith, Martin C., Haverty, Peter M., Weng, Zhiping
Detecting overrepresented known transcription factor binding motifs in a set of promoter sequences of co-regulated genes has become an important approach to deciphering transcriptional regulatory...
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
Hu, Zhenjun, Fu, Yutao, Halees, Anason S., Kielbasa, Szymon M., Weng, Zhiping
Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques...
Fu, Yutao, O'Kelly, Charles, Sieracki, Michael, Distel, Daniel L.
Selective grazing by protists can profoundly influence bacterial community structure, and yet direct, quantitative observation of grazing selectivity has been difficult to achieve. In this...
Detection of functional DNA motifs via statistical over-representation
Frith, Martin C., Fu, Yutao, Yu, Liqun, Chen, Jiang-Fan, Hansen, Ulla, Weng, Zhiping
The interaction of proteins with DNA recognition motifs regulates a number of fundamental biological processes, including transcription. To understand these processes, we need to know which motifs...
MotifViz: an analysis and visualization tool for motif discovery
Fu, Yutao, Frith, Martin C., Haverty, Peter M., Weng, Zhiping
Detecting overrepresented known transcription factor binding motifs in a set of promoter sequences of co-regulated genes has become an important approach to deciphering transcriptional regulatory...
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
Hu, Zhenjun, Fu, Yutao, Halees, Anason S., Kielbasa, Szymon M., Weng, Zhiping
Transcriptional regulation is one of the most basic regulatory mechanisms in the cell. The accumulation of multiple metazoan genome sequences and the advent of high-throughput experimental techniques...
Global mapping of c-Myc binding sites and target gene networks in human B cells
Zeller, Karen I., Zhao, XiaoDong, Lee, Charlie W. H., Chiu, Kuo Ping, Yao, Fei, Yustein, Jason T., ...
The protooncogene MYC encodes the c-Myc transcription factor that regulates cell growth, cell proliferation, cell cycle, and apoptosis. Although deregulation of MYC contributes to tumorigenesis, it...
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...
Zhang, Zhengdong D., Paccanaro, Alberto, Fu, Yutao, Weissman, Sherman, Weng, Zhiping, Chang, Joseph, ...
The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of...
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1
Xi, Hualin, Yu, Yong, Fu, Yutao, Foley, Jonathan, Halees, Anason, Weng, Zhiping
A set of 723 high-quality human core promoter sequences were compiled and analyzed for overrepresented motifs. Beside the two well-characterized core promoter motifs (TATA and Inr), several known...
Transcription factor binding and modified histones in human bidirectional promoters
Lin, Jane M., Collins, Patrick J., Trinklein, Nathan D., Fu, Yutao, Xi, Hualin, Myers, Richard M., ...
Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of...
Nucleosome positioning signals in genomic DNA
Peckham, Heather E., Thurman, Robert E., Fu, Yutao, Stamatoyannopoulos, John A., Noble, William Stafford, Struhl, Kevin, ...
Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae...
Fu, Yutao, Sinha, Manisha, Peterson, Craig L., Weng, Zhiping
Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent...
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...
McKernan, Kevin Judd, Peckham, Heather E., Costa, Gina L., McLaughlin, Stephen F., Fu, Yutao, Tsung, Eric F., ...
We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw...