Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae (2005)
Chih Long Liu, Tommy Kaplan, Minkyu Kim, Stephen Buratowski, Stuart L. Schreiber, Nir Friedman, ...
High-resolution microarrays were used to investigate 12 histone modifications across thousands of yeast nucelosomes in vivo. Two main groups co-occurred, consistent with the redundant histone code...
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae (2005)
Chih Long Liu, Tommy Kaplan, Minkyu Kim, Stephen Buratowski, Stuart L. Schreiber, Nir Friedman, ...
Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has...
Development and validation of a T7 based linear amplification for genomic DNA (2003)
Liu, Chih Long, Schreiber, Stuart L, Bernstein, Bradley E
Abstract Background Genomic maps of transcription factor binding sites and histone modification patterns provide unique insight into the nature of gene regulatory networks and chromatin structure....
Stereotyped and specific gene expression programs in human innate immune responses to bacteria
Boldrick, Jennifer C., Alizadeh, Ash A., Diehn, Maximilian, Dudoit, Sandrine, Liu, Chih Long, Belcher, Christopher E., ...
The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene...
Precision and functional specificity in mRNA decay
Wang, Yulei, Liu, Chih Long, Storey, John D., Tibshirani, Robert J., Herschlag, Daniel, Brown, Patrick O.
Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal...
Diehn, Maximilian, Alizadeh, Ash A., Rando, Oliver J., Liu, Chih Long, Stankunas, Kryn, Botstein, David, ...
Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic...
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Yoav, Wang, Yulei, Storey, John D., Liu, Chih Long, Brown, Patrick O., Herschlag, Daniel
We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the...
Global nucleosome occupancy in yeast
Bernstein, Bradley E, Liu, Chih Long, Humphrey, Emily L, Perlstein, Ethan O, Schreiber, Stuart L
A genome-wide study of nucleosome occupancy at yeast promoters shows that promoters that regulate active genes, contain multiple conserved motifs, or contain Rap1 binding sites tend to be depleted of...
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
Liu, Chih Long, Kaplan, Tommy, Kim, Minkyu, Buratowski, Stephen, Schreiber, Stuart L, Friedman, Nir, ...
Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has...
Stereotyped and specific gene expression programs in human innate immune responses to bacteria
Boldrick, Jennifer C., Alizadeh, Ash A., Diehn, Maximilian, Dudoit, Sandrine, Liu, Chih Long, Belcher, Christopher E., ...
The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene...
Precision and functional specificity in mRNA decay
Wang, Yulei, Liu, Chih Long, Storey, John D., Tibshirani, Robert J., Herschlag, Daniel, Brown, Patrick O.
Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal...
Diehn, Maximilian, Alizadeh, Ash A., Rando, Oliver J., Liu, Chih Long, Stankunas, Kryn, Botstein, David, ...
Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic...
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Yoav, Wang, Yulei, Storey, John D., Liu, Chih Long, Brown, Patrick O., Herschlag, Daniel
We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the...
Global nucleosome occupancy in yeast
Bernstein, Bradley E, Liu, Chih Long, Humphrey, Emily L, Perlstein, Ethan O, Schreiber, Stuart L
A genome-wide study of nucleosome occupancy at yeast promoters shows that promoters that regulate active genes, contain multiple conserved motifs, or contain Rap1 binding sites tend to be depleted of...
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
Liu, Chih Long, Kaplan, Tommy, Kim, Minkyu, Buratowski, Stephen, Schreiber, Stuart L, Friedman, Nir, ...
Covalent modification of histone proteins plays a role in virtually every process on eukaryotic DNA, from transcription to DNA repair. Many different residues can be covalently modified, and it has...
Liu, Chih Long, Prapong, Wijan, Natkunam, Yasodha, Alizadeh, Ash, Montgomery, Kelli, Gilks, C. Blake, ...
The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development...
Nielsen, Torsten O., Hsu, Forrest D., O’Connell, John X., Gilks, C. Blake, Sorensen, Poul H.B., Linn, Sabine, ...
Histological diagnosis of synovial sarcoma can be difficult. Genome-wide expression profiling has identified a number of genes expressed at higher levels in synovial sarcoma than in other soft tissue...
The Stanford Tissue Microarray Database
Marinelli, Robert J., Montgomery, Kelli, Liu, Chih Long, Shah, Nigam H., Prapong, Wijan, Nitzberg, Michael, ...
The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University...