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...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge (2005)
Tommy Kaplan, Nir Friedman, Hanah Margalit
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
Modeling Dependencies in Protein-DNA Binding Sites (2003)
Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan
The availability of whole genome sequences and high-throughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and...
Modeling Dependencies in Protein-DNA Binding Sites (2003)
Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan
The availability of whole genome sequences and high-throughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Kaplan, Tommy, Friedman, Nir, Margalit, Hanah
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
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...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Kaplan, Tommy, Friedman, Nir, Margalit, Hanah
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
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...
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
Habib, Naomi, Kaplan, Tommy, Margalit, Hanah, Friedman, Nir
Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences...
Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast
Kaplan, Tommy, Liu, Chih Long, Erkmann, Judith A., Holik, John, Grunstein, Michael, Kaufman, Paul D., ...
Acetylation of histone H3 lysine 56 is a covalent modification best known as a mark of newly replicated chromatin, but it has also been linked to replication-independent histone replacement. Here, we...