Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Shultzaberger, Ryan K., Roberts, Lindsey R., Lyakhov, Ilya G., Sidorov, Igor A., Stephen, Andrew G., Fisher, Robert J., ...
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics...
Anatomy of Escherichia coli {sigma}70 promoters (2007)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Flexible promoter architecture requirements for coactivator recruitment (2006)
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Abstract Background The spatial organization of transcription factor binding sites in regulatory DNA, and the composition of intersite sequences, influences the assembly of the multiprotein complexes...
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen, Derek Y Chiang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
Anatomy of Escherichia coli {sigma}70 promoters (2006)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Anatomy of Escherichia coli {sigma}70 promoters (2006)
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold
Corbett, Kevin D., Shultzaberger, Ryan K., Berger, James M.
DNA gyrase is unique among enzymes for its ability to actively introduce negative supercoils into DNA. This function is mediated in part by the C-terminal domain of its A subunit (GyrA CTD). Here, we...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold
Corbett, Kevin D., Shultzaberger, Ryan K., Berger, James M.
DNA gyrase is unique among enzymes for its ability to actively introduce negative supercoils into DNA. This function is mediated in part by the C-terminal domain of its A subunit (GyrA CTD). Here, we...
Flexible promoter architecture requirements for coactivator recruitment
Chiang, Derek Y, Nix, David A, Shultzaberger, Ryan K, Gasch, Audrey P, Eisen, Michael B
Anatomy of Escherichia coli σ70 promoters
Shultzaberger, Ryan K., Chen, Zehua, Lewis, Karen A., Schneider, Thomas D.
Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base...
Correlation between binding rate constants and individual information of E. coli Fis binding sites
Shultzaberger, Ryan K., Roberts, Lindsey R., Lyakhov, Ilya G., Sidorov, Igor A., Stephen, Andrew G., Fisher, Robert J., ...
Individual protein binding sites on DNA can be measured in bits of information. This information is related to the free energy of binding by the second law of thermodynamics, but binding kinetics...
Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Discovery of Fur binding site clusters in Escherichia coli by information theory models
Chen, Zehua, Lewis, Karen A., Shultzaberger, Ryan K., Lyakhov, Ilya G., Zheng, Ming, Doan, Bernard, ...
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur...