Discovery of novel tumor suppressor p53 response elements using information theory (2008)
Lyakhov, Ilya G., Krishnamachari, Annangarachari, Schneider, Thomas D.
An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 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...
Molecular flip-flops formed by overlapping Fis sites (2003)
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA‐binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
Lyakhov, Ilya G., Hengen, Paul N., Rubens, Denise, Schneider, Thomas D.
The RepA protein from bacteriophage P1 binds DNA to initiate replication. RepA covers one face of the DNA and the binding site has a completely conserved T that directly faces RepA from the minor...
Molecular flip–flops formed by overlapping Fis sites
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
Lyakhov, Ilya G., Hengen, Paul N., Rubens, Denise, Schneider, Thomas D.
The RepA protein from bacteriophage P1 binds DNA to initiate replication. RepA covers one face of the DNA and the binding site has a completely conserved T that directly faces RepA from the minor...
Molecular flip–flops formed by overlapping Fis sites
Hengen, Paul N., Lyakhov, Ilya G., Stewart, Lisa E., Schneider, Thomas D.
The DNA-binding protein Fis frequently uses pairs of sites 7 or 11 base pairs (bp) apart. Two overlapping Fis sites separated by 11 bp are found in the Escherichia coli origin of chromosomal...
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...
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...
Discovery of novel tumor suppressor p53 response elements using information theory
Lyakhov, Ilya G., Krishnamachari, Annangarachari, Schneider, Thomas D.
An accurate method for locating genes under tumor suppressor p53 control that is based on a well-established mathematical theory and built using naturally occurring, experimentally proven p53 sites...