DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Supercoiling Induces Denaturation Bubbles in Circular DNA

(2010) Jae-Hyung Jeon et al.   PHYSICAL REVIEW LETTERS

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Inherited Variation in Gene Expression

(2009) Daniel A. Skelly et al.   Annual Review of Genomics and Human Genetics

A nonlinear dynamic model of DNA with a sequence-dependent stacking term

(2009) B. S. Alexandrov et al.   NUCLEIC ACIDS RESEARCH

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

(2009) Boian S. Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter

(2009) Boian S. Alexandrov et al.   PLoS Computational Biology

Profiling the Thermodynamic Softness of Adenoviral Promoters

(2008) Chu H. Choi et al.   BIOPHYSICAL JOURNAL