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Analytical study of the effect of recombination on evolution via DNA shuffling
Weiqun Peng, Herbert Levine, Terence Hwa +1
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selecti…
Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction
Ulrich Gerland, J. David Moroz, Terence Hwa
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (…
On the Selection and Evolution of Regulatory DNA Motifs
Ulrich Gerland, Terence Hwa
The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and ind…
DNA Sequence Evolution with Neighbor-Dependent Mutation
Peter F. Arndt, Christopher B. Burge, Terence Hwa
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this cl…
Scaling Laws and Similarity Detection in Sequence Alignment with Gaps
Dirk Drasdo, Terence Hwa, Michael Lassig
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignme…