This paper is a first step towards a computational account of Binding Theory (BT). Two algorithms that compute, respectively, Principle A and B have been provided. Particular atte...
Background: Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition moti...
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
We present a foundation for a computational meta-theory of languages with bindings implemented in a computer-aided formal reasoning environment. Our theory provides the ability to...
Aleksey Nogin, Alexei Kopylov, Xin Yu, Jason Hicke...
The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e., unpaired, and the energy gained from...