User:Xi Chen/Notebook/BIOMOD

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Literature and Software

 * This page shows a collection of papers and software that UT BIOMOD team members should be familiar with.

DNA biophysics

 * 1) SantaLucia, Annu Rev.
 * 2) Pierce review

DNA Circuitry

 * 1) Enzyme-free Logic networks (Seelig et al., 2006 Science)
 * 2) Entropy-driven circuits (Zhang et al., 2007 Science)
 * 3) Kinetics of toehold-mediated strand displacement (Zhang et al., 2009 JACS)
 * 4) Theoretical framework DNA circuits based on Seesaw Gates (Qian et al., 2011 J R Soc Interface)
 * 5) Programmed and catalyzed hairpin assembly (Yin et al., 2008 Science)

DNA self-assembly and DNA origami

 * 1) 2D DNA origami (Rothemund 2006 Nature)
 * 2) 3D origami (Douglas et al., 2009 Nature)
 * 3) Twisted 3D origami (Dietz et al., 2009 Science)

DNA/RNA secondary structure prediction

 * 1) Mfold/UNAFOLD
 * 2) NUPACK

Chemical kinetics simulation

 * 1) KinTek Explorer
 * 2) Visual SPiM
 * 3) Microsoft DSD

Sequence design

 * 1) NUPACK
 * 2) CircDesigNA (Backup site of CircDesigNA)
 * 3) caDNAno


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