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.

[Papers]

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)

[Software]

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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