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BMC Bioinformatics|March 8, 2018
Comparison of discriminative motif optimization using matrix and DNA shape-based modelsShuxiang Ruan, Gary D StormoPlos Computational Biology|July 8, 2017
Inherent limitations of probabilistic models for protein-DNA binding specificityShuxiang Ruan, Gary D StormoBioinformatics (Oxford, England)|April 6, 2017
BEESEM: estimation of binding energy models using HT-SELEX dataShuxiang Ruan, S Joshua Swamidass, Gary D StormoGenetics|April 17, 2012
Improved models for transcription factor binding site identification using nonindependent interactionsYue Zhao, Shuxiang Ruan, Manishi Pandey, et al.Current Protocols in Bioinformatics|April 23, 2008
An overview of RNA structure prediction and applications to RNA gene prediction and RNAi designGary D StormoCurrent Protocols in Bioinformatics|August 14, 2015
An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi DesignGary D StormoCurrent Protocols in Bioinformatics|September 4, 2015
DNA Motif Databases and Their UsesGary D StormoMolecular Cell|June 25, 2003
New tricks for an old dogma: riboswitches as cis-only regulatory systemsGary D StormoGenetics|February 9, 2011
Maximally efficient modeling of DNA sequence motifs at all levels of complexityGary D StormoCurrent Protocols in Bioinformatics|September 4, 2009
An introduction to sequence similarity ("homology") searchingGary D StormoPageof 12