Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs

PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling

(2011) Rahul Siddharthan   PLoS Computational Biology

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

Assessing phylogenetic motif models for predicting transcription factor binding sites

(2009) J. Hawkins et al.   BIOINFORMATICS

Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution

(2009) Xin He et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Complexity reduction in context-dependent DNA substitution models

(2008) William H. Majoros et al.   BIOINFORMATICS

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

(2008) Rahul Satija et al.   BIOINFORMATICS

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing

(2008) Pradipta Ray et al.   PLoS Computational Biology