Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Finding regulatory DNA motifs using alignment-free evolutionary conservation information

(2010) Raluca Gordân et al.   NUCLEIC ACIDS RESEARCH

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse

(2009) Miriam R. Kantorovitz et al.   DEVELOPMENTAL CELL

Alignment-Free Sequence Comparison (I): Statistics and Power

(2009) Gesine Reinert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

(2009) G. A. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approximate word matches between two random sequences

(2008) Conrad J. Burden et al.   ANNALS OF APPLIED PROBABILITY

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

(2008) Qi Dai et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale

(2008) Tomasz Zemojtel et al.   TRENDS IN GENETICS