A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites

(2012) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

(2009) Seth Frietze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

3D-footprint: a database for the structural analysis of protein–DNA complexes

(2009) Bruno Contreras-Moreira   NUCLEIC ACIDS RESEARCH

Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells

(2008) D. Xie et al.   GENOME RESEARCH

Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources

(2008) Harri Lähdesmäki et al.   PLoS One