TherMos: Estimating protein–DNA binding energies from in vivo binding profiles

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets

(2011) D. S. Castro et al.   GENES & DEVELOPMENT

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy et al.   BIOINFORMATICS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

(2009) Eivind Valen et al.   PLoS Computational Biology

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Purification, crystallization and preliminary X-ray diffraction analysis of the HMG domain of Sox17 in complex with DNA

(2008) Calista Keow Leng Ng et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

(2008) Elizabeth D. Wederell et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

(2007) Ralf Jauch et al.   JOURNAL OF MOLECULAR BIOLOGY