Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers

iBBiG: iterative binary bi-clustering of gene sets

(2012) Daniel Gusenleitner et al.   BIOINFORMATICS

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity

(2012) B. W. Busser et al.   DEVELOPMENT

Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis

(2012) Abraham P. Fong et al.   DEVELOPMENTAL CELL

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

(2011) Federico De Masi et al.   NUCLEIC ACIDS RESEARCH

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

(2011) Raluca Gordân et al.   GENOME BIOLOGY

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

(2010) Tracey L. Campbell et al.   PLoS Pathogens

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

(2009) Peter C. Hollenhorst et al.   PLoS Genetics

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

(2008) Anthony A. Philippakis et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA