ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

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

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

(2010) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

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

Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families

(2009) Larry N. Singh et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database provides mutant phenotype data

(2009) S. R. Engel et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology in 2010: extensions and refinements

(2009)   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

(2008) Troels T. Marstrand et al.   PLoS One

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch et al.   PLOS BIOLOGY