Identifying transcription factor complexes and their roles

Activities at the Universal Protein Resource (UniProt)

(2014)   NUCLEIC ACIDS RESEARCH

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

(2013) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

(2013) Diego Diez et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Protein complex prediction based on maximum matching with domain–domain interaction

(2012) Wenji Ma et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators

(2012) Shwe L. Chin et al.   FEBS Journal

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

IDDI: integrated domain-domain interaction and protein interaction analysis system

(2012) Yul Kim et al.   Proteome Science

Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter

(2011) Lu Bai et al.   MOLECULAR CELL

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Conservation of transcription factor binding events predicts gene expression across species

(2011) Martin Hemberg et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

(2011) Jonathan Göke et al.   PLoS Computational Biology

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

(2010) Yosuke Ozawa et al.   BMC BIOINFORMATICS

Computational approaches for detecting protein complexes from protein interaction networks: a survey

(2010) Xiaoli Li et al.   BMC GENOMICS

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina et al.   NUCLEIC ACIDS RESEARCH

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae

(2010) D. T.-H. Chang et al.   NUCLEIC ACIDS RESEARCH

Protein complex prediction based on simultaneous protein interaction network

(2009) Suk Hoon Jung et al.   BIOINFORMATICS

Epigenetic reprogramming and induced pluripotency

(2009) K. Hochedlinger et al.   DEVELOPMENT

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast

(2009) Caroline C. Friedel et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

(2009) Nurcan Tuncbag et al.   Molecular BioSystems

Exploring functional roles of multibinding protein interfaces

(2009) Manoj Tyagi et al.   PROTEIN SCIENCE

From pull-down data to protein interaction networks and complexes with biological relevance

(2008) B. Zhang et al.   BIOINFORMATICS

Topological comparison of methods for predicting transcriptional cooperativity in yeast

(2008) Daniel Aguilar et al.   BMC GENOMICS

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH