Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Binding

(2014) Trevor Siggers et al.   MOLECULAR CELL

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network

(2013) John S. Reece-Hoyes et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

(2013) Peng Jiang et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Early evolution of the T-box transcription factor family

(2013) A. Sebe-Pedros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-binding specificity changes in the evolution of forkhead transcription factors

(2013) S. Nakagawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

(2012) Mihail Sarov et al.   CELL

Sex determination

(2012) Tony Gamble et al.   CURRENT BIOLOGY

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

C. elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments

(2012) Qian Liu et al.   Cell and Bioscience

Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans

(2012) Guoyan Zhao et al.   G3-Genes Genomes Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

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

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

E2F transcription factor-1 regulates oxidative metabolism

(2011) Emilie Blanchet et al.   NATURE CELL BIOLOGY

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

(2011) John S Reece-Hoyes et al.   NATURE METHODS

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

(2011) Kathy N. Lam et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

DAF-12 Regulates a Connected Network of Genes to Ensure Robust Developmental Decisions

(2011) Daniel Hochbaum et al.   PLoS Genetics

Recent advances in understanding the molecular mechanisms regulatingC. eleganstranscription

(2010) Jeb Gaudet et al.   DEVELOPMENTAL DYNAMICS

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

Structural Basis of TBX5–DNA Recognition: The T-Box Domain in Its DNA-Bound and -Unbound Form

(2010) Christian U. Stirnimann et al.   JOURNAL OF MOLECULAR BIOLOGY

Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network

(2010) H Efsun Arda et al.   Molecular Systems Biology

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

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

(2009) Christian A. Grove et al.   CELL

Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans

(2009) B. J. Lesch et al.   GENES & DEVELOPMENT

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements

(2009) Monica C. Sleumer et al.   NUCLEIC ACIDS RESEARCH

The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors

(2009) John S. Reece-Hoyes et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

(2008) Wilfried Haerty et al.   BMC GENOMICS

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

(2008) Michael F. Berger et al.   CELL

The magic of the hypoxia-signaling cascade

(2008) E. Benizri et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS