A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The T-box transcription factor Eomesodermin acts upstream of Mesp1 to specify cardiac mesoderm during mouse gastrulation

(2011) Ita Costello et al.   NATURE CELL BIOLOGY

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Small-sample precision of ROC-related estimates

(2010) B. Hanczar et al.   BIOINFORMATICS

Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo

(2010) J. Enriquez et al.   DEVELOPMENT

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Diversification of muscle types: Recent insights from Drosophila

(2010) Vanessa Tixier et al.   EXPERIMENTAL CELL RESEARCH

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE 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

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny

(2010) H. Rouault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

(2010) Justin Crocker et al.   Nature Communications

Effects of sample size on robustness and prediction accuracy of a prognostic gene signature

(2009) Seon-Young Kim   BMC BIOINFORMATICS

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse

(2009) Miriam R. Kantorovitz et al.   DEVELOPMENTAL CELL

A Systematic Analysis of Tinman Function Reveals Eya and JAK-STAT Signaling as Essential Regulators of Muscle Development

(2009) Ya-Hsin Liu et al.   DEVELOPMENTAL CELL

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Identifying Cis-Regulatory Sequences by Word Profile Similarity

(2009) Garmay Leung et al.   PLoS One

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

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

Teasing out T-box targets in early mesoderm

(2008) Fiona C Wardle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Toward a systems-level understanding of developmental regulatory networks

(2008) Brian W Busser et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

(2008) A. K. Holloway et al.   GENOME RESEARCH

Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes

(2008) Michele Markstein et al.   NATURE GENETICS

The genetics of vertebrate myogenesis

(2008) Robert J. Bryson-Richardson et al.   NATURE REVIEWS GENETICS

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

(2008) Andra Ivan et al.   GENOME BIOLOGY

Muscle development: Forming the head and trunk muscles

(2007) Hung Ping Shih et al.   ACTA HISTOCHEMICA