Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development

(2017) Frédéric Laurent et al.   Cell Reports

gkmSVM: an R package for gapped-kmer SVM

(2016) Mahmoud Ghandi et al.   BIOINFORMATICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures

(2015) Karel van Duijvenboden et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

(2015) Matthew S Wilken et al.   Epigenetics & Chromatin

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

(2015) Nergiz Dogan et al.   Epigenetics & Chromatin

Genome-wide identification of signaling center enhancers in the developing limb

(2014) J. E. VanderMeer et al.   DEVELOPMENT

Loss of Hand2 in a population of Periostin lineage cells results in pronounced bradycardia and neonatal death

(2014) Nathan J. VanDusen et al.   DEVELOPMENTAL BIOLOGY

HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme

(2014) Marco Osterwalder et al.   DEVELOPMENTAL CELL

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila

(2014) Federico Comoglio et al.   PLoS Computational Biology

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

(2012) G. M. Burzynski et al.   GENOME RESEARCH

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Downregulation of Dlx5 and Dlx6 expression by Hand2 is essential for initiation of tongue morphogenesis

(2011) F. Barron et al.   DEVELOPMENT

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Roles of Hand2 in Initiating Polarity and Posterior Shh Expression during the Onset of Mouse Limb Bud Development

(2010) Antonella Galli et al.   PLoS Genetics

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

(2009) Rolf Zeller et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY