The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Deep learning of immune cell differentiation

(2020) Alexandra Maslova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals

(2020) Eric M Sanford et al.   eLife

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Multi-omics profiling of calcium-induced human keratinocytes differentiation reveals modulation of unfolded protein response signaling pathways

(2019) Michaletti Anna et al.   CELL CYCLE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Clustering gene expression time series data using an infinite Gaussian process mixture model

(2018) Ian C. McDowell et al.   PLoS Computational Biology

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4

(2016) Bruno Di Stefano et al.   NATURE CELL BIOLOGY

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers

(2016) Emma K. Farley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Lineage Reprogramming: Strategies, Mechanisms, and Applications

(2015) Jun Xu et al.   Cell Stem Cell

A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation

(2015) Vanessa Lopez-Pajares et al.   DEVELOPMENTAL CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis

(2015) Lavinia Paternoster et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

QuASAR: quantitative allele-specific analysis of reads

(2014) Chris T. Harvey et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

ZNF750 interacts with KLF4 and RCOR1, KDM1A, and CTBP1/2 chromatin regulators to repress epidermal progenitor genes and induce differentiation genes

(2014) Lisa D. Boxer et al.   GENES & DEVELOPMENT

AHR: Making the Keratinocytes Thick Skinned

(2014) Marco Colonna   IMMUNITY

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

(2014) S. S. McDade et al.   NUCLEIC ACIDS RESEARCH

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation

(2012) George L. Sen et al.   DEVELOPMENTAL CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Genetic pathways in disorders of epidermal differentiation

(2012) Vanessa Lopez-Pajares et al.   TRENDS IN GENETICS

GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program

(2012) Amelia Soto Hopkin et al.   PLoS Genetics

EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair

(2011) E. Ezhkova et al.   GENES & DEVELOPMENT

Deconstructing the skin: cytoarchitectural determinants of epidermal morphogenesis

(2011) Cory L. Simpson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells

(2009) Elena Ezhkova et al.   CELL

C/EBPα and β couple interfollicular keratinocyte proliferation arrest to commitment and terminal differentiation

(2009) Rodolphe G. Lopez et al.   NATURE CELL BIOLOGY

Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3

(2008) G. L. Sen et al.   GENES & DEVELOPMENT