DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

Decoding gene regulation in the fly brain

(2022) Jasper Janssens et al.   NATURE

Sequence determinants of human gene regulatory elements

(2022) Biswajyoti Sahu et al.   NATURE GENETICS

Enhancer grammar in development, evolution, and disease: dependencies and interplay

(2021) Granton A. Jindal et al.   DEVELOPMENTAL CELL

Systematic analysis of binding of transcription factors to noncoding variants

(2021) Jian Yan et al.   NATURE

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

(2021) Žiga Avsec et al.   NATURE GENETICS

Ultraconserved enhancer function does not require perfect sequence conservation

(2021) Valentina Snetkova et al.   NATURE GENETICS

Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks

(2021) Peter K. Koo et al.   PLoS Computational Biology

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

(2021) Payam Dibaeinia et al.   NUCLEIC ACIDS RESEARCH

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

(2021) Daniel S. Kim et al.   NATURE GENETICS

Effective gene expression prediction from sequence by integrating long-range interactions

(2021) Žiga Avsec et al.   NATURE METHODS

Analysis of long and short enhancers in melanoma cell states

(2021) David Mauduit et al.   eLife

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

(2020) Dana M King et al.   eLife

Cross-species analysis of enhancer logic using deep learning

(2020) Liesbeth Minnoye et al.   GENOME RESEARCH

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Prediction Of Histone Post-Translational Modifications Using Deep Learning

(2020) Dipankar Ranjan Baisya et al.   BIOINFORMATICS

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

(2019) Nicholas Bogard et al.   CELL

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

(2019) Rajiv Movva et al.   PLoS One

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification

(2018) Jean-François Boisclair Lachance et al.   GENES & DEVELOPMENT

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

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

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhancer Logic and Mechanics in Development and Disease

(2018) Ryan Rickels et al.   TRENDS IN CELL BIOLOGY

Factor cooperation for chromosome discrimination in Drosophila

(2018) Christian Albig et al.   NUCLEIC ACIDS RESEARCH

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Interactions between pluripotency factors specifycis-regulation in embryonic stem cells

(2016) Chris Fiore et al.   GENOME RESEARCH

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

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

An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS

(2016) Ryan Rickels et al.   MOLECULAR CELL

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors

(2016) Justin Crocker et al.   NATURE GENETICS

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

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

(2016) Rupinder Sayal et al.   eLife

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

Progress and challenges in bioinformatics approaches for enhancer identification

(2015) Dimitrios Kleftogiannis et al.   BRIEFINGS IN BIOINFORMATICS

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Transcriptional regulators form diverse groups with context-dependent regulatory functions

(2015) Gerald Stampfel et al.   NATURE

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

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

(2015) Jian Zhou et al.   NATURE METHODS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

(2015) Dmitry Svetlichnyy et al.   PLoS Computational Biology

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

(2014) J. O. Yanez-Cuna et al.   GENOME RESEARCH

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

(2014) Jelena Erceg et al.   PLoS Genetics

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

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

(2013) Robin P Smith et al.   NATURE GENETICS

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

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

(2012) Guillaume Junion et al.   CELL

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

(2012) Yongheng Chen et al.   Cell Reports

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules

(2012) Feng Liu et al.   PLoS Genetics

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

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

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

The role of PU.1 and GATA-1 transcription factors during normal and leukemogenic hematopoiesis

(2010) P Burda et al.   LEUKEMIA

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

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

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

(2008) Justin Crocker et al.   PLOS BIOLOGY