Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

(2021) Houda Belaghzal et al.   NATURE GENETICS

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

(2021) Žiga Avsec et al.   NATURE GENETICS

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Alteration of genome folding via contact domain boundary insertion

(2020) Di Zhang et al.   NATURE GENETICS

DeepC: predicting 3D genome folding using megabase-scale transfer learning

(2020) Ron Schwessinger et al.   NATURE METHODS

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

Selene: a PyTorch-based deep learning library for sequence data

(2019) Kathleen M. Chen et al.   NATURE METHODS

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

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

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

(2018) Jiao Sima et al.   CELL

Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock

(2018) Ramon Amat et al.   GENOME RESEARCH

Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9

(2018) Brittany Croft et al.   Nature Communications

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan 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

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon 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

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE