UNADON: transformer-based model to predict genome-wide chromosome spatial position

Machine learning methods for exploring sequence determinants of 3D genome organization

(2022) Muyu Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2022) Jian Zhou   NATURE GENETICS

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

(2022) Lorenzo Boninsegna et al.   NATURE METHODS

p53 mediates target gene association with nuclear speckles for amplified RNA expression

(2021) Katherine A. Alexander et al.   MOLECULAR CELL

Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture

(2021) Andrew S. Belmont   Cold Spring Harbor Perspectives in Biology

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

(2018) Derek H. Janssens et al.   Epigenetics & Chromatin

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

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

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

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 high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

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

(2012) W. Meuleman et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Biogenesis of Nuclear Bodies

(2010) M. Dundr et al.   Cold Spring Harbor Perspectives in Biology

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

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