Complex small-world regulatory networks emerge from the 3D organisation of the human genome

Bridging-induced phase separation induced by cohesin SMC protein complexes

(2021) Je-Kyung Ryu et al.   Science Advances

How subtle changes in 3D structure can create large changes in transcription

(2021) Jordan Yupeng Xiao et al.   eLife

Polymer compaction and bridging-induced clustering of protein-inspired patchy particles

(2020) C A Brackley   JOURNAL OF PHYSICS-CONDENSED MATTER

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods

(2019) Antonio Jordán-Pla et al.   METHODS

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

Cohesin-dependent regulation of gene expression during differentiation is lost in Cohesin-mutated myeloid malignancies

(2019) Daniel Sasca et al.   BLOOD

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

(2019) Alessandra Dall’Agnese et al.   MOLECULAR CELL

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II

(2018) Barbara Steurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

(2018) Wilberforce Zachary Ouma et al.   PLoS Computational Biology

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

(2018) Peter R Cook et al.   NUCLEIC ACIDS RESEARCH

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

(2018) Adam Buckle et al.   MOLECULAR CELL

Orientation and repositioning of chromosomes correlate with cell geometry–dependent gene expression

(2017) Yejun Wang et al.   MOLECULAR BIOLOGY OF THE CELL

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

(2017) Henri Niskanen et al.   NUCLEIC ACIDS RESEARCH

Nonequilibrium Chromosome Looping via Molecular Slip Links

(2017) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Exploring regulation in tissues with eQTL networks

(2017) Maud Fagny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Position-effect variegation revisited: HUSHing up heterochromatin in human cells

(2016) Richard T. Timms et al.   BIOESSAYS

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Gene Regulation: Activation through Space

(2016) Felix Muerdter et al.   CURRENT BIOLOGY

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Multivalency governs HP1α association dynamics with the silent chromatin state

(2015) Sinan Kilic et al.   Nature Communications

Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and Autism Spectrum Disorder

(2015) Maria Jalbrzikowski et al.   PLoS One

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes

(2013) Anne Katrine Alsing et al.   NUCLEIC ACIDS RESEARCH

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Simplified Models of Biological Networks

(2010) Kim Sneppen et al.   Annual Review of Biophysics

Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence

(2008) Mark D. Humphries et al.   PLoS One