Formation of new chromatin domains determines pathogenicity of genomic duplications

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

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Copy number variation of two separate regulatory regions upstream ofSOX9causes isolated 46,XY or 46,XX disorder of sex development

(2015) Gwang-Jin Kim et al.   JOURNAL OF MEDICAL GENETICS

The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers

(2015) B. Yao et al.   NUCLEIC ACIDS RESEARCH

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice

(2015) Katerina Kraft et al.   Cell Reports

Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish

(2015) Shipra Bhatia et al.   PLoS Genetics

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

(2014) Suhas S.P. Rao et al.   CELL

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Identification of Novel Craniofacial Regulatory Domains Located far Upstream ofSOX9and Disrupted in Pierre Robin Sequence

(2014) Christopher T. Gordon et al.   HUMAN MUTATION

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Copy-number changes in evolution: rates, fitness effects and adaptive significance

(2013) Vaishali Katju et al.   Frontiers in Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An inwardly rectifying K+ channel is required for patterning

(2012) G. R. Dahal et al.   DEVELOPMENT

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Disruption of a long distance regulatory region upstream of SOX9 in isolated disorders of sex development

(2011) S. Benko et al.   JOURNAL OF MEDICAL GENETICS

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The brachydactylies: a molecular disease family

(2009) S Mundlos   CLINICAL GENETICS

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia

(2009) Ingo Kurth et al.   NATURE GENETICS

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

Sex determination involves synergistic action of SRY and SF1 on a specific Sox9 enhancer

(2008) Ryohei Sekido et al.   NATURE