Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

Regulatory integration of Hox factor activity with T-box factors in limb development

(2018) Deepak Jain et al.   DEVELOPMENT

Reassessing the Role of Hox Genes during Vertebrate Development and Evolution

(2018) Moisés Mallo   TRENDS IN GENETICS

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

(2017) Ryohei Seki et al.   Nature Communications

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

(2017) Remo Monti et al.   PLoS Computational Biology

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

CTCF-mediated topological boundaries during development foster appropriate gene regulation

(2016) Varun Narendra et al.   GENES & DEVELOPMENT

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Distal Limb Patterning Requires Modulation of cis -Regulatory Activities by HOX13

(2016) Rushikesh Sheth et al.   Cell Reports

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

(2016) Betty M. Booker et al.   PLoS Genetics

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

(2016) Isabel Guerreiro et al.   eLife

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

(2016) Eric T Domyan et al.   eLife

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin 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

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng 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

Long bone development requires a threshold of Hox function

(2014) Mª Carmen González-Martín et al.   DEVELOPMENTAL BIOLOGY

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

(2014) Nicola H. Dryden et al.   GENOME RESEARCH

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

(2014) Fabrice P. A. David et al.   PLoS One

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

(2014) Daan Noordermeer et al.   eLife

Deserts and Waves in Gene Expression

(2013) A. R. Rodrigues et al.   SCIENCE

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Heterochronically early decline of Hox expression prior to cartilage formation in the avian hindlimb zeugopod

(2012) Namiko Kamiyama et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

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

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

Evolutionary and Developmental Aspects of Avian-Specific Traits in Limb Skeletal Pattern

(2012) Ryohei Seki et al.   ZOOLOGICAL SCIENCE

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Functional characterization of novel mutations in GNPAT and AGPS, causing rhizomelic chondrodysplasia punctata (RCDP) types 2 and 3

(2011) Brandon Itzkovitz et al.   HUMAN MUTATION

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

A regulatory ‘landscape effect’ over the HoxD cluster

(2010) Patrick Tschopp et al.   DEVELOPMENTAL BIOLOGY

Functional Analysis of CTCF During Mammalian Limb Development

(2010) Natalia Soshnikova et al.   DEVELOPMENTAL CELL

Homeobox genes d11–d13 and a13 control mouse autopod cortical bone and joint formation

(2010) Pablo Villavicencio-Lorini et al.   JOURNAL OF CLINICAL INVESTIGATION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A Systematic Enhancer Screen Using Lentivector Transgenesis Identifies Conserved and Non-Conserved Functional Elements at the Olig1 and Olig2 Locus

(2010) Marc Friedli et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code

(2009) Joost M. Woltering et al.   DEVELOPMENTAL BIOLOGY

Ectopic Meis1 expression in the mouse limb bud alters P-D patterning in a Pbx1-independent manner

(2009) Nadia Mercader et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

(2009) Rolf Zeller et al.   NATURE REVIEWS GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Growing models of vertebrate limb development

(2008) M. Towers et al.   DEVELOPMENT

Normal developmental stages of the Madagascar ground geckoParoedura pictuswith special reference to limb morphogenesis

(2008) Miyuki Noro et al.   DEVELOPMENTAL DYNAMICS