Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

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

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

Histone Demethylase Activity of Utx Is Essential for Viability and Regulation ofHOXGene Expression inDrosophila

(2017) Ömer Copur et al.   GENETICS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Histone Demethylase Activity of Utx Is Essential for Viability and Regulation ofHOXGene Expression inDrosophila

(2017) Ömer Copur et al.   GENETICS

Genetic enhancement of limb defects in a mouse model of Cornelia de Lange syndrome

(2016) Martha E. Lopez-Burks et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state

(2016) Yacine Kherdjemil et al.   NATURE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

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

(2016) Rushikesh Sheth et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Nanoscale spatial organization of theHoxDgene cluster in distinct transcriptional states

(2015) Pierre J. Fabre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clustering of mammalianHoxgenes with other H3K27me3 targets within an active nuclear domain

(2015) Maxence Vieux-Rochas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

SnapShot: Hox Gene Regulation

(2014) Guillaume Andrey et al.   CELL

Human UTY(KDM6C) Is a Male-specificNϵ-Methyl Lysyl Demethylase

(2014) Louise J. Walport et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients

(2014) J. Raspopovic et al.   SCIENCE

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence

(2013) M. Sadaie et al.   GENES & DEVELOPMENT

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

(2013) G. Andrey et al.   SCIENCE

A function for all posterior Hoxd genes during digit development?

(2012) Saskia Delpretti et al.   DEVELOPMENTAL DYNAMICS

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

Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism

(2012) R. Sheth et al.   SCIENCE

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Hoxd13 binds in vivo and regulates the expression of genes acting in key pathways for early limb and skeletal patterning

(2008) Valentina Salsi et al.   DEVELOPMENTAL BIOLOGY

Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness

(2008) T. Montavon et al.   GENES & DEVELOPMENT

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

On the nature of thumbs

(2008) Günter P Wagner et al.   GENOME BIOLOGY

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY