A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

(2022) Aleksandr Ianevski et al.   Nature Communications

Limb positioning and initiation: An evolutionary context of pattern and formation

(2021) Samantha R. Royle et al.   DEVELOPMENTAL DYNAMICS

Emergence of co-expression in gene regulatory networks

(2021) Wencheng Yin et al.   PLoS One

Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity

(2021) Jonas Malkmus et al.   Nature Communications

Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors

(2021) Irene Delgado et al.   Nature Communications

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

(2021) Ana Rita Amândio et al.   GENES & DEVELOPMENT

Zfhx4 regulates endochondral ossification as the transcriptional platform of Osterix in mice

(2021) Eriko Nakamura et al.   Communications Biology

The regulatory landscapes of developmental genes

(2020) Christopher Chase Bolt et al.   DEVELOPMENT

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

(2020) Evgeny Z. Kvon et al.   CELL

Proximo-distal positional information encoded by an Fgf-regulated gradient of homeodomain transcription factors in the vertebrate limb

(2020) Irene Delgado et al.   Science Advances

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

(2020) Laure Bridoux et al.   PLoS Genetics

A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates

(2019) Hugo J. Parker et al.   Nature Communications

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

‘Building a perfect body’: control of vertebrate organogenesis by PBX-dependent regulatory networks

(2019) Licia Selleri et al.   GENES & DEVELOPMENT

Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development

(2019) Natalie H. Kelly et al.   MATRIX BIOLOGY

Face morphogenesis is promoted by Pbx-dependent EMT via regulation of Snail1 during frontonasal prominence fusion

(2018) Marta Losa et al.   DEVELOPMENT

Pbx loss in cranial neural crest, unlike in epithelium, results in cleft palate only and a broader midface

(2018) Ian C. Welsh et al.   JOURNAL OF ANATOMY

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

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

(2018) P. J. Fabre et al.   BMC BIOLOGY

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

(2017) Jacqueline Deschamps et al.   GENES & DEVELOPMENT

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets

(2017) Bony De Kumar et al.   GENOME RESEARCH

PBX transcription factors drive pulmonary vascular adaptation to birth

(2017) David J. McCulley et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2017) Remo Monti et al.   PLoS Computational Biology

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree

(2017) Marta Losa et al.   eLife

Using combined evidence from replicates to evaluate ChIP-seq peaks

(2015) Vahid Jalili et al.   BIOINFORMATICS

Homeodomain proteins: an update

(2015) Thomas R. Bürglin et al.   CHROMOSOMA

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

(2015) Shilu Amin et al.   DEVELOPMENTAL CELL

Pbx Regulates Patterning of the Cerebral Cortex in Progenitors and Postmitotic Neurons

(2015) Olga Golonzhka et al.   NEURON

Development of five digits is controlled by a bipartite long-range cis-regulator

(2014) L. A. Lettice et al.   DEVELOPMENT

HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme

(2014) Marco Osterwalder et al.   DEVELOPMENTAL CELL

TALE Factors Poise Promoters for Activation by Hox Proteins

(2014) Seong-Kyu Choe et al.   DEVELOPMENTAL CELL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

GATA6 Is a Crucial Regulator of Shh in the Limb Bud

(2014) Elena Kozhemyakina et al.   PLoS Genetics

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Compensatory regulation of theSnai1andSnai2genes during chondrogenesis

(2013) Ying Chen et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Analysis of the DNA-Binding Profile and Function of TALE Homeoproteins Reveals Their Specialization and Specific Interactions with Hox Genes/Proteins

(2013) Dmitry Penkov et al.   Cell Reports

Congenital Asplenia in Mice and Humans with Mutations in a Pbx/Nkx2-5/p15 Module

(2012) Matthew Koss et al.   DEVELOPMENTAL CELL

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

(2012) Laura A. Lettice et al.   DEVELOPMENTAL CELL

Characterization ofTALEgenes expression during the first lineage segregation in mammalian embryos

(2012) Wendy Sonnet et al.   DEVELOPMENTAL DYNAMICS

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

A Conserved Pbx-Wnt-p63-Irf6 Regulatory Module Controls Face Morphogenesis by Promoting Epithelial Apoptosis

(2011) Elisabetta Ferretti et al.   DEVELOPMENTAL CELL

Control of pelvic girdle development by genes of the Pbx family and Emx2

(2011) Terence D. Capellini et al.   DEVELOPMENTAL DYNAMICS

Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth

(2011) Terence D. Capellini et al.   DEVELOPMENTAL DYNAMICS

Msx1 and Msx2 in limb mesenchyme modulate digit number and identity

(2011) Vardina Bensoussan-Trigano et al.   DEVELOPMENTAL DYNAMICS

Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome

(2011) Georgette Moyle-Heyrman et al.   JOURNAL OF MOLECULAR BIOLOGY

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A computational pipeline for comparative ChIP-seq analyses

(2011) Anaïs F Bardet et al.   Nature Protocols

Axial Hox9 activity establishes the posterior field in the developing forelimb

(2011) B. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1

(2010) T. D. Capellini et al.   DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Roles of Hand2 in Initiating Polarity and Posterior Shh Expression during the Onset of Mouse Limb Bud Development

(2010) Antonella Galli et al.   PLoS Genetics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

LIM homeobox transcription factors integrate signaling events that control three-dimensional limb patterning and growth

(2009) I. Tzchori et al.   DEVELOPMENT

Meis Cofactors Control HDAC and CBP Accessibility at Hox-Regulated Promoters during Zebrafish Embryogenesis

(2009) Seong-Kyu Choe et al.   DEVELOPMENTAL CELL

Fgf-Dependent Etv4/5 Activity Is Required for Posterior Restriction of Sonic hedgehog and Promoting Outgrowth of the Vertebrate Limb

(2009) Junhao Mao et al.   DEVELOPMENTAL CELL

Tamoxifen-dependent, inducible Hoxb6CreERT recombinase function in lateral plate and limb mesoderm, CNS isthmic organizer, posterior trunk neural crest, hindgut, and tailbud

(2009) Minh-Thanh Nguyen et al.   DEVELOPMENTAL DYNAMICS

PBX1 is dispensable for neural commitment of RA-treated murine ES cells

(2009) Anne S. Jürgens et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL

KLF4 and PBX1 Directly RegulateNANOGExpression in Human Embryonic Stem Cells

(2009) Ken Kwok-Keung Chan et al.   STEM CELLS

Pbx/Meis Deficiencies Demonstrate Multigenetic Origins of Congenital Heart Disease

(2008) Kryn Stankunas et al.   CIRCULATION RESEARCH

Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and Hox in mesoderm and Pax1/Pax9 in sclerotome

(2008) Terence D. Capellini et al.   DEVELOPMENTAL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY