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

Uncovering tissue-specific binding features from differential deep learning

(2020) Mike Phuycharoen et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Licia Selleri et al.   GENES & DEVELOPMENT

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

A novelk-mer set memory (KSM) motif representation improves regulatory variant prediction

(2018) Yuchun Guo et al.   GENOME RESEARCH

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

(2018) Jelle Jacobs et al.   NATURE GENETICS

Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors

(2018) Amélie Dard et al.   Cell Reports

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

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

MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1

(2017) Ann-Christin Hau et al.   JOURNAL OF CELL BIOLOGY

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

(2017) Marta Losa et al.   eLife

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins

(2016) Samir Merabet et al.   TRENDS IN GENETICS

KPC2 relocalizes HOXA2 to the cytoplasm and decreases its transcriptional activity

(2015) Laure Bridoux et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Homeodomain proteins: an update

(2015) Thomas R. Bürglin et al.   CHROMOSOMA

Cellular and molecular insights into Hox protein action

(2015) R. Rezsohazy et al.   DEVELOPMENT

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

(2015) Shilu Amin et al.   DEVELOPMENTAL CELL

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose)

(2015) Matthias Altmeyer et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes

(2013) Alexander Cumberworth et al.   BIOCHEMICAL JOURNAL

The Homeodomain Transcription Factor Hoxa2 Interacts with and Promotes the Proteasomal Degradation of the E3 Ubiquitin Protein Ligase RCHY1

(2013) Isabelle Bergiers et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Protein interactions of the transcription factor Hoxa1

(2012) Barbara Lambert et al.   BMC DEVELOPMENTAL BIOLOGY

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Genome-wide occupancy links Hoxa2 to Wnt–β-catenin signaling in mouse embryonic development

(2012) Ian J. Donaldson et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of Hoxa9 binding sites in hematopoietic cells

(2011) Y. Huang et al.   BLOOD

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome

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

An autoinhibitory effect of the homothorax domain of Meis2

(2010) Cathy Hyman-Walsh et al.   FEBS Journal

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

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

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

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

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

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Six2 functions redundantly immediately downstream of Hoxa2

(2008) E. Kutejova et al.   DEVELOPMENT

Coordinated Actions of the Forkhead Protein Foxp1 and Hox Proteins in the Columnar Organization of Spinal Motor Neurons

(2008) David L. Rousso et al.   NEURON

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY