A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets

Better, Faster, Cheaper: Recent Advances in Cryo–Electron Microscopy

(2022) Eugene Y.D. Chua et al.   Annual Review of Biochemistry

Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells

(2022) Jiyoon Beon et al.   eLife

TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex

(2020) Dario Zimmerli et al.   eLife

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Occurrence of the potent mutagens 2- nitrobenzanthrone and 3-nitrobenzanthrone in fine airborne particles

(2019) Aldenor G. Santos et al.   Scientific Reports

Reactivation of a developmental Bmp2 signaling center is required for therapeutic control of the murine periosteal niche

(2019) Valerie S Salazar et al.   eLife

Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

(2019) Michael P. Meers et al.   MOLECULAR CELL

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

Improved CUT&RUN chromatin profiling tools

(2019) Michael P Meers et al.   eLife

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

TCF/LEF dependent and independent transcriptional regulation of Wnt/β‐catenin target genes

(2018) Nikolaos Doumpas et al.   EMBO JOURNAL

Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling

(2018) Claudio Cantù et al.   GENES & DEVELOPMENT

Genome-wide analysis of canonical Wnt target gene regulation inXenopus tropicalischallenges β-catenin paradigm

(2017) Yukio Nakamura et al.   GENESIS

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

A Single TCF Transcription Factor, Regardless of Its Activation Capacity, Is Sufficient for Effective Trilineage Differentiation of ESCs

(2017) Steven Moreira et al.   Cell Reports

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Wnt-induced transcriptional activation is exclusively mediated by TCF/LEF

(2014) Jurian Schuijers et al.   EMBO JOURNAL

Functional analysis of limb transcriptional enhancers in the mouse

(2014) Mark J. Nolte et al.   EVOLUTION & DEVELOPMENT

FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units

(2014) et al.   LABORATORY ANIMALS

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition

(2014) Nate P. Hoverter et al.   NUCLEIC ACIDS RESEARCH

GATA6 Is a Crucial Regulator of Shh in the Limb Bud

(2014) Elena Kozhemyakina et al.   PLoS Genetics

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

(2014) Yajie Yang et al.   Computational and Structural Biotechnology Journal

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

The many faces and functions of β-catenin

(2012) Tomas Valenta et al.   EMBO JOURNAL

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

TCF/LEFs and Wnt Signaling in the Nucleus

(2012) K. M. Cadigan et al.   Cold Spring Harbor Perspectives in Biology

Islet1-mediated activation of the  -catenin pathway is necessary for hindlimb initiation in mice

(2011) Y. Kawakami et al.   DEVELOPMENT

Ezh2 regulates anteroposterior axis specification and proximodistal axis elongation in the developing limb

(2011) L. A. Wyngaarden et al.   DEVELOPMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Shox2 function couples neural, muscular and skeletal development in the proximal forelimb

(2010) Lori Vickerman et al.   DEVELOPMENTAL BIOLOGY

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transforming Growth Factor-β Regulates Basal Transcriptional Regulatory Machinery to Control Cell Proliferation and Differentiation in Cranial Neural Crest-derived Osteoprogenitor Cells

(2009) Jun-ichi Iwata et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

β-Catenin hits chromatin: regulation of Wnt target gene activation

(2009) Christian Mosimann et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY