An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion

The invasin D protein fromYersinia pseudotuberculosisselectively binds the Fab region of host antibodies and affects colonization of the intestine

(2018) Pooja Sadana et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Constitutive centromere-associated network contacts confer differential stability on CENP-A nucleosomes in vitro and in the cell

(2018) Shengya Cao et al.   MOLECULAR BIOLOGY OF THE CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Identification of regulatory elements from nascent transcription using dREG

(2018) Zhong Wang et al.   GENOME RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast

(2018) Gonzalo I. Mendoza-Ochoa et al.   YEAST

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

(2017) André L Martins et al.   NUCLEIC ACIDS RESEARCH

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle

(2017) Clarissa Scholes et al.   Cell Systems

Cofactor squelching: Artifact or fact?

(2016) Søren Fisker Schmidt et al.   BIOESSAYS

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Mechanisms of auxin signaling

(2016) Meirav Lavy et al.   DEVELOPMENT

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

(2016) Fabiana M. Duarte et al.   GENES & DEVELOPMENT

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

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

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

CENP-A Is Dispensable for Mitotic Centromere Function after Initial Centromere/Kinetochore Assembly

(2016) Sebastian Hoffmann et al.   Cell Reports

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

A Review of Auxin Response Factors (ARFs) in Plants

(2016) Si-Bei Li et al.   Frontiers in Plant Science

Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells

(2016) Qiupeng Zheng et al.   BIOTECHNIQUES

Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers

(2015) Søren Fisker Schmidt et al.   GENOME RESEARCH

The CENP-L-N Complex Forms a Critical Node in an Integrated Meshwork of Interactions at the Centromere-Kinetochore Interface

(2015) Kara L. McKinley et al.   MOLECULAR CELL

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPAR -driven enhancers

(2014) S. E. Step et al.   GENES & DEVELOPMENT

Auxin-induced Rapid Degradation of Inhibitor of Caspase-activated DNase (ICAD) Induces Apoptotic DNA Fragmentation, Caspase Activation, and Cell Death

(2014) Kumiko Samejima et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transient Estrogen Receptor Binding and p300 Redistribution Support a Squelching Mechanism for Estradiol-Repressed Genes

(2014) Michael J. Guertin et al.   MOLECULAR ENDOCRINOLOGY

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression

(2014) D. A. Korasick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for oligomerization of auxin transcriptional regulators

(2014) Max H. Nanao et al.   Nature Communications

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11

(2013) Richard Patryk Ngondo-Mbongo et al.   NUCLEIC ACIDS RESEARCH

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

An expanded tool kit for the auxin-inducible degron system in budding yeast

(2013) Magdalena Morawska et al.   YEAST

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A combinatorial TIR1/AFB–Aux/IAA co-receptor system for differential sensing of auxin

(2012) Luz Irina A Calderón Villalobos et al.   Nature Chemical Biology

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

High-Resolution Genome-wide Mapping of AHR and ARNT Binding Sites by ChIP-Seq

(2012) Raymond Lo et al.   TOXICOLOGICAL SCIENCES

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L.)

(2010) ChenJia Shen et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Auxin Perception--Structural Insights

(2010) L. I. Calderon-Villalobos et al.   Cold Spring Harbor Perspectives in Biology

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

(2010) Michael J. Guertin et al.   PLoS Genetics

Mechanism of Auxin-Regulated Gene Expression in Plants

(2009) Elisabeth J. Chapman et al.   Annual Review of Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Spt6 enhances the elongation rate of RNA polymerase II in vivo

(2009) M Behfar Ardehali et al.   EMBO JOURNAL

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mediator-Dependent Recruitment of TFIIH Modules in Preinitiation Complex

(2008) Cyril Esnault et al.   MOLECULAR CELL

TOPLESS Mediates Auxin-Dependent Transcriptional Repression During Arabidopsis Embryogenesis

(2008) H. Szemenyei et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE