Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems

High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing

(2016) Takayasu Mikuni et al.   CELL

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

(2016) Bastiaan Evers et al.   NATURE BIOTECHNOLOGY

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Overview of the roles of Sox2 in stem cell and development

(2015) Ruopeng Feng et al.   BIOLOGICAL CHEMISTRY

An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors

(2015) Andrew T. Chang et al.   GENES & DEVELOPMENT

Avoiding the Ends: Internal Epitope Tagging of Proteins Using Transposon Tn7

(2015) R. E. Zordan et al.   GENETICS

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

Antibody anarchy: A call to order

(2015) Monya Baker   NATURE

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

(2015) Sándor Spisák et al.   NATURE MEDICINE

Inntags: small self-structured epitopes for innocuous protein tagging

(2015) Maya V Georgieva et al.   NATURE METHODS

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems

(2015) Tetsushi Sakuma et al.   Nature Protocols

A human transcription factor in search mode

(2015) Kevin Hauser et al.   NUCLEIC ACIDS RESEARCH

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

(2015) Douglas Vernimmen et al.   TRENDS IN GENETICS

A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

(2015) Mathieu Dalvai et al.   Cell Reports

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Pioneer transcription factors in cell reprogramming

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

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alanine repeats influence protein localization in splicing speckles and paraspeckles

(2014) Shuo-Hsiu Chang et al.   NUCLEIC ACIDS RESEARCH

The GOA database: Gene Ontology annotation updates for 2015

(2014) Rachael P. Huntley et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm

(2014) Kazutoshi Takahashi et al.   Nature Communications

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

Dual role for Hox genes and Hox co-factors in conferring leg motoneuron survival and identity in Drosophila

(2013) M. Baek et al.   DEVELOPMENT

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Matthew Slattery et al.   CELL

Embryonic stem cell–based mapping of developmental transcriptional programs

(2011) Esteban O Mazzoni et al.   NATURE METHODS

Transposon Assisted Gene Insertion Technology (TAGIT): A Tool for Generating Fluorescent Fusion Proteins

(2010) James A. Gregory et al.   PLoS One

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs

(2009) Peter Maye et al.   BMC BIOTECHNOLOGY

Persistent Expression of FLAG-tagged Micro dystrophin in Nonhuman Primates Following Intramuscular and Vascular Delivery

(2009) Louise R Rodino-Klapac et al.   MOLECULAR THERAPY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DEVELOPMENTAL BIOLOGY: Pluripotent Chromatin State

(2009) A. S. Chi et al.   SCIENCE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies

(2008) Xiaodong Zhang et al.   NATURE METHODS

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS