HOT or not: examining the basis of high-occupancy target regions

A reassessment of DNA-immunoprecipitation-based genomic profiling

(2018) Antonio Lentini et al.   NATURE METHODS

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

(2016) Lamia Wahba et al.   GENES & DEVELOPMENT

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

G-quadruplex structures mark human regulatory chromatin

(2016) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability

(2016) Peter Zeller et al.   NATURE GENETICS

A proposal for validation of antibodies

(2016) Mathias Uhlen et al.   NATURE METHODS

ViableRNaseH1knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function

(2016) Walt F. Lima et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

(2015) Dhawal Jain et al.   NUCLEIC ACIDS RESEARCH

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome

(2015) Yoong Wearn Lim et al.   eLife

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

Extreme HOT regions are CpG-dense promoters in C. elegans and humans

(2014) R. A.- J. Chen et al.   GENOME RESEARCH

A promoter-level mammalian expression atlas

(2014)   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

(2014) Wolfgang Krebs et al.   NUCLEIC ACIDS RESEARCH

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hitchhiker antigens: Inconsistent ChIP results, questionable immunohistology data, and poor antibody performance may have a common factor

(2013) Missag Hagop Parseghian   Biochemistry and Cell Biology

Discriminative motif analysis of high-throughput dataset

(2013) Zizhen Yao et al.   BIOINFORMATICS

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

p185, an Immunodominant Epitope, Is an Autoantigen Mimotope

(2011) Sanjeev Kumar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Specific cross-reaction of anti-dsDNA antibody with platelet integrin GPIIIa49-66

(2010) Wei Zhang et al.   AUTOIMMUNITY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Requirement for DNA CpG Content in TLR9-Dependent Dendritic Cell Activation Induced by DNA-Containing Immune Complexes

(2009) K. Yasuda et al.   JOURNAL OF IMMUNOLOGY

Autoimmunogenicity of the helix-loop-helix DNA-binding domain

(2009) Natalia Petrakova et al.   MOLECULAR IMMUNOLOGY

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Specific recognition of a dsDNA sequence motif by an immunoglobulin VH homodimer

(2004) Hulin Jin et al.   PROTEIN SCIENCE