List of works by Alan P. Boyle

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A proximity-based graph clustering method for the identification and application of transcription factor clusters

scientific article published on 29 November 2017

Annotation of functional variation in personal genomes using RegulomeDB

scientific article (publication date: September 2012)

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain

scientific article

Broad noncoding transcription suggests genome surveillance by RNA polymerase V

scientific article published on 16 November 2020

Cas9 targeted enrichment of mobile elements using nanopore sequencing

scientific article published on 11 June 2021

Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression

scientific article published on 28 December 2018

Comparative analysis of regulatory information and circuits across distant species

scientific article

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

scientific article published on 19 January 2018

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution

scientific article published in Nature

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2

scientific article

Deciphering ENCODE.

scientific article published on 5 March 2016

Dynamic trans-acting factor colocalization in human cells

scientific article published on 24 October 2013

Evidence-ranked motif identification

scientific article published on 15 February 2010

Extensive variation in chromatin states across humans

scientific article

F-Seq: a feature density estimator for high-throughput sequence tags

scientific article

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development

scientific article published on 27 December 2017

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

scientific article

Heritable individual-specific and allele-specific chromatin signatures in humans

scientific article

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

scientific article

High-resolution mapping and characterization of open chromatin across the genome

scientific article

High-resolution mapping studies of chromatin and gene regulatory elements

scientific article

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

scientific article published on 23 June 2019

Linking disease associations with regulatory information in the human genome

scientific article

Mango: a bias-correcting ChIA-PET analysis pipeline

scientific article

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms

scientific article published on 06 December 2016

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

scientific article

Personal omics profiling reveals dynamic molecular and medical phenotypes

scientific article (publication date: 16 March 2012)

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions

scientific article published on 06 February 2020

Predicting functional variants in enhancer and promoter elements using RegulomeDB

scientific article published on 22 June 2019

Predicting the effects of SNPs on transcription factor binding affinity

scientific article published on 01 January 2020

Principles of regulatory information conservation between mouse and human

scientific article

Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve

scientific article

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

scientific article published on August 2014

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

scientific article published on 5 June 2014

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

scientific article published on 06 July 2020

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

scientific article published on 27 June 2019

Transcription factor co-binding patterns drive conserved regulatory outcomes

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes

scientific article published on 14 April 2020

Visualization of aligned genomic open reading frame data

scholarly article by Alan P. Boyle published in January 2003

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