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

por Ouyang, Ningxin, Boyle, Alan P.
Publicado 2020

F-Seq2: improving the feature density based peak caller with dynamic statistics

por Zhao, Nanxiang, Boyle, Alan P
Publicado 2021

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome

por Dong, Shengcheng, Boyle, Alan P
Publicado 2021

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions

por Nishizaki, Sierra S., Boyle, Alan P.
Publicado 2022

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

por Diehl, Adam G, Boyle, Alan P
Publicado 2018

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets

por Diehl, Adam G., Boyle, Alan P.
Publicado 2019

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

por Diehl, Adam G., Boyle, Alan P.
Publicado 2020

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

por Spadafore, Maxwell, Najarian, Kayvan, Boyle, Alan P.
Publicado 2017

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

por Amemiya, Haley M., Kundaje, Anshul, Boyle, Alan P.
Publicado 2019

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

por Diehl, Adam G., Ouyang, Ningxin, Boyle, Alan P.
Publicado 2020

Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes

por Castro, Christopher P., Diehl, Adam G., Boyle, Alan P.
Publicado 2023

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

por Boyle, Alan P., Guinney, Justin, Crawford, Gregory E., Furey, Terrence S.
Publicado 2008

Linking disease associations with regulatory information in the human genome

por Schaub, Marc A., Boyle, Alan P., Kundaje, Anshul, Batzoglou, Serafim, Snyder, Michael
Publicado 2012

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

por Phanstiel, Douglas H., Boyle, Alan P., Araya, Carlos L., Snyder, Michael P.
Publicado 2014

Evidence-ranked motif identification

por Georgiev, Stoyan, Boyle, Alan P, Jayasurya, Karthik, Ding, Xuan, Mukherjee, Sayan, Ohler, Uwe
Publicado 2010

LRphase: an efficient method for assigning haplotype identity to long reads

por Holmes, Monica J., Mahjour, Babak, Castro, Christopher P., Farnum, Gregory A., Diehl, Adam G., Boyle, Alan P.
Publicado 2023

Multiplexed long-read plasmid validation and analysis using OnRamp

por Mumm, Camille, Drexel, Melissa L., McDonald, Torrin L., Diehl, Adam G., Switzenberg, Jessica A., Boyle, Alan P.
Publicado 2023

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

por Babbitt, Courtney C., Fedrigo, Olivier, Pfefferle, Adam D., Boyle, Alan P., Horvath, Julie E., Furey, Terrence S., Wray, Gregory A.
Publicado 2010

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

por Xu, Xueqing, Tsumagari, Koji, Sowden, Janet, Tawil, Rabi, Boyle, Alan P., Song, Lingyun, Furey, Terrence S., Crawford, Gregory E., Ehrlich, Melanie
Publicado 2009

Cas9 targeted enrichment of mobile elements using nanopore sequencing

por McDonald, Torrin L., Zhou, Weichen, Castro, Christopher P., Mumm, Camille, Switzenberg, Jessica A., Mills, Ryan E., Boyle, Alan P.
Publicado 2021