Publications by authors named "Alan Boyle"

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The IGVF catalog-from genetic variation to function.
Daofeng Li, Shane Liu, Pedro R Assis, Mingjie Li, Shengcheng Dong, Alan P Boyle

Nucleic Acids Res· December 2025

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A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex.
Weichen Zhou, Camille Mumm, Yanming Gan, Jessica A Switzenberg, Jinhao Wang, Alan P Boyle

bioRxiv· October 2025

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Multi-platform framework for mapping somatic retrotransposition in human tissues.
Seunghyun Wang, Mingyun Bae, Jinhao Wang, Boxun Zhao, Khue Nguyen, Alan P Boyle

bioRxiv· October 2025

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Draft genome construction of sp. PRP1: identified from single-cell sequencing library preparation.
Preston Parana, Camille Mumm, Michael J McConnell, Alan P Boyle

Microbiol Resour Announc· September 2025

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Long-term immune reprogramming of classical monocytes with altered ontogeny mediates enhanced lung injury in sepsis survivors.
Scott J Denstaedt, Breanna McBean, Alan P Boyle, Brett C Arenberg, Matthias Mack

bioRxiv· August 2025

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Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation.
Shannon L Miller, Katelyn M Green, Bradley Crone, Jessica A Switzenberg, Elizabeth M H Tank, Alan P Boyle

Proc Natl Acad Sci U S A· August 2025

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The Somatic Mosaicism across Human Tissues Network.
Tim H H Coorens, Ji Won Oh, Yujin Angelina Choi, Nam Seop Lim, Boxun Zhao, Alan P Boyle

Nature· July 2025

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Author Correction: An activity-regulated transcriptional program directly drives synaptogenesis.
Callista Yee, Yutong Xiao, Hongwen Chen, Anay R Reddy, Bing Xu, Alan P Boyle

Nat Neurosci· May 2025

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Fast and Accurate Draft Genome Patching with GPatch.
Adam Diehl, Alan Boyle

bioRxiv· May 2025

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Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders.
Sool Lee, Jessica C McAfee, Jiseok Lee, Alejandro Gomez, Austin T Ledford, Alan P Boyle

Cell· March 2025

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MELK as a Mediator of Stemness and Metastasis in Aggressive Subtypes of Breast Cancer.
Breanna McBean, Reine Abou Zeidane, Samuel Lichtman-Mikol, Benjamin Hauk, Johnathan Speers, Alan P Boyle

Int J Mol Sci· March 2025

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Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.
Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd, Alan P Boyle

Nucleic Acids Res· January 2025

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An activity-regulated transcriptional program directly drives synaptogenesis.
Callista Yee, Yutong Xiao, Hongwen Chen, Anay R Reddy, Bing Xu, Alan P Boyle

Nat Neurosci· September 2024

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AAGGG repeat expansions trigger -independent synaptic dysregulation in human CANVAS neurons.
Connor J Maltby, Amy Krans, Samantha J Grudzien, Yomira Palacios, Jessica Muiños, Alan P Boyle

Sci Adv· September 2024

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Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration.
Bradley Crone, Alan P Boyle

PLoS Genet· August 2024

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Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing.
Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd, Alan P Boyle

medRxiv· May 2024

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HaplotagLR: An efficient and configurable utility for haplotagging long reads.
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle

PLoS One· March 2024

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Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants.
Jessica C McAfee, Sool Lee, Jiseok Lee, Jessica L Bell, Oleh Krupa, Alan P Boyle

Cell Genom· October 2023

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Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1.
Lindsay Moritz, Samantha B Schon, Mashiat Rabbani, Yi Sheng, Ritvija Agrawal, Alan P Boyle

Nat Struct Mol Biol· August 2023

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Challenges in screening for noncoding variants contributing to genetically complex phenotypes.
Christopher P Castro, Adam G Diehl, Alan P Boyle

HGG Adv· July 2023

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Multiplexed long-read plasmid validation and analysis using OnRamp.
Camille Mumm, Melissa L Drexel, Torrin L McDonald, Adam G Diehl, Jessica A Switzenberg, Alan P Boyle

Genome Res· May 2023

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Annotating and prioritizing human non-coding variants with RegulomeDB v.2.
Shengcheng Dong, Nanxiang Zhao, Emma Spragins, Meenakshi S Kagda, Mingjie Li, Alan P Boyle

Nat Genet· May 2023

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LRphase: an efficient method for assigning haplotype identity to long reads.
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle

bioRxiv· January 2023

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SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.
Sierra S Nishizaki, Alan P Boyle

BMC Bioinformatics· August 2022

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Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.
Tingting Qin, Christopher Lee, Shiting Li, Raymond G Cavalcante, Peter Orchard, Alan P Boyle

Genome Biol· April 2022

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