Alan P Boyle

ResearcherID Scopus Author ID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 32

Top Venues

PloS one

PLoS genetics

Nature communications

Nature neuroscience

University of Michigan

Duke University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Michigan

United States

Assistant Professor :: Computational Medicine & Bioinformatics

Stanford University School of Medicine

United States

Postdoctoral Scholar :: Genetics

Education History

Duke University

United States

PHD :: Computational Biology & Bioinformatics

Publications

Bradley Crone, Alan P Boyle
Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration. PLoS genetics 20 (8) (2024)
Bradley Crone, Alan P Boyle
Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration. PLoS genetics 20 (8) (2024)
Bradley Crone, Alan P Boyle
Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration. PLoS genetics 20 (8) (2024)
Callista Yee, Yutong Xiao, Hongwen Chen, Anay R Reddy, Bing Xu, Taylor N Medwig-Kinney, Wan Zhang, Alan P Boyle, Wendy A Herbst, Yang Kevin Xiang, David Q Matus, Kang Shen
An activity-regulated transcriptional program directly drives synaptogenesis. Nature neuroscience (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
HaplotagLR: An efficient and configurable utility for haplotagging long reads. PloS one 19 (3) (2024)
Connor J Maltby, Amy Krans, Samantha J Grudzien, Yomira Palacios, Jessica Muiños, Andrea Suárez, Melissa Asher, Sydney Willey, Kinsey Van Deynze, Camille Mumm, Alan P Boyle, Andrea Cortese, Alain Ndayisaba, Vikram Khurana, Sami J Barmada, Anke A Dijkstra, Peter K Todd
AAGGG repeat expansions trigger RFC1 -independent synaptic dysregulation in human CANVAS neurons. Science advances 10 (36) (2024)
Callista Yee, Yutong Xiao, Hongwen Chen, Anay R Reddy, Bing Xu, Taylor N Medwig-Kinney, Wan Zhang, Alan P Boyle, Wendy A Herbst, Yang Kevin Xiang, David Q Matus, Kang Shen
An activity-regulated transcriptional program directly drives synaptogenesis. Nature neuroscience (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
HaplotagLR: An efficient and configurable utility for haplotagging long reads. PloS one 19 (3) (2024)
Connor J Maltby, Amy Krans, Samantha J Grudzien, Yomira Palacios, Jessica Muiños, Andrea Suárez, Melissa Asher, Sydney Willey, Kinsey Van Deynze, Camille Mumm, Alan P Boyle, Andrea Cortese, Alain Ndayisaba, Vikram Khurana, Sami J Barmada, Anke A Dijkstra, Peter K Todd
AAGGG repeat expansions trigger RFC1 -independent synaptic dysregulation in human CANVAS neurons. Science advances 10 (36) (2024)
Bradley Crone, Alan P Boyle
Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration. PLoS genetics 20 (8) (2024)
Callista Yee, Yutong Xiao, Hongwen Chen, Anay R Reddy, Bing Xu, Taylor N Medwig-Kinney, Wan Zhang, Alan P Boyle, Wendy A Herbst, Yang Kevin Xiang, David Q Matus, Kang Shen
An activity-regulated transcriptional program directly drives synaptogenesis. Nature neuroscience (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
HaplotagLR: An efficient and configurable utility for haplotagging long reads. PloS one 19 (3) (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
HaplotagLR: An efficient and configurable utility for haplotagging long reads. PloS one 19 (3) (2024)
Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd, Alan P Boyle
Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing. medRxiv : the preprint server for health sciences (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
HaplotagLR: An efficient and configurable utility for haplotagging long reads. PloS one 19 (3) (2024)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
LRphase: an efficient method for assigning haplotype identity to long reads. bioRxiv : the preprint server for biology (2023)
Shengcheng Dong, Nanxiang Zhao, Emma Spragins, Meenakshi S Kagda, Mingjie Li, Pedro Assis, Otto Jolanki, Yunhai Luo, J Michael Cherry, Alan P Boyle, Benjamin C Hitz
Annotating and prioritizing human non-coding variants with RegulomeDB v.2. Nature genetics 55 (5) (2023)
Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle
LRphase: an efficient method for assigning haplotype identity to long reads. bioRxiv : the preprint server for biology (2023)
Lindsay Moritz, Samantha B Schon, Mashiat Rabbani, Yi Sheng, Ritvija Agrawal, Juniper Glass-Klaiber, Caleb Sultan, Jeannie M Camarillo, Jourdan Clements, Michael R Baldwin, Adam G Diehl, Alan P Boyle, Patrick J O'Brien, Kaushik Ragunathan, Yueh-Chiang Hu, Michael P Snyder, Jayakrishnan Nandakumar, Jun Z Li, Kyle E Orwig, Sy Redding, Saher Sue Hammoud
Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. Nature structural & molecular biology (2023)
Shengcheng Dong, Nanxiang Zhao, Emma Spragins, Meenakshi S Kagda, Mingjie Li, Pedro Assis, Otto Jolanki, Yunhai Luo, J Michael Cherry, Alan P Boyle, Benjamin C Hitz
Annotating and prioritizing human non-coding variants with RegulomeDB v.2. Nature genetics 55 (5) (2023)
Camille Mumm, Melissa L Drexel, Torrin L McDonald, Adam G Diehl, Jessica A Switzenberg, Alan P Boyle
Multiplexed long-read plasmid validation and analysis using OnRamp. Genome research (2023)
Sierra S Nishizaki, Alan P Boyle
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. BMC bioinformatics 23 (1) (2022)
Shengcheng Dong, Alan P Boyle
Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome. Nucleic acids research (2021)
Nanxiang Zhao, Alan P Boyle
F-Seq2: improving the feature density based peak caller with dynamic statistics. NAR genomics and bioinformatics 3 (1) (2021)
Torrin L McDonald, Weichen Zhou, Christopher P Castro, Camille Mumm, Jessica A Switzenberg, Ryan E Mills, Alan P Boyle
Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nature communications 12 (1) (2021)
Ningxin Ouyang, Alan P Boyle
TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence. Genome research 30 (7) (2020)
Masayuki Tsuzuki, Shriya Sethuraman, Adriana N Coke, M Hafiz Rothi, Alan P Boyle, Andrzej T Wierzbicki
Broad noncoding transcription suggests genome surveillance by RNA polymerase V. Proceedings of the National Academy of Sciences of the United States of America 117 (48) (2020)
Adam G Diehl, Ningxin Ouyang, Alan P Boyle
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nature communications 11 (1) (2020)
Christopher T Lee, Raymond G Cavalcante, Chee Lee, Tingting Qin, Snehal Patil, Shuze Wang, Zing T Y Tsai, Alan P Boyle, Maureen A Sartor
Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. NAR genomics and bioinformatics 2 (1) (2020)
Haley M Amemiya, Anshul Kundaje, Alan P Boyle
The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific reports 9 (1) (2019)
Arushi Varshney, Hadley VanRenterghem, Peter Orchard, Alan P Boyle, Michael L Stitzel, Duygu Ucar, Stephen C J Parker
Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 211 (2) (2018)
Bo Yang, Wei Zhou, Jiao Jiao, Jonas Bille Nielsen, Michael R Mathis, Mahyar Heydarpour, Guillaume Lettre, Lasse Folkersen, Siddharth Prakash, Claudia Schurmann, Lars G Fritsche, Gregory A Farnum, Maoxuan Lin, Mohammad Othman, Whitney Hornsby, Anisa Driscoll, Alexandra Levasseur, Marc Thomas, Linda Farhat, Marie-Pierre Dubé, Eric M Isselbacher, Anders Franco-Cereceda, Dong-Chuan Guo, Erwin P Bottinger, G Michael Deeb, Anna Booher, Sachin Kheterpal, Y Eugene Chen, Hyun Min Kang, Jacob Kitzman, Heather J Cordell, Bernard D Keavney, Judith A Goodship, Santhi K Ganesh, Gonçalo Abecasis, Kim A Eagle, Alan P Boyle, Ruth J F Loos, Per Eriksson, Jean-Claude Tardif, Chad M Brummett, Dianna M Milewicz, Simon C Body, Cristen J Willer
Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. Nature communications 8 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Alan P Boyle