Alan P. Boyle
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View article: The IGVF catalog—from genetic variation to function
The IGVF catalog—from genetic variation to function Open
Genomic variation between individuals is essential for understanding how differences in the genome sequence affect molecular and cellular processes. The Impact of Genomic Variation on Function (IGVF) Consortium aims to uncover the relation…
View article: Multi-platform framework for mapping somatic retrotransposition in human tissues
Multi-platform framework for mapping somatic retrotransposition in human tissues Open
Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fracti…
View article: Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation
Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation Open
Intronic GGGGCC hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Despite its intronic location, this repeat avidly supports synthesis of…
View article: Draft <i>de novo</i> genome construction of <i>Scytonema</i> sp. PRP1: identified from single-cell sequencing library preparation
Draft <i>de novo</i> genome construction of <i>Scytonema</i> sp. PRP1: identified from single-cell sequencing library preparation Open
We present the genome sequence of Scytonema sp. PRP1, a cyanobacterium identified during single-cell sequencing library preparation of de-identified human brain samples associated with the Brain Somatic Mosaicism Network. Our 8,266,022 bp …
View article: Fast and Accurate Draft Genome Patching with GPatch
Fast and Accurate Draft Genome Patching with GPatch Open
Recent advancements in sequencing technologies have yielded numerous long-read draft genomes, promising to enhance our understanding of genomic variation. However, draft genomes are typically highly fragmented, posing significant challenge…
View article: Long-term immune reprogramming of classical monocytes with altered ontogeny mediates enhanced lung injury in sepsis survivors
Long-term immune reprogramming of classical monocytes with altered ontogeny mediates enhanced lung injury in sepsis survivors Open
Patients who survive sepsis are predisposed to new hospitalizations for respiratory failure, but the underlying mechanisms are unknown. Using a murine model in which prior sepsis predisposes to enhanced lung injury, we previously discovere…
View article: Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation
Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation Open
Intronic GGGGCC hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Despite its intronic location, this repeat avidly supports synthesis of…
View article: MELK as a Mediator of Stemness and Metastasis in Aggressive Subtypes of Breast Cancer
MELK as a Mediator of Stemness and Metastasis in Aggressive Subtypes of Breast Cancer Open
Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest prognosis and lacks actionable molecular targets for treatment. Maternal embryonic leucine zipper kinase (MELK) is highly expressed in TNBC and has been imp…
View article: Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing
Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing Open
Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization of disease-associated repeat loci remains resource intensive and often lacks high r…
View article: TEnCATS - Transposable Element nanopore Cas9-Targeted Sequencing v2
TEnCATS - Transposable Element nanopore Cas9-Targeted Sequencing v2 Open
This is the Boyle lab's protocol for using Cas9 to target transposable elements within genomic DNA using Oxford Nanopore Technologies (ONT) R10 flow cells.
View article: TEnCATS - Transposable Element nanopore Cas9-Targeted Sequencing v1
TEnCATS - Transposable Element nanopore Cas9-Targeted Sequencing v1 Open
This is the Boyle lab's protocol for using Cas9 to target transposable elements within genomic DNA using Oxford Nanopore Technologies (ONT) R10 flow cells.
View article: AAGGG repeat expansions trigger <i>RFC1</i> -independent synaptic dysregulation in human CANVAS neurons
AAGGG repeat expansions trigger <i>RFC1</i> -independent synaptic dysregulation in human CANVAS neurons Open
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recessively inherited neurodegenerative disorder caused by intronic biallelic, nonreference CCCTT/AAGGG repeat expansions within RFC1 . To investigate how th…
View article: Deciphering the impact of genomic variation on function
Deciphering the impact of genomic variation on function Open
Our genomes influence nearly every aspect of human biology-from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously …
View article: Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration
Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration Open
Portability of trans-ancestral polygenic risk scores is often confounded by differences in linkage disequilibrium and genetic architecture between ancestries. Recent literature has shown that prioritizing GWAS SNPs with functional genomic …
View article: An activity-regulated transcriptional program directly drives synaptogenesis
An activity-regulated transcriptional program directly drives synaptogenesis Open
Although the molecular composition and architecture of synapses have been widely explored, much less is known about what genetic programs directly activate synaptic gene expression and how they are modulated. Here, using Caenorhabditis ele…
View article: Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing
Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing Open
Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization of disease-associated repeat loci remains resource intensive and often lacks high r…
View article: HaplotagLR: An efficient and configurable utility for haplotagging long reads
HaplotagLR: An efficient and configurable utility for haplotagging long reads Open
Understanding the functional effects of sequence variation is crucial in genomics. Individual human genomes contain millions of variants that contribute to phenotypic variability and disease risks at the population level. Because variants …
View article: Enhancing Portability of Trans-Ancestral Polygenic Risk Scores through Tissue-Specific Functional Genomic Data Integration
Enhancing Portability of Trans-Ancestral Polygenic Risk Scores through Tissue-Specific Functional Genomic Data Integration Open
Portability of trans-ancestral polygenic risk scores is often confounded by differences in linkage disequilibrium and genetic architecture between ancestries. Recent literature has shown that prioritizing GWAS SNPs with functional genomic …
View article: Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants Open
Genome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel r…
View article: Organ-specific prioritization and annotation of non-coding regulatory variants in the human genome
Organ-specific prioritization and annotation of non-coding regulatory variants in the human genome Open
Identifying non-coding regulatory variants in the human genome remains a challenging task in genomics. Recently we advanced our leading regulatory variant database, RegulomeDB, to its second version. Building upon this comprehensive databa…
View article: Multiplexed long-read plasmid validation and analysis using OnRamp
Multiplexed long-read plasmid validation and analysis using OnRamp Open
Recombinant plasmid vectors are versatile tools that have facilitated discoveries in molecular biology, genetics, proteomics, and many other fields. As the enzymatic and bacterial processes used to create recombinant DNA can introduce erro…
View article: Explain-seq: an end-to-end pipeline from training to interpretation of sequence-based deep learning models
Explain-seq: an end-to-end pipeline from training to interpretation of sequence-based deep learning models Open
Interpreting predictive machine learning models to derive biological knowledge is the ultimate goal of developing models in the era of genomic data exploding. Recently, sequence-based deep learning models have greatly outperformed other ma…