Devon Ryan
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View article: Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression
Selective vulnerability of the aging cholinergic system to amyloid pathology revealed by induced APP overexpression Open
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by amyloid beta (Aβ) accumulation, tau pathology, and cognitive decline, with aging as the primary risk factor. To investigate whether age influences suscep…
View article: Intermittent fasting boosts sexual behavior by limiting the central availability of tryptophan and serotonin
Intermittent fasting boosts sexual behavior by limiting the central availability of tryptophan and serotonin Open
Aging affects reproductive capabilities in males through physiological and behavioral alterations, including endocrine changes and decreased libido. In this study, we investigated the influence of intermittent fasting (IF) on these aging-r…
View article: Correcting Methylation Calls in Clinically Relevant Low-Mappability Regions
Correcting Methylation Calls in Clinically Relevant Low-Mappability Regions Open
DNA methylation is an important component in vital biological functions such as embryonic development, carcinogenesis, and heritable regulation. Accurate methods to assess genomic methylation status are crucial to its effective use in many…
View article: Foxd3 controls heterochromatin‐mediated repression of repeat elements and 2‐cell state transcription
Foxd3 controls heterochromatin‐mediated repression of repeat elements and 2‐cell state transcription Open
Repeat element transcription plays a vital role in early embryonic development. The expression of repeats such as MERVL characterises mouse embryos at the 2-cell stage and defines a 2-cell-like cell (2CLC) population in a mouse embryonic s…
View article: Foxd3 controls heterochromatin-mediated silencing of repeat elements in mouse embryonic stem cells and represses the 2-cell transcription program
Foxd3 controls heterochromatin-mediated silencing of repeat elements in mouse embryonic stem cells and represses the 2-cell transcription program Open
Repeat element transcription plays a vital role in early embryonic development. Expression of repeats such as MERVL characterises mouse embryos at the 2-cell stage, and defines a 2-cell-like cell (2CLC) population in a mouse embryonic stem…
View article: Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia Open
Background Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcri…
View article: Repeat to Gene Expression Ratios in Leukemic Blast Cells Can Stratify Risk Prediction in Acute Myeloid Leukemia
Repeat to Gene Expression Ratios in Leukemic Blast Cells Can Stratify Risk Prediction in Acute Myeloid Leukemia Open
Background Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcri…
View article: snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis Open
Summary Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from …
View article: Test data for running snakePipes : ChIP-seq workflow
Test data for running snakePipes : ChIP-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : HiC workflow
Test data for running snakePipes : HiC workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : ATAC-seq workflow
Test data for running snakePipes : ATAC-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : HiC workflow
Test data for running snakePipes : HiC workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : WGBS workflow
Test data for running snakePipes : WGBS workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : ATAC-seq workflow
Test data for running snakePipes : ATAC-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : ChIP-seq workflow
Test data for running snakePipes : ChIP-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : RNA-seq workflow
Test data for running snakePipes : RNA-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : WGBS workflow
Test data for running snakePipes : WGBS workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : RNA-seq workflow
Test data for running snakePipes : RNA-seq workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: snakePipes enable flexible, scalable and integrative epigenomic analysis
snakePipes enable flexible, scalable and integrative epigenomic analysis Open
The scale and diversity of epigenomics data has been rapidly increasing and ever more studies now present analyses of data from multiple epigenomic techniques. Performing such integrative analysis is time-consuming, especially for explorat…
View article: Test data for running snakePipes : DNA-mapping workflow
Test data for running snakePipes : DNA-mapping workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test data for running snakePipes : DNA-mapping workflow
Test data for running snakePipes : DNA-mapping workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Test Data For Running Snakepipes : Dna-Mapping Workflow
Test Data For Running Snakepipes : Dna-Mapping Workflow Open
Test files for running snakePipes workflows snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes. This folder contains test files…
View article: Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing
Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing Open
Summary This paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples. Starting with user requests, Parkour allows tracking and assessing samples based on predef…
View article: Ultra-parallel ChIP-seq by barcoding of intact nuclei
Ultra-parallel ChIP-seq by barcoding of intact nuclei Open
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. However, sample preparation is still a largely individual and labor-intensive process that hinders assay …
View article: Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice
Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice Open
Significance Aging-associated diseases are increasingly common in an aging global population. However, the contributors and origins of differential risk for unhealthy aging remain poorly understood. Using a mouse model, we found that offsp…