Alec Eames
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View article: Profiling Epigenetic Aging at Cell‐Type Resolution Through Long‐Read Sequencing
Profiling Epigenetic Aging at Cell‐Type Resolution Through Long‐Read Sequencing Open
DNA methylation can give rise to robust biomarkers of aging, yet most studies profile it at the bulk tissue level, which masks cell type‐specific alterations that may follow distinct aging trajectories. Long‐read sequencing technology enab…
View article: Profiling Epigenetic Aging at Cell-Type Resolution Through Long-Read Sequencing
Profiling Epigenetic Aging at Cell-Type Resolution Through Long-Read Sequencing Open
DNA methylation can give rise to robust biomarkers of aging, yet most studies profile it at the bulk tissue level, which masks cell type-specific alterations that may follow distinct aging trajectories. Long-read sequencing technology enab…
View article: MethylGPT: a foundation model for the DNA methylome
MethylGPT: a foundation model for the DNA methylome Open
DNA methylation serves as a powerful biomarker for disease diagnosis and biological age assessment. However, current analytical approaches often rely on linear models that cannot capture the complex, context-dependent nature of methylation…
View article: A Unified Framework for Systematic Curation and Evaluation of Aging Biomarkers
A Unified Framework for Systematic Curation and Evaluation of Aging Biomarkers Open
Aging biomarkers are essential for understanding and quantifying the aging process and developing targeted longevity interventions. However, validation of these tools has been hindered by the lack of standardized approaches for cross-popul…
View article: Integrative epigenetics and transcriptomics identify aging genes in human blood
Integrative epigenetics and transcriptomics identify aging genes in human blood Open
Recent epigenome-wide studies have identified a large number of genomic regions that consistently exhibit changes in their methylation status with aging across diverse populations, but the functional consequences of these changes are large…
View article: Plasma-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems
Plasma-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems Open
Aging is a complex process manifesting at the molecular, cell, organ and organismal levels. It leads to functional decline, disease and ultimately death, but the relationship between these fundamental biomedical features remains elusive. B…
View article: Maresin 1 repletion improves muscle regeneration after volumetric muscle loss
Maresin 1 repletion improves muscle regeneration after volumetric muscle loss Open
The acute traumatic or surgical loss of skeletal muscle, known as volumetric muscle loss (VML), is a devastating type of injury that results in exacerbated and persistent inflammation followed by fibrosis. The mechanisms that mediate the m…
View article: Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth
Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth Open
Quiescence, a temporary withdrawal from the cell cycle, plays a key role in tissue homeostasis and regeneration. Quiescence is increasingly viewed as a continuum between shallow and deep quiescence, reflecting different potentials to proli…
View article: A Unified Framework for Systematic Curation and Evaluation of Aging Biomarkers
A Unified Framework for Systematic Curation and Evaluation of Aging Biomarkers Open
Aging biomarkers are essential for understanding and quantifying the aging process and developing targeted longevity interventions. However, validation of these tools has been hindered by the lack of standardized approaches for cross-popul…
View article: Maresin 1 Repletion Improves Muscle Regeneration After Volumetric Muscle Loss
Maresin 1 Repletion Improves Muscle Regeneration After Volumetric Muscle Loss Open
The acute traumatic or surgical loss of skeletal muscle, known as volumetric muscle loss (VML), is a devastating type of injury that results in exacerbated and persistent inflammation followed by fibrosis. The mechanisms that mediate the m…
View article: Dynamic metabolic network modeling of a mammalian cell cycle using time-course multi-omics data
Dynamic metabolic network modeling of a mammalian cell cycle using time-course multi-omics data Open
Cell cycle is a fundamental process for cell growth and proliferation, and its dysregulation leads to many diseases. How metabolic networks are regulated and rewired during the cell cycle is unknown. Here we apply a dynamic genome-scale me…
View article: Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms
Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms Open
Genome-scale metabolic models (GEMs) are powerful tools for understanding metabolism from a systems-level perspective. However, GEMs in their most basic form fail to account for cellular regulation. A diverse set of mechanisms regulate cel…