Handan Melike Dönertaş

Temporal multi-omic profiling of immune, gut, and microbiome responses to ischemic stroke reveals convergence of host and microbial perturbations one week after brain injury

This paper uses multi-omic profiling in a mouse stroke model to show that host and microbial changes converge around day 7 post-injury.

Aging-associated decline of phosphatidylcholine synthesis is a malleable trigger of natural mitochondrial aging.

The paper identifies a decline in phosphatidylcholine synthesis as a driver of mitochondrial aging that can be reversed by dietary interventions in both worms and human cells.

Integrative transcriptomic identification of cellular senescence beyond marker limitations

The paper develops a machine learning classifier to identify cellular senescence using single-cell RNA-seq data, finding it outperforms marker-based approaches and reveals new mechanistic insights.

The Evolution of Human Ageing Under the Shadow of Demographic Transition

This paper uses demographic data to show how human ageing has changed due to demographic transition, with reduced selection pressure on late-life traits.

Age-dependent gut microbiota dynamics and their association with male fitness traits in Drosophila melanogaster

This study links gut microbiota variation to male life history traits in Drosophila melanogaster, showing that Acetobacter species influence aging and reproduction across different life stages.

Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity

The paper analyzes gene expression in multiple tissues across development and ageing in mice, finding that tissues converge in expression patterns with age, associated with loss of tissue identity.

Common genetic associations between age-related diseases

This study identifies genetic associations between age-related diseases, finding four clusters with shared age-of-onset profiles and aging-related genes, and suggests drug repurposing for multiple age-dependent diseases.

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice

This study compares transcriptomic changes in long- and short-lived mouse models of ageing, identifying mitochondrial metabolism as a key factor and showing that progeroid mice exhibit gene expression patterns similar to normal ageing.

Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences

This study shows that gene expression heterogeneity increases with aging in the human brain and is linked to lifespan regulation and neuronal functions.

The variability of expression of many genes and most functional pathways is observed to increase with age in brain transcriptome data

The paper examines age-related changes in transcriptome heterogeneity using human brain data, finding a consistent increase in gene and pathway variability with age.

Using the drug-protein interactome to identify anti-ageing compounds for humans

The paper identifies anti-ageing drug candidates by analyzing drug-protein interactions and validates one candidate in C. elegans.

Gene Expression-Based Drug Repurposing to Target Ageing

This study uses gene expression data to identify drugs that may combat ageing by comparing age-related gene changes with drug-induced profiles.

Characterising Complex Enzyme Reaction Data

The paper analyzes the relationship between enzyme-catalyzed reactions and EC numbers, finding that one-third of EC numbers are linked to multiple reactions in secondary databases.

Convergent evolution of primate testis transcriptomes reflects mating strategy

The paper analyzes testis transcriptomes across primates to show convergent evolution linked to mating strategies, finding both tissue composition shifts and cell-autonomous changes.