Manolis Maragkakis

SenCat catalogs senescence markers across 14 human cell types using transcriptomic and proteomic profiling, revealing shared metabolic pathways and enabling machine learning-based identification of senescent cells.

This study shows HSV-1 infection induces Aβ clustering and neurodegeneration pathways in iPSC-derived neurons, supporting the pathogen infection hypothesis for Alzheimer's disease.

This study identifies cell-type-specific RNA isoform changes in aging mouse brain using single-cell and long-read sequencing, revealing altered coding potential and senescence markers in immune cells.

This study shows that DNA hydroxymethylation in gene bodies limits transcriptional changes with age in mouse and human tissues.

The paper introduces RNAkinet, a deep learning model that uses nanopore sequencing to analyze RNA dynamics and cis-regulatory elements at single molecule resolution.

The paper shows that loss of TDP-43 function leads to the expression of de novo proteins from mis-spliced mRNA transcripts in ALS/FTD.

This study shows MOV10 restricts LINE1 retrotransposition in mice in a dosage-dependent manner, affecting reproductive fitness and transcriptome regulation.

The paper investigates how senescence affects the integrated stress response and secretory phenotype in human cells, finding that translational repression of ATF4 reduces stress response and enhances inflammation.

SamQL provides an SQL-like query language for SAM/BAM files to enable efficient and structured querying without data transformation.

GenOO is a Perl framework for HTS analysis that models biological entities as objects, enabling flexible and efficient development of custom tools.