Nicola Neretti

Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases

The paper improves the SNS-seq protocol to better detect DNA replication origins and reduce non-origin biases in yeast.

SenoQuant: One-stop AI software for senescence marker analysis and prediction

SenoQuant is an AI software for analyzing and predicting senescence markers in tissues, offering spatial quantification across imaging modalities and supporting custom models.

Plasma proteomics reveals divergent sex-specific senescence and bone biology signatures across neurodegenerative diseases

This study identifies sex-specific changes in bone and senescence-related proteins in neurodegenerative diseases using plasma proteomics.

Senescence-Associated Chromatin Rewiring Promotes Inflammation and Transposable Element Activation

This study presents high-resolution Hi-C maps of human fibroblasts during senescence, revealing chromatin remodeling that promotes inflammation and transposable element activation.

Single Cell Transcriptomics Reveals Global Markers of Transcriptional Diversity Across Different Forms of CellularSenescence

The paper identifies common transcriptional subpopulations across different senescence types and shows their differential response to a senolytic agent.

Expression of retrotransposons contributes to aging in Drosophila

This study investigates the role of retrotransposon expression and insertions in aging using Drosophila, finding that expression, not insertion, is linked to longevity.

LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5'-single cell RNA-Seq

The paper develops a method to measure LINE-1 retrotransposon expression in single cells and identifies its presence in epithelial and neuronal cells, with age-related increases.

Single-cell transcriptomics of peripheral blood in the aging mouse

This study uses single-cell RNA-sequencing to analyze aging mouse peripheral blood, identifying age-related changes in cell-type composition and transcriptional profiles.

Single cell analysis of the aging female hypothalamus

This study uses single nuclei RNA-sequencing to identify cell-specific aging signatures in the hypothalamus of aged female mice, revealing Xist as a novel marker of neuronal aging in females.

Towards A 3D Chromosome Shape Alphabet

This paper introduces a method to represent chromosome 3D shapes as sequences of shape letters, enabling analysis of structural variability using generalized sequence logos.

Notch signalling mediates secondary senescence

The paper identifies Notch signalling as essential for secondary senescence, distinguishing it from primary senescence through molecular endpoints.

Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data

The paper develops a Bayesian method to infer 3D chromosomal structures from single-cell Hi-C data, incorporating bulk Hi-C as a prior to improve accuracy.

A comparative study of metagenomics analysis pipelines at the species level

This study compares metagenomics tools for species-level classification, finding kallisto outperforms others in sensitivity and accuracy while highlighting issues with full reference genome approaches.