Nicola Neretti

Nicola Neretti is an Associate Professor of Molecular Biology, Cell Biology, and Biochemistry at Brown University and serves as Associate Director for the Center on the Biology of Aging. He is affiliated with the Center for Computational Molecular Biology (CCMB) and leads the Neretti Lab, which combines genomics and computational biology to study the biology of aging and age-associated diseases.

His educational background includes:

• PhD in Computational Biology from Brown University (2001)
• MS from Brown University (1999)

Dr. Neretti's research focuses on the application of high throughput techniques such as RNA-seq to study changes in transcriptional networks caused by genetic and environmental interventions that extend lifespan. His work integrates computational methods with experimental biology to detect age-associated chromatin changes and activation of transposable elements. He develops computational tools to analyze 3D chromosome structure and has made significant contributions to understanding the role of genomic instability in aging.

Analysis of Dr. Neretti's recent publications reveals a strong focus on cellular senescence, chromatin remodeling, and transposable element activation in aging. His work spans multiple model organisms and human tissues, with an increasing emphasis on single-cell and spatial transcriptomics approaches. A consistent theme across his publications is the connection between genomic instability, particularly through transposable element activation, and age-related inflammation.

Dr. Neretti teaches several courses at Brown University:

• BIOL 2010 - Quantitative Approaches to Biology
• BIOL 2010B - Introduction to Data Science in Molecular Biology
• BIOL 2350 - The Biology of Aging

The Neretti Lab has developed several important software tools for genomic analysis:

• SIMBA3D: Statistical method for inferring 3D chromosome structure from single-cell Hi-C data
• GINOM: Statistical framework for assessing interval overlap of multiple genomic features
• RepEnrich: Method to estimate repetitive element enrichment using high-throughput sequencing data
• CORaL: Software for comparing expression profiles across experiments
• FISH-MDS: Multidimensional scaling for chromosome structure inference with FISH constraints