Michele Di Pierro

Quantifying the influence of genetic context on duplicated mammalian genes

This study quantifies how genetic context influences evolutionary rates in duplicated mammalian genes, finding that target copies in new genomic locations evolve faster than source copies.

Random, fragile, or correlated: Mechanisms of synteny decay in mammals

The paper evaluates three models of genome evolution by comparing their fit to empirical synteny block size distributions across 200 mammalian genomes, finding that fragile and correlated breakage models better explain synteny decay than the random breakage model.

Understanding the physical processes behind DNA-DNA proximity ligation assays

This study uses numerical experiments and theoretical modeling to investigate the physical processes in DNA-DNA proximity ligation assays and their impact on experimental outcomes.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

3D genome architecture regulates the traffic of transcription factors throughout human chromosomes

This study shows how 3D genome architecture influences transcription factor movement and reduces time spent commuting between binding sites.

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues

The paper uses physical simulations to study the 3D genome architecture of Aedes aegypti, revealing liquid crystalline structures and sensitivity to nuclear deformation.

The Nucleome Data Bank: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome

The paper introduces the Nucleome Data Bank, a web-based platform for simulating and analyzing the 3D genome using epigenetic data, and provides tools for visualization and data analysis.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

A Transferable Model For Chromosome Architecture

The paper introduces a theoretical model that explains and accurately reproduces the three-dimensional structure of interphase chromosomes using experimental data.