Tancredi Massimo Pentimalli

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics

InterScale models both local and global cellular interactions in spatial transcriptomics data, revealing spatially restricted differentiation programs and disease-associated tissue remodeling.

Spatiotemporal dynamics of tumor microenvironment remodelling

This study uses spatial transcriptomics to analyze tumor microenvironment remodeling dynamics in triple-negative breast cancer, identifying early stromal programs as potential therapeutic targets.

OpenDVP: An experimental and computational framework for community-empowered deep visual proteomics

The paper introduces openDVP, a framework for deep visual proteomics, demonstrating its application in three tissue studies to integrate spatial single-cell phenotypes with proteomic data.

UBE3C links ubiquitin signaling to epitranscriptomic control of cortical neurogenesis

The paper shows UBE3C regulates cortical neurogenesis and glial fate through m6A methylation, with mutations disrupting this process and offering therapeutic targets.

Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure

This study shows that mutant Huntingtin causes neurodevelopmental issues in human brain organoids by disrupting CHCHD2, leading to mitochondrial and metabolic problems.

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease

The paper identifies repurposable drugs for mitochondrial disease by using deep learning to screen for compounds that improve neuronal commitment and neurogenesis in Leigh syndrome organoids.

Open-ST: High-resolution spatial transcriptomics in 3D

Open-ST provides a high-resolution, 3D spatial transcriptomics method to study tissue molecular organization, revealing spatially contiguous structures and biomarkers in tumors and lymph nodes.

High-resolution molecular atlas of a lung tumor in 3D

This paper presents a 3D spatial atlas of a human lung carcinoma, revealing tumor microenvironment niches and their associated immune interactions and survival outcomes.

SURF1 mutations causative of Leigh syndrome impair human neurogenesis

This study shows SURF1 mutations impair human neurogenesis by generating patient-derived iPS cells and demonstrating defects in neuronal differentiation and bioenergetics.

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1

This study infects human brain organoids with HSV-1 and identifies molecular and cellular changes associated with neurodegeneration.