Matthew Ruffalo

The paper introduces the SenNet Portal, a resource for senescent cell data and tools, and discusses its usage and future developments.

This paper introduces RIBCA, a tool for automated cell type annotation in multiplexed tissue images, capable of annotating over 3 million cells across 40 human tissues without manual intervention.

3DCellComposer uses 2D segmentation models to generate accurate 3D cell segmentations without requiring additional training or human annotations.

This paper introduces GIANT, a method for integrating atlas-scale single cell data from multiple modalities and tissues, creating a unified gene embedding space that reflects gene functions and regulations.

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

The paper introduces HBM-CITEseq, a CITE-seq processing pipeline for the HuBMAP Consortium that aligns with existing RNA-seq pipelines and is available on GitHub.

CINS infers differential cell-cell interactions between conditions using scRNA-Seq data and identifies the proteins involved in these interactions.

scQuery provides a web server for supervised comparison of single-cell RNA-seq datasets, showing supervised methods outperform unsupervised approaches in cell type identification.