Joshua Orvis

SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication

SEngEAR is a web platform for annotating senescent cells, visualizing communication networks, and comparing senescence signatures across datasets and contexts.

A comparative single-cell transcriptomic atlas for diverse populations of vertebrate hair cells

The paper constructs a cross-species single-cell transcriptomic atlas of hair cells across multiple vertebrates and identifies conserved and species-specific gene expression programs.

Distinct fibroblast and perivascular senotypes define spatial niches that regulate fibrosis

The paper identifies distinct fibroblast and perivascular senescence subtypes in fibrosis using single-cell and spatial transcriptomics, showing their spatial organization and roles in fibrosis progression.

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

The paper compiles a large transcriptomic dataset of neocortical development and uses joint matrix decomposition to identify conserved transcriptome dynamics across mammals and developmental stages.

The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain

The paper describes the Neuroscience Multi-Omic Archive, a repository for single-cell transcriptomic and epigenomic data from mammalian brains, providing tools for data access and analysis.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

gEAR provides a community-driven portal for multi-omic data visualization, analysis, and sharing across species and data types.

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo- derived strain and reveals exceptional intra-specific genetic diversity

The paper develops a capture-based DNA enrichment method to assemble the first buffalo-derived T. parva genome, revealing high genetic diversity between cattle- and buffalo-associated strains.

Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms

The paper re-annotates the Theileria parva genome, refining 53% of the proteome and uncovering a minimal N-glycosylation pathway.