Ricky S. Adkins

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.

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.

Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas

The paper identifies multi-omic phenotypes in pancreatic precursor lesions to distinguish progressive from indolent precancers using integrative transcriptomic, genomic, and spatial data.

Deciphering Bacterial and Archaeal Transcriptional Dark Matter and Its Architectural Complexity

The paper predicts bacterial and archaeal transcripts using ONT direct RNA sequencing and public data, revealing novel and previously characterized transcripts across multiple strains.

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.

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.

FADU: A Feature Counting Tool for Prokaryotic RNA-Seq Analysis

FADU improves RNA-Seq quantification for prokaryotes by better detecting genes missed by HTSeq and featurecounts, especially in organisms with overlapping transcriptional units and polycistronic transcripts.