Joshua Gould

Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples

The paper develops a tool to detect viral integrations in human genomes and applies it to over 30,000 tumor samples, identifying virus-human chimeric transcripts and insertion hotspots.

Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

PerturbView enables highly multiplexed optical pooled screens in primary cells and tissues by improving barcode amplification, revealing regulators of NFκB signaling and enabling spatial transcriptomics integration.

STOmicsDB: a database of Spatial Transcriptomic data

STOmicsDB provides a database for spatial transcriptomics data with tools for dataset visualization, publication search, and data archiving.

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

This study uses single-nucleus and spatial transcriptomics to analyze pancreatic cancer before and after neoadjuvant treatment, revealing changes in cell states and immune infiltration that may inform therapy.

Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq

Cumulus is a cloud-based framework for analyzing large-scale sc/snRNA-seq data, improving efficiency and scalability while maintaining result quality.

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

High-density spatial transcriptomics arrays for in situ tissue profiling

This paper introduces HDST, a high-resolution spatial transcriptomics method, and demonstrates its application in mouse brain tissue to resolve spatial expression patterns and cell types.

scSVA: an interactive tool for big data visualization and exploration in single-cell omics

scSVA provides a lightweight R package for interactive visualization and exploration of large single-cell omics datasets using efficient 3D embedding methods.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

The paper creates a proteomic resource profiling 90 drugs in six cell lines, revealing cell-specific responses and enabling integration with transcriptional data to identify therapeutic opportunities.

The GCTx format and cmap{Py, R, M} packages: resources for the optimized storage and integrated traversal of dense matrices of data and annotations

The paper introduces the GCTx format and associated software packages for efficiently storing and analyzing large dense matrices of perturbation data and annotations.

A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles

The paper introduces the L1000 platform, a high-throughput gene expression profiling method, and reports 1.3 million perturbational profiles expanding the Connectivity Map for drug mechanism discovery and functional annotation.