Jeremy Goecks

Verifiable Agentic Science on Public Infrastructure

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

A Web-based software toolkit for accessible and best-practice machine learning analyses in biomedical research

GLEAM provides a web-based toolkit for accessible and rigorous machine learning analyses in biomedical research, producing accurate models across three tasks.

Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets

Galaxy-ME is a web-based software hub for analyzing and visualizing multiplex tissue imaging datasets, demonstrating its utility on normal and cancerous tissue data.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.

Accessible, Reproducible, and Scalable Machine Learning for Biomedicine

The paper introduces Galaxy-ML, a web-based platform for reproducible and scalable supervised machine learning in biomedicine, extending the Galaxy computational workbench.

Adding software to package management systems can increase their citation by 280%

This study shows that publishing software in package management systems increases its cited scholarly papers by 280%.

A new long-read RNA-seq analysis approach identifies and quantifies novel transcripts of very large genes

The paper introduces a long-read RNA-seq analysis approach that identifies and quantifies novel transcripts of very large genes, revealing differential exon usage and phasing across muscle types.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Cloud Bursting Galaxy: Federated Identity and Access Management

The paper develops a secure method for accessing distributed biomedical datasets across cloud platforms using OpenID Connect and OAuth2 integrated with Galaxy.

G-OnRamp: A Galaxy-based platform for creating genome browsers for collaborative genome annotation

G-OnRamp provides a web-based platform for collaborative genome annotation using UCSC Assembly Hubs and JBrowse/Apollo browsers with various evidence tracks.

Practical computational reproducibility in the life sciences

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser

The paper introduces Iso-Seq Browser, a tool for interactive analysis of long-read RNA sequencing data, enabling visualization and exploration of gene isoforms.