The paper introduces ARCHER-LD, a GPU-accelerated method to compute long-range linkage disequilibrium at biobank scale, achieving significant speedups over existing tools.

bioRxiv · Sep 21, 2026 · PreprintBioinformatics

Genome-wide Association Study of Long COVID

Vilma Lammi, Tomoko Nakanishi, Samuel E. Jones, Shea J. Andrews, Juha M Karjalainen, Beatriz Cortés, Heath O’Brien, Ana Ochoa-Guzmán, Brian Fulton‐Howard, Martin E. Broberg, Hele Haapaniemi, Masahiro Kanai, Matti Pirinen, Axel Schmidt, Ruth E. Mitchell, , Sergi Papiol

This study performs a genome-wide association study for Long COVID, identifying a significant association with the FOXP4 locus and highlighting the role of pulmonary dysfunction and COVID-19 severity.

Nature Genetics · May 21, 2025Peer-reviewedGenetic & Genomic Medicine

Genome-Wide Assessment of Pleiotropy Across >1000 Traits from Global Biobanks

Michael G. Levin, Satoshi Koyama, Jakob Woerner, David Y Zhang, Alexis Rodriguez, Tarak Nandi, Buu Minh Thanh Truong, Sarah A. Abramowitz, Hritvik Gupta, Himani Kamineni, Whitney Hornsby, Zilinghan Li, Taylor Cohron, Jennifer E. Huffman, Patrick T. Ellinor, , Pradeep Natarajan

The paper identifies pleiotropic loci across 1,167 traits using GWAS meta-analysis and shows they are enriched for functional annotations and improve polygenic score predictions.

medRxiv · Apr 18, 2025 · PreprintGenetic & Genomic Medicine

MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline

Joseph Y. Moon, Peer‐Timo Bremer, Pratik Mukherjee, Amy J. Markowitz, Eva M. Palacios, Lanya Tianhao Cai, Alexis Rodriguez, Yukai Xiao, Geoffrey A. Manley, Ravi Madduri

MaPPeRTrac streamlines and accelerates large-scale diffusion MRI tractography by automating the pipeline and leveraging HPC resources.

bioRxiv · Dec 23, 2020 · PreprintNeuroscience

Reproducible big data science: A case study in continuous FAIRness

Ravi Madduri, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W. Deutsch, Cory C. Funk, Ben Heavner, Matthew A. Richards, Paul T. Shannon, Gustavo Glusman, Nathan D. Price, Carl Kesselman, Ian T Foster

The paper presents tools for ensuring FAIRness in big biomedical data analysis through a case study on creating a transcription factor binding site atlas from ENCODE data.

PLoS ONE · Apr 11, 2019Peer-reviewedBioinformatics