Selected Publications

For a complete list of papers citing AnVIL, please see the Citations page.

AnVIL Platform, Data, Tools and Components

Open-source Tools for Training Resources – OTTR

Candace Savonen, Carrie Wright, Ava M. Hoffman, John Muschelli, Katherine Cox, et al. (2022). Journal of Statistics and Data Science Education. https://doi.org/10.1080/26939169.2022.2118646.

National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians

Jennifer L. Hall, Sally Honeycutt, Nicole Gonzalez, Anne O'Donnell-Luria, Cassy Overby Taylor, et al. (2023). Circulation: Genomic and Precision Medicine. https://doi.org/10.1161/CIRCGEN.122.003936.

Diversifying the genomic data science research community

The Genomic Data Science Community Network, et al. (2022). Genome Research. https://doi.org/10.1101/gr.276496.121.

seqr: A web‐based analysis and collaboration tool for rare disease genomics

Lynn S. Pais, Hana Snow, Ben Weisburd, Shifa Zhang, Samantha M. Baxter, et al. (2022). Human Mutation. https://doi.org/10.1002/humu.24366.

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

Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, et al. (2022). Cell Genomics. https://doi.org/10.1101/2021.04.22.436044.

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, et al. (2021). Nucleic Acids Research. https://doi.org/10.1093/nar/gkab346.

Orchestrating single-cell analysis with Bioconductor

Robert A. Amezquita, Aaron T. L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, et al. (2020). Nature Methods. https://doi.org/10.1038/s41592-019-0654-x.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, et al. (2020). Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa434.

Parliament2: Accurate structural variant calling at scale

Samantha Zarate, Andrew Carroll, Medhat Mahmoud, Olga Krasheninina, Goo Jun, et al. (2020). GigaScience. https://doi.org/10.1093/gigascience/giaa145.

Centers for Mendelian Genomics: A decade of facilitating gene discovery

Samantha M. Baxter, Jennifer E. Posey, Nicole J. Lake, Nara Sobreira, Jessica X. Chong, et al. (2021). medRxiv. https://doi.org/10.1101/2021.08.24.21261656.

Cloud bursting galaxy: federated identity and access management

Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks, et al. (2020). Bioinformatics. https://doi.org/10.1093/bioinformatics/btz472.

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