publications.mdx

description	Selected publications about the AnVIL platform, data, tools, and components.
layoutStyle	LAYOUT_STYLE_NO_CONTRAST_LIGHTEST
title	Selected Publications
publications	title cardLink category citation Open-source Tools for Training Resources – OTTR https://www.tandfonline.com/doi/full/10.1080/26939169.2022.2118646 ABOUT_ANVIL authors doi journal publisher year Candace Savonen Carrie Wright Ava M. Hoffman John Muschelli Katherine Cox Frederick J. Tan Jeffrey T. Leek https://doi.org/10.1080/26939169.2022.2118646 Journal of Statistics and Data Science Education 2022 title cardLink category citation National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians https://www.sciencedirect.com/science/article/abs/pii/S1098360023008973 ABOUT_ANVIL authors doi journal publisher year Jennifer L. Hall Sally Honeycutt Nicole Gonzalez Anne O'Donnell-Luria Cassy Overby Taylor Laura Stevens Anthony A. Philippakis Michael C. Schatz https://doi.org/10.1161/CIRCGEN.122.003936 Circulation: Genomic and Precision Medicine 2023 title cardLink category citation Diversifying the genomic data science research community https://genome.cshlp.org/content/32/7/1231 ABOUT_ANVIL authors doi journal publisher year The Genomic Data Science Community Network https://doi.org/10.1101/gr.276496.121 Genome Research 2022 title cardLink category citation seqr: A web‐based analysis and collaboration tool for rare disease genomics https://onlinelibrary.wiley.com/doi/epdf/10.1002/humu.24366 ABOUT_ANVIL authors doi journal publisher year Lynn S. Pais Hana Snow Ben Weisburd Shifa Zhang Samantha M. Baxter Stephanie DiTroia Emily O'Heir Eleina England Katherine R. Chao Gabrielle Lemire Ikeoluwa Osei‐Owusu Grace E. VanNoy Michael Wilson Kevin Nguyen Harindra Arachchi William Phu Matthew Solomonson Stacy Mano Melanie O'Leary Alysia Lovgren Lawrence Babb Christina A. Austin‐Tse Heidi L. Rehm Daniel G. MacArthur Anne O'Donnell‐Luria https://doi.org/10.1002/humu.24366 Human Mutation 2022 title cardLink category citation Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) https://www.cell.com/cell-genomics/fulltext/S2666-979X(21)00106-3 ABOUT_ANVIL authors doi journal publisher year Michael C. Schatz Anthony A. Philippakis Enis Afgan Eric Banks Vincent J. Carey Robert J. Carroll Alessandro Culotti Kyle Ellrott Jeremy Goecks Robert L. Grossman Ira M. Hall Kasper D. Hansen Jonathan Lawson Jeffrey T. Leek Anne O’Donnell Luria Stephen Mosher Martin Morgan Anton Nekrutenko Brian D. O’Connor Kevin Osborn Benedict Paten Candace Patterson Frederick J. Tan Casey Overby Taylor Jennifer Vessio Levi Waldron Ting Wang Kristin Wuichet AnVIL Team https://doi.org/10.1101/2021.04.22.436044 Cell Genomics 2022 title cardLink category citation The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols https://academic.oup.com/nar/article/49/W1/W624/6274534 ABOUT_ANVIL authors doi journal publisher year Denis Yuen Louise Cabansay Andrew Duncan Gary Luu Gregory Hogue Charles Overbeck Natalie Perez Walt Shands David Steinberg Chaz Reid Nneka Olunwa Richard Hansen Elizabeth Sheets Ash O’Farrell Kim Cullion Brian D O’Connor Benedict Paten Lincoln Stein https://doi.org/10.1093/nar/gkab346 Nucleic Acids Research 2021 title cardLink category citation Orchestrating single-cell analysis with Bioconductor https://www.nature.com/articles/s41592-019-0654-x ABOUT_ANVIL authors doi journal publisher year Robert A. Amezquita Aaron T. L. Lun Etienne Becht Vince J. Carey Lindsay N. Carpp Ludwig Geistlinger Federico Marini Kevin Rue-Albrecht Davide Risso Charlotte Soneson Levi Waldron Hervé Pagès Mike L. Smith Wolfgang Huber Martin Morgan Raphael Gottardo Stephanie C. Hicks https://doi.org/10.1038/s41592-019-0654-x Nature Methods 2020 title cardLink category citation The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update https://academic.oup.com/nar/article/48/W1/W395/5849904 ABOUT_ANVIL authors doi journal publication year Vahid Jalili Enis Afgan Qiang Gu Dave Clements Daniel Blankenberg Jeremy Goecks James Taylor Anton Nekrutenko https://doi.org/10.1093/nar/gkaa434 Nucleic Acids Research 2020 title cardLink category citation Parliament2: Accurate structural variant calling at scale https://academic.oup.com/gigascience/article/9/12/giaa145/6042728?login=true ABOUT_ANVIL authors doi journal publisher year Samantha Zarate Andrew Carroll Medhat Mahmoud Olga Krasheninina Goo Jun William J Salerno Michael C Schatz Eric Boerwinkle Richard A Gibbs Fritz J Sedlazeck https://doi.org/10.1093/gigascience/giaa145 GigaScience 2020 title cardLink category citation Centers for Mendelian Genomics: A decade of facilitating gene discovery https://www.medrxiv.org/content/10.1101/2021.08.24.21261656v1.full ABOUT_ANVIL authors doi journal publisher year Samantha M. Baxter Jennifer E. Posey Nicole J. Lake Nara Sobreira Jessica X. Chong Steven Buyske Elizabeth E. Blue Lisa H. Chadwick Zeynep H. Coban-Akdemir Kimberly F. Doheny Colleen P. Davis Monkol Lek Christopher Wellington Shalini N. Jhangiani Mark Gerstein Richard A. Gibbs Richard P. Lifton Daniel G. MacArthur Tara C. Matise James R. Lupski David Valle Michael J. Bamshad Ada Hamosh Shrikant Mane Deborah A. Nickerson Centers for Mendelian Genomics Consortium Heidi L. Rehm Anne O’Donnell-Luria https://doi.org/10.1101/2021.08.24.21261656 medRxiv Cold Spring Harbor Laboratory Press 2021 title cardLink category citation Cloud bursting galaxy: federated identity and access management https://academic.oup.com/bioinformatics/article/36/1/1/5514039 ABOUT_ANVIL authors doi journal publisher year Vahid Jalili Enis Afgan James Taylor Jeremy Goecks https://doi.org/10.1093/bioinformatics/btz472 Bioinformatics 2020

Selected Publications

For a complete list of papers citing AnVIL, please see the [Citations](/explore/citations) page.

AnVIL Platform, Data, Tools and Components