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A Draft Human Pangenome Reference

Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, et al. (2023). Nature. https://doi.org/10.1038/s41586-023-05896-x.

Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing

Stephanie A. Felker, James M.J. Lawlor, Susan M. Hiatt, Michelle L. Thompson, Donald R. Latner, et al. (2023). Genetics in Medicine. https://doi.org/10.1016/j.gim.2023.100884.

Jasmine and Iris: population-scale structural variant comparison and analysis

Melanie Kirsche, Gautam Prabhu, Rachel Sherman, Bohan Ni, Alexis Battle, et al. (2023). Nature Methods. https://doi.org/10.1038/s41592-022-01753-3.

Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing

Sam Kovaka, Shujun Ou, Katharine M. Jenike, Michael C. Schatz, et al. (2023). Nature Methods. https://doi.org/10.1038/s41592-022-01716-8.

The complete sequence of a human Y chromosome

Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, et al. (2022). https://www.biorxiv.org/. https://doi.org/10.1101/2022.12.01.518724.

The Human Pangenome Project: a global resource to map genomic diversity

Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, et al. (2022). Nature. https://doi.org/10.1038/s41586-022-04601-8.

A complete reference genome improves analysis of human genetic variation

Sergey Aganezov, Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, et al. (2022). Science. https://doi.org/10.1126/science.abl3533.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, et al. (2021). Science. https://doi.org/10.1126/science.abe3261.

The Need for a Human Pangenome Reference Sequence

Karen H. Miga, Ting Wang, et al. (2021). Annual Review of Genomics and Human Genetics. https://doi.org/10.1146/annurev-genom-120120-081921.

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Kristoffer Sahlin, Paul Medvedev, et al. (2021). Nature Communications. https://doi.org/10.1038/s41467-020-20340-8.

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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