Channel:  Human Pangenome Reference Consortium (HPRC)

bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive.

50 Articles

A complete reference genome improves analysis of human genetic variation
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Rhie, A., Meredith, M., Martin, S., Lee, J., Koren, S., Rosenfeld, J., Paten, B., Layer, R., Chin, C.-S., Sedlazeck, F. J., Hansen, N. F., Miller, D. E., Phillippy, A. M., Miga, K. H., McCoy, R. C., Dennis, M. Y., Zook, J. M., Schatz, M. C.
10.1101/2021.07.12.452063 — Posted: 2021-07-13
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., Altemose, N., Core, L., Gerton, J. L., Makalowski, W., Olson, D., Rosen, J., Smit, A. F. A., Straight, A. F., Vollger, M. R., Wheeler, T., Schatz, M., Eichler, E., Phillippy, A. M., Timp, W., Miga, K. H., O'Neill, R. J.
10.1101/2021.07.12.451456 — Posted: 2021-07-12
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Mc Cartney, A. M., Shafin, K., Alonge, M., Bzikadze, A. V., Formenti, G., Fungtammasan, A., Howe, K., Jain, C., Koren, S., Logsdon, G. A., Miga, K. H., Mikheenko, A., Paten, B., Shumate, A., Soto, D. C., Sovic, I., Wood, J. M., Zook, J. M., Phillippy, A. M., Rhie, A.
10.1101/2021.07.02.450803 — Posted: 2021-07-02
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., Caldas, G. V., Cheng, H., Chin, C.-S., Chow, W., de Lima, L. G., Dishuck, P. C., Durbin, R., Dvorkina, T., Fiddes, I. T., Formenti, G., Fulton, R. S., Fungtammasan, A., Garrison, E., Grady, P. G. S., Graves-Lindsay, T. A., Hall, I. M., Hansen, N. F., Hartley, G. A., Haukness, M., Howe, K., Hunkapiller, M. W., Jain, C., Jain, M.
10.1101/2021.05.26.445798 — Posted: 2021-05-27
Epigenetic Patterns in a Complete Human Genome
Gershman, A., Sauria, M. E. G., Hook, P. W., Hoyt, S., Razaghi, R., Koren, S., Altemose, N., Caldas, G. V., Vollger, M. R., Logsdon, G., Rhie, A., Eichler, E., Schatz, M., O'Neill, R. J., Phillippy, A. M., Miga, K. H., Timp, W.
10.1101/2021.05.26.443420 — Posted: 2021-05-27
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. M., Hoekzema, K., Porubsky, D., Li, R., Nurk, S., Koren, S., Miga, K. H., Phillippy, A. M., Timp, W., Ventura, M., Eichler, E. E.
10.1101/2021.05.26.445678 — Posted: 2021-05-26
A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development
Modzelewski, A. J., Shao, W., Chen, J., Lee, A., Qi, X., Noon, M., Tjokro, K., Sales, G., Biton, A., Speed, T., Xuan, Z., Wang, T., Risso, D., He, L.
10.1101/2021.03.24.436683 — Posted: 2021-03-25
Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks
Shafin, K., Pesout, T., Chang, P.-C., Nattestad, M., Kolesnikov, A., Goel, S., Baid, G., Eizenga, J. M., Miga, K. H., Carnevali, P., Jain, M., Carroll, A., Paten, B.
10.1101/2021.03.04.433952 — Posted: 2021-03-05
Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
Siren, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., Gupta, N., Gabriel, S., Blackwell, T. W., Ratan, A., Taylor, K. D., Rich, S. S., Rotter, J. I., Haussler, D., Garrison, E., Paten, B.
10.1101/2020.12.04.412486 — Posted: 2021-02-02
De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., Yilmaz, F., Zhao, X., Hsieh, P., Lee, J., Kumar, S., Lin, J., Rausch, T., Chen, Y., Ren, J., Santamarina, M., Hoeps, W., Ashraf, H., Chuang, N. T., Yang, X., Munson, K. M., Lewis, A. P., Fairley, S., Tallon, L. J., Clarke, W. E., Basile, A. O., Byrska-Bishop, M., Corvelo, A., Chaisson, M. J. P., Chen, J., Li, C., Brand, H., Wenger, A. M., Ghareghani, M., Harvey, W., Raeder, B., Hasenfeld, P., Regier, A., Abel, H., Hall, I., Flicek, P., Stegle, O., Gerstein, M
10.1101/2020.12.16.423102 — Posted: 2020-12-16

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