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.

95 Articles

Genotyping sequence-resolved copy-number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes
Ma, W., Chaisson, M.
10.1101/2024.08.11.607269 — Posted: 2025-02-20
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
Billingsley, K. J., Meredith, M., Daida, K., Alvarez Jerez, P., Negi, S., Malik, L., Genner, R. M., Moller, A., Zheng, X., Gibson, S. B., Mastoras, M., Baker, B., Kouam, C., Paquette, K., Jarreau, P., Makarious, M. B., Moore, A., Hong, S., Vitale, D., Shah, S., Monlong, J., Pantazis, C. B., Asri, M., Shafin, K., Carnevali, P., Marenco, S., Auluck, P., Mandal, A., Miga, K. H., Rhie, A., Reed, X., Ding, J., Cookson, M. R., Nalls, M., Singleton, A., Miller, D. E., Chaisson, M., Timp, W., Gibbs, J. R., Phillippy, A. M., Kolmogorov, M., Jain, M., Sedlazeck, F. J., Paten, B., Blauwendraat, C.
10.1101/2024.12.16.628723 — Posted: 2024-12-18
Characterizing cytosine methylation of polymorphic human transposable element insertions using human pangenome resources
Zhuo, X., Tomlinson, C., Belter, E. A., Kuntala, P. K., Saintilnord, W. N., Lindsay, T., Macias, J., Fulton, R. S., Wang, T.
10.1101/2024.11.22.623804 — Posted: 2024-11-23
Telomere-to-Telomere Phased Genome Assembly Using HERRO-Corrected Simplex Nanopore Reads
Stanojevic, D., Lin, D., Nurk, S., Florez De Sessions, P., Sikic, M.
10.1101/2024.05.18.594796 — Posted: 2024-10-15
SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings
Rubin, J. D., van Waaij, J., Kraft, L. M., Siren, J., Sackett, P. W., Renaud, G.
10.1101/2024.08.12.607489 — Posted: 2024-10-08
Building pangenome graphs
Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., Ashbrook, D. G., Thorell, K., Rusholme-Pilcher, R. L., Liti, G., Rudbeck, E., Nahnsen, S., Yang, Z., Mwaniki, M. N., Nobrega, F. L., Wu, Y., Chen, H., de Ligt, J., Sudmant, P. H., Soranzo, N., Colonna, V., Williams, R. W., Prins, P.
10.1101/2023.04.05.535718 — Posted: 2024-10-02
Gene expansions contributing to human brain evolution
Soto, D. C., Uribe-Salazar, J. M., Kaya, G., Valdarrago, R., Sekar, A., Haghani, N. K., Hino, K., La, G. N., Mariano, N. A. F., Ingamells, C., Baraban, A. E., Turner, T. N., Green, E. D., Simo, S., Quon, G., Andres, A., Dennis, M. Y.
10.1101/2024.09.26.615256 — Posted: 2024-09-26
Highly accurate assembly polishing with DeepPolisher
Mastoras, M., Asri, M., Brambrink, L., Hebbar, P., Kolesnikov, A., Cook, D. E., Nattestad, M., Lucas, J., Won, T. S., Chang, P.-C., Carroll, A., Paten, B., Shafin, K.
10.1101/2024.09.17.613505 — Posted: 2024-09-19
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Negi, S., Stenton, S. L., Berger, S., McNulty, B., Violich, I., Gardner, J., Hillaker, T., O'Rourke, S. M., O'Leary, M. C., Carbonell, E., Austin-Tse, C., Lemire, G., Serrano, J., Mangilog, B., VanNoy, G., Kolmogorov, M., Vilain, E., O'Donnell-Luria, A., Delot, E., Miga, K. H., Monlong, J., Paten, B.
10.1101/2024.08.22.24312327 — Posted: 2024-08-22
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies
Park, J., Cook, D. E., Chang, P.-C., Kolesnikov, A., Brambrink, L., Mier, J. C., Gardner, J., McNulty, B., Sacco, S., Keskus, A., Bryant, A., Ahmad, T., Shetty, J., Zhao, Y., Tran, B., Narzisi, G., Helland, A., Yoo, B., Pushel, I., Lansdon, L. A., Bi, C., Walter, A., Gibson, M., Pastinen, T., Farooqi, M. S., Robine, N., Miga, K. H., Carroll, A., Kolmogorov, M., Paten, B., Shafin, K.
10.1101/2024.08.16.608331 — Posted: 2024-08-19

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