Channel:  Human Pangenome Reference Consortium (HPRC)

158 Articles

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DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks
Cheng, W., Song, Z., Zhang, Y., Wang, S., Wang, D., Yang, M., Li, L., Ma, J.
10.1101/2025.01.06.631595 — Posted: 2025-01-08
Learning a Pairwise Epigenomic and Transcription Factor Binding Association Score Across the Human Genome
Kwon, S. B., Ernst, J.
10.1101/2024.12.19.629547 — Posted: 2024-12-22
Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells
Yan, J., Luo, R., Rosen, B. P., Liu, D., Wong, W., Leslie, C. S., Huangfu, D.
10.1101/2024.12.21.628413 — Posted: 2024-12-21
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
L2G: Repurposing Language Models for Genomics Tasks
Cheng, W., Shen, J., Khodak, M., Ma, J., Talwalkar, A.
10.1101/2024.12.09.627422 — Posted: 2024-12-11
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
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
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Rosen, B. P., Li, Q. V., Cho, H. S., Liu, D., Yang, D., Graff, S., Yan, J., Luo, R., Verma, N., Damodaran, J. R., Kale, H. T., Kaplan, S. J., Beer, M. A., Sidoli, S., Huangfu, D.
10.1101/2023.05.03.539283 — Posted: 2024-09-01

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