HPRC Publications

Notes:
The table below shows the selected publications. Please refer to NCBI PubMed Collection and bioRxiv channel for the full collection.
Please refer to the complete protocol via HPRC Publication Protocol.

TITLE
AUTHORS
DATE
DOI
A draft human pangenome reference
Liao et al.
2023
10.1038/s41586-023-05896-x
Increased mutation rate and gene conversion within human segmental duplications
Vollger et al.
2023
10.1038/s41586-023-05895-y
Recombination between heterologous human acrocentric chromosomes
Guarracino et al.
2023
10.1038/s41586-023-05976-y
Pangenome graph construction from genome alignment with minigraph-cactus
Hickey et al.
2023
10.1038/s41587-023-01793-w
Gaps and complex structurally variant loci in phased genome assemblies
Porubsky et al.
2023
10.1101/gr.277334.122
AGC: compact representation of assembled genomes with fast queries and updates
Deorowicz S, Danek A, Li H.
2023-03-01
PMC9994791
Unbiased pangenome graphs
Erik Garrison, Andrea Guarracino
2022-11-20
PMC9805579
GBZ File Format for Pangenome Graphs
Sirén, Jouni, and Benedict Paten
2022-11-15
PMC9665857 (available on 2023-09-30)
Automated assembly of high-quality diploid human reference genomes
Jarvis, Erich D., Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey et al.
2022-10-19
PMC9668749
Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
Tan, K.-T., Slevin, M., Meyerson, M., Li, H.
2022-08-26
PMC9414165
KmerKeys: a web resource for searching indexed genome assemblies and variants
Dmitri Pavilichin, Hojoon Lee, H. Ji et al.
2022-07-05
PMC9252721
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders
Porubsky, D., Höps, W., Ashraf, H., Hsieh, P., Rodriguez-Martin, B., Yilmaz, F., Ebler, J., Hallast, P., Maggiolini, F. A. M., Harvey, W. T., Henning, B., Audano, P. A., Gordon, D. S., Ebert, P., Hasenfeld, P., Benito, E., Zhu, Q., Human Genome Structural Variation Consortium, , Lee, C., Antonacci, F., Steinrücken, M., Beck, C. R., Sanders, A. D., Marschall, T., Eichler, E. E., Korbel, J. O.
2022-05-26
PMC9563103 (available on 2023-05-26)
Metagenome assembly of high-fidelity long reads with hifiasm-met
Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li
2022-05-09
PMC9343089
The Human Pangenome Project: a global resource to map genomic diversity.
Wang T., Antonacci-Fulton L., Howe K., et al.
2022-04-20
10.1038/s41586-022-04601-8
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.
Ebler J, Ebert P, Clarke WE, Rausch T, Audano PA, Houwaart T, Mao Y, Korbel JO, Eichler EE, Zody MC, Dilthey AT, Marschall T.
2022-04-11
10.1038/s41588-022-01043-w
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.
Bailey AD, Talkish J, Ding H, Igel H, Duran A, Mantripragada S, Paten B, Ares M. Elife
2022-04-06
10.7554/eLife.76562
Segmental duplications and their variation in a complete human genome.
Vollger MR, Guitart X, Dishuck PC, et al.
2022-04-01
10.1126/science.abj6965
StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps.
Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE.
2022-01-10
10.1093/bioinformatics/btac018
The UCSC Genome Browser database: 2022 update.
Lee BT, Barber GP, Benet-Pagès A, et al.
2022-01-07
10.1093/nar/gkab959
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Tsung-Yu Lu, Human Genome Structural Variation Consortium, Mark Chaisson.
2021-07-12
10.1038/s41467-021-24378-0
Targeted long-read sequencing identifies missing disease-causing variation
Miller, D., Sulovari, A., Wang, T., et al.
2021-07-02
10.1016/j.ajhg.2021.06.006
lra: A long read aligner for sequences and contigs
Jingwen Ren, Mark Chaisson.
2021-06-21
10.1371/journal.pcbi.1009078
The qBED track: a novel genome browser visualization for point processes
Moudgil, A., Li, D., Hsu, S., et al.
2021-05-23
10.1093/bioinformatics/btaa771
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis
Karlow, J., Miao, B., Xing, X., et al.
2021-05-21
10.1038/s42003-021-02094-1
A high-quality bonobo genome refines the analysis of hominid evolution
Mao, Y., Catacchio, C., Hillier, L., et al.
2021-05-05
10.1038/s41586-021-03519-x
The Need for a Human Pangenome Reference Sequence
Miga, K., Wang, T.
2021-04-30
10.1146/annurev-genom-120120-081921
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease
Zhang, B., Kim, B., Elliot, G., et al.
2021-04-20
10.1016/j.devcel.2021.04.001
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
Lau, B., Pavlichin, D., Hooker, A., et al.
2021-04-19
10.1186/s13073-021-00882-2
The structure, function and evolution of a complete human chromosome 8
Logsdon, G., Vollger, M., Hsieh, P., et al.
2021-04-07
10.1038/s41586-021-03420-7
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P., Zhu, Q., et al.
2021-02-25
10.1126/science.abf7117
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G., Feng, X., et al.
2021-02-01
10.1038/s41592-020-01056-5
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Porubsky, D., et al.
2020-12-07
10.1038/s41587-020-0719-5
Chromosome-scale, haplotype-resolved assembly of human genomes
Garg, S., Fungtammasan, A., Carroll, A., et al.
2020-12-07
10.1038/s41587-020-0711-0
A map of cis-regulatory elements and 3D genome structures in zebrafish
Yang, H., Luan, Y., Liu, T., et al.
2020-11-25
10.1038/s41586-020-2962-9
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., Chu, C.
2020-10-16
10.1186/s13059-020-02168-z
Cell-type-specific 3D epigenomes in the developing human cortex
Song, M., Pebworth, M., Yang, X., et al.
2020-10-14
10.1038/s41586-020-2825-4
Tissue-specific usage of transposable element-derived promoters in mouse development
Miao, B., Fa, S., Lyu, C., et al.
2020-09-28
10.1186/s13059-020-02164-3
Telomere-to-telomere assembly of a complete human X chromosome
Miga, K., Koren, S., Rhie, A. et al.
2020-07-14
10.1038/s41586-020-2547-7
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human
Liu, S., Yu, Y., Zhang, S., et al.
2020-07-03
10.1186/s12915-020-00792-6
The design and construction of reference pangenome graphs
Li, H., Feng, X., Chu, C.
2020-03-13
arXiv:2003.06079
Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey, G., Heller, D., Monlong, J., et al.
2020-02-12
10.1186/s13059-020-1941-7
A fully phased accurate assembly of an individual human genome
Porubsky, D., Ebert, P., Audano, P., et al.
2019-11-26
10.1101/855049
Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., et al.
2019-10-09
10.1101/730531
Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
Shafin, K., Pesout, T., Lorig-Roach, R., et al.
2019-07-26
10.1101/715722
We would like to acknowledge the National Genome Research Institute (NHGRI) for funding the following grants supporting the creation of the human pangenome reference: 1U41HG010972, 1U01HG010971, 1U01HG010961, 1U01HG010973, 1U01HG010963, and the Human Pangenome Reference Consortium.