HPRC Publications

Note: The table below shows the selected publications. Please refer to NCBI PubMed Collection and bioRxiv channel for the full collection.

HPRC Publication and Data Use Protocol


TITLE
AUTHORS
DOI
DATE
The Human Pangenome Project: a global resource to map genomic diversity.
Wang T., Antonacci-Fulton L., Howe K., et al.
2022-04-20

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

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

Segmental duplications and their variation in a complete human genome.
Vollger MR, Guitart X, Dishuck PC, et al.
2022-04-01

StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps.
Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE.
2022-01-10

The UCSC Genome Browser database: 2022 update.
Lee BT, Barber GP, Benet-Pag├Ęs A, et al.
2022-01-07

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

Targeted long-read sequencing identifies missing disease-causing variation
Miller, D., Sulovari, A., Wang, T., et al.
2021-07-02

lra: A long read aligner for sequences and contigs
Jingwen Ren, Mark Chaisson.
2021-06-21

The qBED track: a novel genome browser visualization for point processes
Moudgil, A., Li, D., Hsu, S., et al.
2021-05-23

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

A high-quality bonobo genome refines the analysis of hominid evolution
Mao, Y., Catacchio, C., Hillier, L., et al.
2021-05-05

The Need for a Human Pangenome Reference Sequence
Miga, K., Wang, T.
2021-04-30

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease
Zhang, B., Kim, B., Elliot, G., et al.
2021-04-20

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

The structure, function and evolution of a complete human chromosome 8
Logsdon, G., Vollger, M., Hsieh, P., et al.
2021-04-07

Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P., Zhu, Q., et al.
2021-02-25

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G., Feng, X., et al.
2021-02-01

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Porubsky, D., et al.
2020-12-07

Chromosome-scale, haplotype-resolved assembly of human genomes
Garg, S., Fungtammasan, A., Carroll, A., et al.
2020-12-07

A map of cis-regulatory elements and 3D genome structures in zebrafish
Yang, H., Luan, Y., Liu, T., et al.
2020-11-25

The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., Chu, C.
2020-10-16

Cell-type-specific 3D epigenomes in the developing human cortex
Song, M., Pebworth, M., Yang, X., et al.
2020-10-14

Tissue-specific usage of transposable element-derived promoters in mouse development
Miao, B., Fa, S., Lyu, C., et al.
2020-09-28

Telomere-to-telomere assembly of a complete human X chromosome
Miga, K., Koren, S., Rhie, A. et al.
2020-07-14

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

The design and construction of reference pangenome graphs
Li, H., Feng, X., Chu, C.
2020-03-13

Genotyping structural variants in pangenome graphs using the vg toolkit
Hickey, G., Heller, D., Monlong, J., et al.
2020-02-12

A fully phased accurate assembly of an individual human genome
Porubsky, D., Ebert, P., Audano, P., et al.
2019-11-26

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

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., et al.
2019-10-09

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.