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  • About Us
    • Consortium Organization
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  • About Us
    • Consortium Organization
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HPRC Publications

There are several HPRC publications in development at this time. Please check back for updates and follow us on Twitter @HumanPangenome.  Below is a selection of publications from the HPRC membership.

Title
Authors
DOI
Date

The Human Pangenome Project: a global resource to map genomic diversity.

Wang T., Antonacci-Fulton L., Howe K., et al.

10.1038/s41586-022-04601-8

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.

10.1038/s41588-022-01043-w

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

10.7554/eLife.76562

2022-04-06

Segmental duplications and their variation in a complete human genome.

Vollger MR, Guitart X, Dishuck PC, et al.

10.1126/science.abj6965

2022-04-01

StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps.

Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE.

10.1093/bioinformatics/btac018

2022-01-10

The UCSC Genome Browser database: 2022 update.

Lee BT, Barber GP, Benet-Pagès A, et al.

10.1093/nar/gkab959

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.

10.1038/s41467-021-24378-0

2021-07-12

Targeted long-read sequencing identifies missing disease-causing variation

Miller, D., Sulovari, A., Wang, T., et al.

https://doi.org/10.1016/j.ajhg.2021.06.006

2021-07-02

lra: A long read aligner for sequences and contigs

Jingwen Ren, Mark Chaisson.

https://doi.org/10.1371/journal.pcbi.1009078

2021-06-21

The qBED track: a novel genome browser visualization for point processes

Moudgil, A., Li, D., Hsu, S., et al.

https://doi.org/10.1093/bioinformatics/btaa771

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.

10.1038/s42003-021-02094-1

2021-05-21

A high-quality bonobo genome refines the analysis of hominid evolution

Mao, Y., Catacchio, C., Hillier, L., et al.

10.1038/s41586-021-03519-x

2021-05-05

The Need for a Human Pangenome Reference Sequence

Miga, K., Wang, T.

https://doi.org/10.1146/annurev-genom-120120-081921

2021-04-30

Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease

Zhang, B., Kim, B., Elliot, G., et al.

https://doi.org/10.1016/j.devcel.2021.04.001

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.

https://doi.org/10.1186/s13073-021-00882-2

2021-04-19

The structure, function and evolution of a complete human chromosome 8

Logsdon, G., Vollger, M., Hsieh, P., et al.

10.1038/s41586-021-03420-7

2021-04-07

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P., Zhu, Q., et al.

https://doi.org/10.1126/science.abf7117

2021-02-25

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Cheng, H., Concepcion, G., Feng, X., et al.

https://doi.org/10.1038/s41592-020-01056-5

2021-02-01

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Porubsky, D., et al.

https://doi.org/10.1038/s41587-020-0719-5

2020-12-07

Chromosome-scale, haplotype-resolved assembly of human genomes

Garg, S., Fungtammasan, A., Carroll, A., et al.

https://doi.org/10.1038/s41587-020-0711-0

2020-12-07

A map of cis-regulatory elements and 3D genome structures in zebrafish

Yang, H., Luan, Y., Liu, T., et al.

https://doi.org/10.1038/s41586-020-2962-9

2020-11-25

The design and construction of reference pangenome graphs with minigraph

Li, H., Feng, X., Chu, C.

https://doi.org/10.1186/s13059-020-02168-z

2020-10-16

Cell-type-specific 3D epigenomes in the developing human cortex

Song, M., Pebworth, M., Yang, X., et al.

https://doi.org/10.1038/s41586-020-2825-4

2020-10-14

Tissue-specific usage of transposable element-derived promoters in mouse development

Miao, B., Fa, S., Lyu, C., et al.

https://doi.org/10.1186/s13059-020-02164-3

2020-09-28

Telomere-to-telomere assembly of a complete human X chromosome

Miga, K., Koren, S., Rhie, A. et al.

https://doi.org/10.1038/s41586-020-2547-7

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.

10.1186/s12915-020-00792-6

2020-07-03

The design and construction of reference pangenome graphs

Li, H., Feng, X., Chu, C.

arXiv:2003.06079

2020-03-13

Genotyping structural variants in pangenome graphs using the vg toolkit

Hickey, G., Heller, D., Monlong, J., et al.

https://doi.org/10.1186/s13059-020-1941-7

2020-02-12

A fully phased accurate assembly of an individual human genome

Porubsky, D., Ebert, P., Audano, P., et al.

https://doi.org/10.1101/855049

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.

https://doi.org/10.1101/715722

2019-07-26

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., et al. 

https://doi.org/10.1101/730531

2019-10-09

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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.

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