Publications with Arang Rhie, PhD
Staff Scientist
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
bioRxiv, March 17, 2024
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM
A high-quality blue whale genome, segmental duplications, and historical demography
Molecular Biology and Evolution, February 20, 2024
Bukhman YV … Rhie A … Phillippy AM … Stewart R
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
The complete sequence and comparative analysis of ape sex chromosomes
bioRxiv, December 1, 2023
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
The complete sequence of a human Y chromosome
The reference genome of the paradise fish (Macropodus opercularis)
bioRxiv, August 10, 2023
Fodor E, Okendo J, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM
A draft human pangenome reference
Recombination between heterologous human acrocentric chromosomes
Nature, May 10, 2023
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Nature Biotechnology, February 16, 2023
A chromosome-level reference genome and pangenome for barn swallow population genomics
Cell Reports, January 31, 2023
Secomandi S … Rhie A … Formenti G
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
Semi-automated assembly of high-quality diploid human reference genomes
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Genome Biology, September 27, 2022
Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J, Durbin R, Formenti G, Brown S, Cantin L, Mello CV, Cho S, Rhie A, Kim H, Jarvis ED
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Nature Methods, April 1, 2022
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JM, Zook JM, Phillippy AM, Rhie A
Long-read mapping to repetitive reference sequences using Winnowmap2
Nature Methods, April 1, 2022
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Nature Methods, April 1, 2022
Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM
Complete genomic and epigenetic maps of human centromeres
Epigenetic Patterns in a Complete Human Genome
Science, April 1, 2022
Gershman A, Sauria ME, Hook PW, Hoyt SJ, Razaghi R, Koren S, Altemose N, Caldas GV, Vollger MR, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O’Neill RJ, Phillippy AM, Miga KH, Timp W
The complete sequence of a human genome
Standards recommendations for the Earth BioGenome Project
Proc Natl Acad Sci USA, January 25, 2022
Lawniczak MKN … Phillippy AM … Rhie A … Richards S
Population genomics of the critically endangered kākāpō
Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution
Molecular ecology resources, June 27, 2021
Peart CR … Rhie A … Wolf JBW
Reference genome and demographic history of the most endangered marine mammal, the vaquita
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Towards complete and error-free genome assemblies of all vertebrate species
Extended haplotype phasing of long-read de novo genome assemblies using Hi-C
Nature Communications, April 28, 2021
Kronenberg ZN, Rhie A, Koren S, Concepcion G, Peluso P, Munson K, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB
Evolutionary and biomedical insights from a marmoset diploid genome assembly
The structure, function and evolution of a complete human chromosome 8
A complete reference genome improves analysis of human genetic variation
Platypus and echidna genomes reveal mammalian biology and evolution
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Improved reference genome of the arboviral vector Aedes albopictus
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Genome Research, August 14, 2020
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S
Telomere-to-telomere assembly of a complete human X chromosome
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Nature Communications, April 29, 2020
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AW, Heaton MP, Phillippy AM, Hiendleder S, Smith TP, Williams JL
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
Gigascience, April 3, 2020
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Vander LB, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TP
De novo assembly of the cattle reference genome with single-molecule sequencing
Gigascience, March 19, 2020
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
BMC Genomics, December 19, 2019
Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
PLoS Computational Biology, August 21, 2019
HLA*LA - HLA typing from linearly projected graph alignments
Bioinformatics, April 3, 2019
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM
De novo assembly of haplotype-resolved genomes with trio binning
Nature Biotechnology, October 22, 2018
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM
Nanopore sequencing and assembly of a human genome with ultra-long reads
Nature Biotechnology, January 29, 2018
De novo assembly and phasing of a Korean human genome
Nature, October 5, 2016
Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, Hastie A, Cao H, Yun J-Y, Kim J, Kuk J, P G H, Kim J, Ryu H, Kim J, Roh M, Baek J, Hunkapiller MW, Korlach J, Shin JY, Kim C
Genomic Copy Number Variations Characterize the Prognosis of Both P16-Positive and P16-Negative Oropharyngeal Squamous Cell Carcinoma After Curative Resection
Medicine, December 1, 2015
Rhie A, Park WS, Choi MK, Kim J-H, Ryu J, Ryu CH, Kim J-I, Jung Y-S
FX: an RNA-Seq analysis tool on the cloud
Bioinformatics, January 17, 2012
Hong D, Rhie A, Park S-S, Lee J, Ju YS, Kim S, Yu S-S, Bleazard T, Park H-S, Rhee H, Chong H, Yang K-S, Lee Y-S, Kim I-H, Lee JS, Kim J-I, Seo J-S