Publications with Arang Rhie, PhD

Postdoctoral Fellow

Complete genomic and epigenetic maps of human centromeres
bioRxiv, July 19, 2021
Altemose N … Rhie A, McCartney AMNurk S, Koren SPhillippy AM … Miga KH
Merfin: improved variant filtering and polishing via k-mer validation
bioRxiv, July 18, 2021
Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM
A complete reference genome improves analysis of human genetic variation
bioRxiv, July 13, 2021
Aganezov S … Avdeyev PRhie AKoren SPhillippy AM … Schatz MC
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
bioRxiv, July 2, 2021
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
The complete sequence of a human genome
bioRxiv, May 27, 2021
Nurk S, Koren S, Rhie A, Rautiainen MJain CMc Cartney AMWalenz BPPhillippy AM
Epigenetic Patterns in a Complete Human Genome
bioRxiv, May 27, 2021
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
Reference genome and demographic history of the most endangered marine mammal, the vaquita
Molecular Ecology Resources, May 21, 2021
Morin PA … Phillippy A, Rhie A … Jarvis ED
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Genome Biology, April 29, 2021
Formenti G, Rhie AKoren SPhillippy AM … The Vertebrate Genomes Project Consortium
Towards complete and error-free genome assemblies of all vertebrate species
Nature, April 28, 2021
Rhie AKoren SGhurye JWalenz BPPhillippy AM, Jarvis ED
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
Nature, April 12, 2021
Yang C … Rhie AKoren SPhillippy AM … Zhang G
False gene and chromosome losses affected by assembly and sequence errors
bioRxiv, April 9, 2021
Kim J, Lee C, Ko BJ, Yoo D, Won S, Phillippy A, 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
The structure, function and evolution of a complete human chromosome 8
Nature, April 7, 2021
Logsdon GA … Koren S, Nurk SRhie AJain CPhillippy AM, Eichler EE
Platypus and echidna genomes reveal mammalian biology and evolution
Nature, January 6, 2021
Zhou Y … Rhie APhillippy AM … Zhang G
A long read mapping method for highly repetitive reference sequences
bioRxiv, November 2, 2020
Jain C, Rhie A, Hansen N, Koren S, Phillippy AM
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Rhie A, Walenz BP, Koren S, Phillippy AM
Improved reference genome of the arboviral vector Aedes albopictus
Genome Biology, August 26, 2020
Palatini U … Koren SGhurye J, Rhie APhillippy AM, Bonizzoni M
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
Nature, July 14, 2020
Miga KH, Koren S, Rhie AChang AMPhillippy AM
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
Jain C, Rhie A, Zhang H, Chu C, Koren S, Phillippy A
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
Rosen BD … Koren SRhie A, Ghurye JPhillippy AM … Medrano JF
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
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S
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
Jain M, Koren SDilthey ATRhie APhillippy AM … & Loose M
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