Publications | The Hsieh lab at the University of Minnesota, Twin Cities

2025

Sauers SC, Huepenbecker B, Hsieh PH. Genome-wide diversity of chromosomal inversions and their disease relationships. bioRxiv. 2025. DOI: 10.1101/2025.09.25.678440.

Hsieh PH, Soisangwan N, Gordon DS, Javidh A, Harvey WT, Porubsky D, Hoekzema K, Baker C, Munson KM, Kinipi C, Leavesley M, Brucato N, Cox MP, Ricaut FX, Gallego Romero I, Eichler EE. A global map for introgressed structural variation and selection in humans. bioRxiv. 2025. DOI: 10.1101/2025.06.24.661368.

Dishuck PC, Munson KM, Lewis AP, Dougherty ML, Underwood JG, Harvey WT, Hsieh PH, Pastinen T, Eichler EE. Structural variation, selection, and diversification of the NPIP gene family from the human pangenome. Cell Genom. 2025; 100977. DOI: 10.1016/j.xgen.2025.100977.

2024

Plender EG, Prodanov T, Hsieh PH, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O'Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. Am J Hum Genet. 2024; 111(8):1700-1716.

2023

Garza R, Atacho DAM, Adami A, Gerdes P, Vinod M, Hsieh PH, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Hammell MG, Barker RA, Kokaia Z, Douse CH, Jakobsson J. LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Sci Adv. 2023; 9(44):eadh9543.

Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh PH, Eichler EE. Increased mutation and gene conversion within human segmental duplications. Nature. 2023; 617(7960):325-334.

2022

Porubsky D, Höps W, Ashraf H, Hsieh PH, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maggiolini FAM, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell. 2022; 185(11):1986-2005.e26.

Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Gerstein MB, Sanders AD, Zody MC, Talkowski ME, Mills RE, Korbel JO, Marschall T, Ebert P, Audano PA, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh PH, Lee J, Kumar S, Rausch T, Chen Y, Chong Z, Munson KM, Chaisson MJP, Chen J, Shi X, Wenger AM, Harvey WT, Hansenfeld P, Regier A, Hall IM, Flicek P, Hastie AR, Fairely S, Zhang C, Human Genome Structural Variation Consortium, Lee C, Devine SE, Eichler EE, Ye K. Mako: A graph-based pattern growth approach to detect complex structural variants. Genomics Proteomics Bioinformatics. 2022; 20(1):205-218.

Johansson PA, Brattås PL, Douse CH, Hsieh PH, Adami A, Pontis J, Grassi D, Garza R, Sozzi E, Cataldo R, Jönsson ME, Atacho DAM, Pircs K, Eren F, Sharma Y, Johansson J, Fiorenzano A, Parmar M, Fex M, Trono D, Eichler EE, Jakobsson J. A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development. Cell Stem Cell. 2022; 29(1):52-69.e8.

2021

Hsieh PH, Dang V, Vollger MR, Mao Y, Huang TH, Dishuck PC, Baker C, Cantsilieris S, Lewis AP, Munson KM, Sorensen M, Welch AE, Underwood JG, Eichler EE. Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans. Nat Commun. 2021; 12(1):5118.

Wilfert AB, Turner TN, Murali SC, Hsieh PH, Sulovari A, Wang T, Coe BP, Guo H, Hoekzema K, Bakken TE, Winterkorn LH, Evani US, Byrska-Bishop M, Earl RK, Bernier RA, Zody MC, Eichler EE. Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet. 2021; 53(8):1125-1134.

Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh PH, Harvey WT, Audano PA, Mercuri L, Piccolo I, Antonacci F, Munson KM, Lewis AP, Baker C, Underwood JG, Hoekzema K, Huang TH, Sorensen M, Walker JA, Hoffman J, Thibaud-Nissen F, Salama SR, Pang AWC, Lee J, Hastie AR, Paten B, Batzer MA, Diekhans M, Ventura M, Eichler EE. A high-quality bonobo genome refines the analysis of hominid evolution. Nature. 2021; 594(7861):77-81.

Logsdon GA, Vollger MR, Hsieh PH, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE. The structure, function and evolution of a complete human chromosome 8. Nature. 2021; 593(7857):101-107.

Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh PH, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021; 372(6537):eabf7117.

2020

Cantsilieris S, Sunkin SM, Johnson ME, Anaclerio F, Huddleston J, Baker C, Dougherty ML, Underwood JG, Sulovari A, Hsieh PH, Mao Y, Catacchio CR, Malig M, Welch AE, Sorensen M, Munson KM, Jiang W, Girirajan S, Ventura M, Lamb BT, Conlon RA, Eichler EE. An evolutionary driver of interspersed segmental duplications in primates. Genome Biol. 2020; 21(1):202.

Porubsky D, Sanders AD, Höps W, Hsieh PH, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE. Recurrent inversion toggling and great ape genome evolution. Nat Genet. 2020; 52(8):849-858.

2019

Hsieh PH, Vollger MR, Dang V, Porubsky D, Baker C, Cantsilieris S, Hoekzema K, Lewis AP, Munson KM, Sorensen M, Kronenberg ZN, Murali S, Nelson BJ, Chiatante G, Maggiolini FAM, Blanché H, Underwood JG, Antonacci F, Deleuze JF, Eichler EE. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes. Science. 2019; 366(6463):eaax2083.

Hallmark B, Karafet TM, Hsieh PH, Osipova LP, Watkins JC, Hammer MF. Genomic evidence of local adaptation to climate and diet in indigenous Siberians. Mol Biol Evol. 2019; 36(2):315-327.

2018

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh PH, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. High-resolution comparative analysis of great ape genomes. Science. 2018; 360(6393):eaar6343.

2017

Prüfer K, De Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh PH, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science. 2017; 358(6363):655-658.

Hsieh PH, Hallmark B, Watkins J, Karafet TM, Osipova LP, Gutenkunst RN, Hammer MF. Exome sequencing provides evidence of polygenic adaptation to a fat-rich animal diet in indigenous Siberian populations. Mol Biol Evol. 2017; 34(11):2913-2926.

2016

Hsieh PH, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF. Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies. Genome Res. 2016; 26(3):291-300.

Ragsdale AP, Coffman AJ, Hsieh PH, Struck TJ, Gutenkunst RN. Triallelic population genomics for inferring correlated fitness effects of same site nonsynonymous mutations. Genetics. 2016; 203(1):513-523.

Hsieh PH, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN. Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection. Genome Res. 2016; 26(3):279-290.

Coffman AJ, Hsieh PH, Gravel S, Gutenkunst RN. Computationally efficient composite likelihood statistics for demographic inference. Mol Biol Evol. 2016; 33(2):591-593.

Edwards T, Tollis M, Hsieh PH, Gutenkunst RN, Liu Z, Kusumi K, Culver M, Murphy RW. Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses. Ecol Evol. 2016; 6(2):379-396.

2004

Hsieh PH, Chen Y, Lin YT, Kuo SY. An XOR based Reed-Solomon algorithm for advanced RAID systems. In: 19th IEEE International Symposium on Defect and Fault Tolerance in VLSI Systems (DFT 2004); 2004. p. 165-172.