HiMWA: A Hierarchical Multiple-wave Admixture Model for Reconstructing Complex Population Admixture Histories.
Yang Y., Zhang R., Yang L., Ni X., Yuan K.* & Xu S. Genomics Proteomics Bioinformatics, qzag046.
PUBLICATIONS
Selected Publications
Fine-mapping across diverse ancestries drives the discovery of putative causal variants underlying human complex traits and diseases.
Yuan K., Longchamps R. J., Pardiñas A. F., Yu M., Chen T.-T., ... Nat. Genet. 56, 1841-1850. Yuan K., Longchamps R. J., Pardiñas A. F., Yu M., Chen T.-T., Lin S.-C., Chen Y., Lam M., Liu R., Xia Y., Guo Z., Shi W., Shen C., The Schizophrenia Workgroup of Psychiatric Genomics Consortium, Daly M. J., Neale B. M., Feng Y.-C. A., Lin Y.-F., Chen C.-Y., O’Donovan M. C., Ge T. & Huang H. Nat. Genet. 56, 1841-1850.
Reconstruct recent multi-population migration history by using identical-by-descent sharing.
Zhang W.*, Yuan K.*, Wen R., Li H. & Ni X. J. Genet. Genomics 51, 642-651.
Reconstructing complex admixture history using a hierarchical model.
Zhang S.*, Zhang R.*, Yuan K.*, Yang L., Liu C., Liu Y., Ni X. & Xu S. Brief. Bioinform. 25, bbad540.
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.
Sazonovs A.*, Stevens C. R.*, Venkataraman G. R.*, Yuan K.*, ... Nat. Genet. 54, 1275-1283. Sazonovs A.*, Stevens C. R.*, Venkataraman G. R.*, Yuan K.*, Avila B., Abreu M. T., Ahmad T., Allez M., Ananthakrishnan A. N., Atzmon G., Baras A., Barrett J. C., Barzilai N., Beaugerie L., Beecham A., Bernstein C. N., Bitton A., Bokemeyer B., Chan A., Chung D., Cleynen I., Cosnes J., Cutler D. J., Daly A., Damas O. M., Datta L. W., Dawany N., Devoto M., Dodge S., Ellinghaus E., Fachal L., Farkkila M., Faubion W., Ferreira M., Franchimont D., Gabriel S. B., Ge T., Georges M., Gettler K., Giri M., Glaser B., Goerg S., Goyette P., Graham D., Hämäläinen E., Haritunians T., Heap G. A., Hiltunen M., Hoeppner M., Horowitz J. E., Irving P., Iyer V., Jalas C., Kelsen J., Khalili H., Kirschner B. S., Kontula K., Koskela J. T., Kugathasan S., Kupcinskas J., Lamb C. A., Laudes M., Lévesque C., Levine A. P., Lewis J. D., Liefferinckx C., Loescher B.-S., Louis E., Mansfield J., May S., McCauley J. L., Mengesha E., Mni M., Moayyedi P., Moran C. J., Newberry R. D., O’Charoen S., Okou D. T., Oldenburg B., Ostrer H., Palotie A., Paquette J., Pekow J., Peter I., Pierik M. J., Ponsioen C. Y., Pontikos N., Prescott N., Pulver A. E., Rahmouni S., Rice D. L., Saavalainen P., Sands B., Sartor R. B., Schiff E. R., Schreiber S., Schumm L. P., Segal A. W., Seksik P., Shawky R., Sheikh S. Z., Silverberg M. S., Simmons A., Skeiceviciene J., Sokol H., Solomonson M., Somineni H., Sun D., Targan S., Turner D., Uhlig H. H., van der Meulen A. E., Vermeire S., Verstockt S., Voskuil M. D., Winter H. S., Young J., Belgium IBD Consortium, Cedars-Sinai IBD, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, NIHR IBD BioResource, Regeneron Genetics Center, SHARE Consortium, SPARC IBD Network, UK IBD Genetics Consortium, Duerr R. H., Franke A., Brant S. R., Cho J., Weersma R. K., Parkes M., Xavier R. J., Rivas M. A., Rioux J. D., McGovern D. P. B., Huang H., Anderson C. A. & Daly M. J. Nat. Genet. 54, 1275-1283.
MultiWaverX: modeling latent sex-biased admixture history.
Zhang R.*, Ni X.*, Yuan K.*, Pan Y. & Xu S. Brief. Bioinform. 23, bbac179.
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0.
Yuan K.*, Ni X.*, Liu C.*, Pan Y., Deng L., Zhang R., Gao Y., Ge X., Liu J., Ma X., Lou H., Wu T. & Xu S. Nat. Commun. 12, 6232.
Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders.
Deng L.*, Zhang C.*, Yuan K.*, Gao Y., Pan Y., ... Natl. Sci. Rev. 6, 1201-1222. Deng L.*, Zhang C.*, Yuan K.*, Gao Y., Pan Y., Ge X., He Y., Yuan Y., Lu Y., Zhang X., Chen H., Lou H., Wang X., Lu D., Liu J., Tian L., Feng Q., Khan A., Yang Y., Jin Z.-B., Yang J., Lu F., Qu J., Kang L., Su B. & Xu S. Natl. Sci. Rev. 6, 1201-1222.
MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures.
Ni X.*, Yuan K.*, Liu C., Feng Q., Tian L., Ma Z. & Xu S. Eur. J. Hum. Genet. 27, 133-139.
Inference of multiple-wave admixtures by length distribution of ancestral tracks.
Ni X.*, Yuan K.*, Yang X.*, Feng Q., Guo W., Ma Z. & Xu S. Heredity 121, 52-63.
Models, methods and tools for ancestry inference and admixture analysis.
Yuan K.*, Zhou Y.*, Ni X.*, Wang Y., Liu C. & Xu S. Quantitative Biology 5, 236-250.
Genetic history of Xinjiang's Uyghurs suggests Bronze Age multiple-way contacts in Eurasia.
Feng Q.*, Lu Y.*, Ni X.*, Yuan K.*, Yang Y., ... Mol. Biol. Evol. 34, 2572-2582. Feng Q.*, Lu Y.*, Ni X.*, Yuan K.*, Yang Y., Yang X., Liu C., Lou H., Ning Z., Wang Y., Lu D., Zhang C., Zhou Y., Shi M., Tian L., Wang X., Zhang X., Li J., Khan A., Guan Y., Tang K., Wang S. & Xu S. Mol. Biol. Evol. 34, 2572-2582.
Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions.
Zhou Y.*, Yuan K.*, Yu Y., Ni X., Xie P., Xing E. P. & Xu S. Heredity 118, 503-510.
Ancestral origins and genetic history of Tibetan Highlanders.
Lu D.*, Lou H.*, Yuan K.*, Wang X., Wang Y., Zhang C., Lu Y., Yang X., Deng L., Zhou Y., Feng Q., Hu Y., Ding Q., Yang Y., Li S., Jin L., Guan Y., Su B., Kang L. & Xu S. Am. J. Hum. Genet. 99, 580-594.
Other Publications
Extending genome-wide association studies to admixed cohorts with high degrees of relatedness.
Tan T., Vergara-Lope A., Martínez-Magaña J. J., Shah N. N., Lin Y.-S., Yuan K., Berumen J., Alegre-Díaz J., Kuri-Morales P., Tapia-Conyer R., Gelenter J., Montalvo-Ortiz J. L., Zhou W., Torres J. M. & Atkinson E. G. Nat. Genet. (2026).
Cross-ancestry analysis of brain QTLs enhances interpretation of schizophrenia genome-wide association studies.
Chen Y., Liu S., Ren Z., Wang F., Liang Q., Jiang Y., Dai R., Duan F., Han C., Ning Z., Xia Y., Li M., Yuan K., ... Am. J. Hum. Genet. 111, 2444-2457. Chen Y., Liu S., Ren Z., Wang F., Liang Q., Jiang Y., Dai R., Duan F., Han C., Ning Z., Xia Y., Li M., Yuan K., Qiu W., Yan X.-X., Dai J., Kopp R. F., Huang J., Xu S., Tang B., Wu L., Gamazon E. R., Bigdeli T., Gershon E., Huang H., Ma C., Liu C. & Chen C. Am. J. Hum. Genet. 111, 2444-2457.
Ancestral origins and post-admixture adaptive evolution of highland Tajiks.
Wen J., Liu J., Feng Q., Lu Y., Yuan K., Zhang X., Zhang C., Gao Y., Wang X., Mamatyusupu D. & Xu S. Natl. Sci. Rev. 11, nwae284.
Multi-ancestry study of the genetics of problematic alcohol use in over 1 million individuals.
Zhou H., Kember R. L., Deak J. D., Xu H., Toikumo S., Yuan K., ... Nat. Med. 29, 3184-3192. Zhou H., Kember R. L., Deak J. D., Xu H., Toikumo S., Yuan K., Lind P. A., Farajzadeh L., Wang L., Hatoum A. S., Johnson J., Lee H., Mallard T. T., Xu J., Johnston K. J. A., Johnson E. C., Nielsen T. T., Galimberti M., Dao C., Levey D. F., Overstreet C., Byrne E. M., Gillespie N. A., Gordon S., Hickie I. B., Whitfield J. B., Xu K., Zhao H., Huckins L. M., Davis L. K., Sanchez-Roige S., Madden P. A. F., Heath A. C., Medland S. E., Martin N. G., Ge T., Smoller J. W., Hougaard D. M., Børglum A. D., Demontis D., Krystal J. H., Gaziano J. M., Edenberg H. J., Agrawal A., Million Veteran Program, Zhao H., Justice A. C., Stein M. B., Kranzler H. R. & Gelernter J. Nat. Med. 29, 3184-3192.
Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries.
Liu Z., Liu R., Gao H., Jung S., Gao X., Sun R., Liu X., Kim Y., Lee H.-S., Kawai Y., Nagasaki M., Umeno J., Tokunaga K., Kinouchi Y., Masamune A., Shi W., Shen C., Guo Z., Yuan K., ... Nat. Genet. 55, 796-806. Liu Z., Liu R., Gao H., Jung S., Gao X., Sun R., Liu X., Kim Y., Lee H.-S., Kawai Y., Nagasaki M., Umeno J., Tokunaga K., Kinouchi Y., Masamune A., Shi W., Shen C., Guo Z., Yuan K., FinnGen, International Inflammatory Bowel Disease Genetics Consortium, Abreu M., Achkar J.-P., Andersen V., Bernstein C., Brant S. R., Bujanda L., Ng S. C., Denson L. A., Duerr R. H., Ferguson L. R., Franchimont D., Franke A., Gearry R., Hakonarson H., Halfvarson J., Heller C., Julià A., Kelsen J., Khalili H., Kugathasan S., Kupcinskas J., Latiano A., Louis E., Malekzadeh R., McCauley J. L., Moran C., Okou D., Orchard T., Palotie A., Parkes M., Pekow J., Potočnik U., Radford-Smith G., Rioux J. D., Rogler G., Sands B., Silverberg M., Sokol H., Vermeire S., Weersma R. K., Xavier R. J., Chinese Inflammatory Bowel Disease Genetics Consortium, Hu N., Cao Q., Wang Y., Miao Y., Zhang H., Lv X., Gao X., Zhang H., Su J., Feng B., Zhao Y., Zhu L., Chen Y., Zhu L., Chen C., Wang Y., Wang Y., Pang Z., Chen Y., Zhang X., Li H., Yu Q., Ye M., Zhang S., Tang W., Wang M., Cao X., Zhu R., Zhou G., Bian Z., Guo X., Wu X., Liu J., Xu W., Li Y., Guo Q., Guo Z., Zhu S., Li D., Liu J., Ge T., Cho J., Daly M. J., McGovern D. P. B., Ye B. D., Song K., Kakuta Y., Li M. & Huang H. Nat. Genet. 55, 796-806.
Human genetic history on the Tibetan Plateau in the past 5100 years.
Wang H., Yang M. A., Wangdue S., Lu H., Chen H., ... Zhang C., Yuan K., ... Sci. Adv. 9, eadd5582. Wang H., Yang M. A., Wangdue S., Lu H., Chen H., Li L., Dong G., Tsring T., Yuan H., He W., Ding M., Wu X., Li S., Tashi N., Yang T., Yang F., Tong Y., Chen Z., He Y., Cao P., Dai Q., Liu F., Feng X., Wang T., Yang R., Ping W., Zhang Z., Gao Y., Zhang M., Wang X., Zhang C., Yuan K., Ko A. M.-S., Aldenderfer M., Gao X., Xu S. & Fu Q. Sci. Adv. 9, eadd5582.
Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0.
Zhang R., Yuan K. & Xu S. STAR Protoc. 3, 101314.
Genetic connections and convergent evolution of tropical indigenous peoples in Asia.
Deng L., Pan Y., Wang Y., Chen H., Yuan K., Chen S., Lu D., Lu Y., Mokhtar S. S., Rahman T. A., Hoh B.-P. & Xu S. Mol. Biol. Evol. 39, msab361.
AdmixSim 2: a forward-time simulator for modeling complex population admixture.
Zhang R., Liu C., Yuan K., Ni X., Pan Y. & Xu S. BMC Bioinformatics 22, 506.
The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans.
Zhang X., Witt K. E., Bañuelos M. M., Ko A., Yuan K., Xu S., Nielsen R. & Huerta-Sanchez E. Proc. Natl. Acad. Sci. U. S. A. 118, e2020803118.
Exome sequencing in 30,000 cases defines novel risk factors for Crohn's disease.
Stevens C., Yuan K., Sazonovs A., Venkataraman G. R., Rivas M. A., Rioux J. D., McGovern D. P., Xavier R., Huang H., Anderson C. & Daly M. J. Gastroenterology 160, S-156.
Shared signature of recent positive selection on the TSBP1-BTNL2-HLA-DRA genes in five native populations from North Borneo.
Hoh B.-P., Zhang X., Deng L., Yuan K., Yew C.-W., Saw W.-Y., Hoque M. Z., Aghakhanian F., Phipps M. E., Teo Y.-Y., Subbiah V. K. & Xu S. Genome Biol. Evol. 12, 2245-2257.
AdmixSim: a forward-time simulator for various complex scenarios of population admixture.
Yang X., Yuan K., Ni X., Zhou Y., Guo W. & Xu S. Front. Genet. 11, 601439.
PGG.Han: the Han Chinese genome database and analysis platform.
Gao Y., Zhang C., Yuan L., Ling Y., Wang X., Liu C., Pan Y., Zhang X., Ma X., Wang Y., Lu Y., Yuan K., ... Nucleic Acids Res. 48, D971-D976. Gao Y., Zhang C., Yuan L., Ling Y., Wang X., Liu C., Pan Y., Zhang X., Ma X., Wang Y., Lu Y., Yuan K., Ye W., Qian J., Chang H., Cao R., Yang X., Ma L., Ju Y., Dai L., Tang Y., The Han100K Initiative, Zhang G. & Xu S. Nucleic Acids Res. 48, D971-D976.
PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations.
Zhang C., Gao Y., Ning Z., Lu Y., Zhang X., Liu J., Xie B., Xue Z., Wang X., Yuan K., Ge X., Pan Y., Liu C., Tian L., Wang Y., Lu D., Hoh B.-P. & Xu S. Genome Biol. 20, 215.
Genome-wide comparison of allele-specific gene expression between African and European populations.
Tian L., Khan A., Ning Z., Yuan K., Zhang C., Lou H., Yuan Y. & Xu S. Hum. Mol. Genet. 27, 1067-1077.
Differentiated demographic histories and local adaptations between Sherpas and Tibetans.
Zhang C., Lu Y., Feng Q., Wang X., Lou H., Liu J., Ning Z., Yuan K., Wang Y., Zhou Y., Deng L., Liu L., Yang Y., Li S., Ma L., Zhang Z., Jin L., Su B., Kang L. & Xu S. Genome Biol. 18, 115.
Length distribution of ancestral tracks under a general admixture model and its applications in population history inference.
Ni X., Yang X., Guo W., Yuan K., Zhou Y., Ma Z. & Xu S. Sci. Rep. 6, 20048.
Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.
Khan A., Tian L., Zhang C., Yuan K. & Xu S. Sci. Rep. 6, 18755.
A probabilistic method for estimating the sharing of identity by descent for populations with migration.
Ni X., Guo W., Yuan K., Yang X., Ma Z., Xu S. & Zhang S. IEEE/ACM Trans. Comput. Biol. Bioinform. 13, 281-290.
Differential natural selection of human zinc transporter genes between African and non-African populations.
Zhang C., Li J., Tian L., Lu D., Yuan K., Yuan Y. & Xu S. Sci. Rep. 5, 9658.
Preprints
Exome sequencing directly implicates 68 genes in inflammatory bowel disease.
Zhu R.*, Zhang Q.*, Yuan K., Zhang R., Turvey A. K., Stevens C. R., ... medRxiv. Zhu R.*, Zhang Q.*, Yuan K., Zhang R., Turvey A. K., Stevens C. R., Fachal L., Ahmad T., Bel Kok K., Bernstein C. N., Bokemeyer B., Brant S. R., Brooks J., Butterworth J., Cho J. H., Clark K., Cummings F., Duerr R. H., Ennis S., Farkkila M., Faubion W. A., Foley S., Franchimont D., Franke A., Hancock L., Hart A., Hooper P., Irving P., Jarvis M., Johnston E., Karlson E. W., Kemp C., Kennedy N., Kupcinskas J., Lamb C. A., Lees C., Lewis J. D., Li A., Limdi J., Loescher B.-S., Louis E., McCauley J. L., McGovern D. P. B., McLaughlin J., Moayyedi P., Moran G., Newberry R. D., Oglesby A., Palotie A., Pekow J., Perez K. J., Pollok R., Prescott N., Raine T., Ramadas A., Ramakrishnan S., Sabic K., Sands B., Satsangi J., Sazonovs A., Schreiber S., Selinger C., Shedwell S., Silverberg M. S., Singh S., Sokol H., Steed H., Steel A., Uhlig H. H., Verma A., Vermeire S., Weersma R. K., Xavier R. J., Yu M., Parkes M., Rioux J. D., Daly M. J., Huang H. & Anderson C. A. medRxiv.
Blended Genome Exome (BGE) as a cost efficient alternative to deep whole genomes or arrays.
DeFelice M., Grimsby J. L., Howrigan D., Yuan K., Chapman S. B., Stevens C., DeLuca S., Townsend M., Buxbaum J., Pericak-Vance M., Qin S., Stein D. J., Teferra S., Xavier R. J., Huang H., Martin A. R. & Neale B. M. bioRxiv.
A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner.
Boltz T. A., Chu B. B., Liao C., Sealock J. M., Ye R., ... Yu M., Yuan K., ... bioRxiv. Boltz T. A., Chu B. B., Liao C., Sealock J. M., Ye R., Majara L., Fu J. M., Service S., Zhan L., Medland S. E., Chapman S. B., Rubinacci S., DeFelice M., Grimsby J. L., Abebe T., Alemayehu M., Ashaba F. K., Atkinson E. G., Bigdeli T., Bradway A. B., Brand H., Chibnik L. B., Fekadu A., Gatzen M., Gelaye B., Gichuru S., Gildea M. L., Hill T. C., Huang H., Hubbard K. M., Injera W. E., James R., Joloba M., Kachulis C., Kalmbach P. R., Kamulegeya R., Kigen G., Kim S., Koen N., Kwobah E. K., Kyebuzibwa J., Lee S., Lennon N. J., Lind P. A., Lopera-Maya E. A., Makale J., Mangul S., McMahon J., Mowlem P., Musinguzi H., Mwema R. M., Nakasujja N., Newman C. P., Nkambule L. L., O’Neil C. R., Olivares A. M., Olsen C. M., Ongeri L., Parsa S. J., Pretorius A., Ramesar R., Reagan F. L., Sabatti C., Schneider J. A., Shiferaw W., Stevenson A., Stricker E., Stroud R. E., Tang J., Whiteman D., Yohannes M. T., Yu M., Yuan K., NeuroGAP-Psychosis, Akena D., Atwoli L., Kariuki S. M., Koenen K. C., Newton C. R. J. C., Stein D. J., Teferra S., Zingela Z., Pato C. N., Pato M. T., Lopez-Jaramillo C., Freimer N., Ophoff R. A., Olde Loohuis L. M., Talkowski M. E., Neale B. M., Howrigan D. P. & Martin A. R. bioRxiv.
