Publications

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2020
Liu S, Tian M, He F, Li J, Xie H, Liu W, Zhang Y, Zhang R, Yi M, Che F, Ma X, Zheng Y, Deng H, Wang G, Chen L, Sun X, Xu Y, Wang J, Zang Y, Han M, Wang X, Guan H, Ge Y, Wu C, Wang H, Liang H, Li H, Ran N, Yang Z, Huang H, Wei Y, Zheng X, Sun X, Feng X, Zheng L, Zhu T, Luo W, Chen Q, Yan Y, Huang Z, Jing Z, Guo Y, Zhang X, Schaaf CP, Xing J, Wang C, Yu F, Guan J-S. Mutations in ASH1L confer susceptibility to Tourette syndrome. Mol Psychiatry. 2020 ;25(2):476-490.
Liu M, Zhong Y, Liu H, Liang D, Liu E, Zhang Y, Tian F, Liang Q, Cram DS, Wang H, Wu L, Yu F. REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis. Mol Genet Genomic Med. 2020 ;8(11):e1488.
Xue C, Rustagi N, Liu X, Raveendran M, Harris RA, Venkata MGorentla, Rogers J, Yu F. Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS One. 2020 ;15(8):e0236285.
Liu S, Tian M, He F, Li J, Xie H, Liu W, Zhang Y, Zhang R, Yi M, Che F, Ma X, Zheng Y, Deng H, Wang G, Chen L, Sun X, Xu Y, Wang J, Zang Y, Han M, Wang X, Guan H, Ge Y, Wu C, Wang H, Liang H, Li H, Ran N, Yang Z, Huang H, Wei Y, Zheng X, Sun X, Feng X, Zheng L, Zhu T, Luo W, Chen Q, Yan Y, Huang Z, Jing Z, Guo Y, Zhang X, Schaaf CP, Xing J, Wang C, Yu F, Guan J-S. Spontaneous hyperactivity in Ash1l mutant mice, a new model for Tourette syndrome. Mol Psychiatry. 2020 ;25(2):241-242.
2018
Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science. 2018 ;361(6409).
Wang J, Chen L, Zhou C, Wang L, Xie H, Xiao Y, Zhu H, Hu T, Zhang Z, Zhu Q, Liu Z, Liu S, Wang H, Xu M, Ren Z, Yu F, Cram DS, Liu H. Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing. Am J Obstet Gynecol. 2018 ;219(3):287.e1-287.e18.
Yang X, Li J, Fang Y, Zhang Z, Jin D, Chen X, Zhao Y, Li M, Huan L, Kent TA, Dong J-fei, Jiang R, Yang S, Jin L, Zhang J, Zhong TP, Yu F. Rho Guanine Nucleotide Exchange Factor Is a Risk Gene for Intracranial Aneurysms. Circ Genom Precis Med. 2018 ;11(7):e002099.
Retshabile G, Mlotshwa BC, Williams L, Mwesigwa S, Mboowa G, Huang Z, Rustagi N, Swaminathan S, Katagirya E, Kyobe S, Wayengera M, Kisitu GP, Kateete DP, Wampande EM, Maplanka K, Kasvosve I, Pettitt ED, Matshaba M, Nsangi B, Marape M, Tsimako-Johnstone M, Brown CW, Yu F, Kekitiinwa A, Joloba M, Mpoloka SW, Mardon G, Anabwani G, Hanchard NA. Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Am J Hum Genet. 2018 ;102(5):731-743.
2017
Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SWai, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017 ;38(6):669-677.
Rustagi N, Zhou A, W Watkins S, Gedvilaite E, Wang S, Ramesh N, Muzny D, Gibbs RA, Jorde LB, Yu F, Xing J. Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics. 2017 ;18(1):396.
Morrison AC, Huang Z, Yu B, Metcalf G, Liu X, Ballantyne C, Coresh J, Yu F, Muzny D, Feofanova E, Rustagi N, Gibbs R, Boerwinkle E. Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits. Am J Hum Genet. 2017 ;100(2):205-215.
2016
Song J, Xue C, Preisser JS, Cramer DW, Houck KL, Liu G, Folsom AR, Couper D, Yu F, Dong J-fei. Association of Single Nucleotide Polymorphisms in the ST3GAL4 Gene with VWF Antigen and Factor VIII Activity. PLoS One. 2016 ;11(9):e0160757.
Xue C, Chen H, Yu F. Base-Biased Evolution of Disease-Associated Mutations in the Human Genome. Hum Mutat. 2016 ;37(11):1209-1214.
Huang Z, Rustagi N, Veeraraghavan N, Carroll A, Gibbs R, Boerwinkle E, Venkata MGorentla, Yu F. A hybrid computational strategy to address WGS variant analysis in >5000 samples. BMC Bioinformatics. 2016 ;17(1):361.
Campbell IM, Gambin T, Jhangiani S, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F, Lupski JR. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat. 2016 ;37(3):231-234.
Xue C, Raveendran M, R Harris A, Fawcett GL, Liu X, White S, Dahdouli M, Deiros DRio, Below JE, Salerno W, Cox L, Fan G, Ferguson B, Horvath J, Johnson Z, Kanthaswamy S, H Kubisch M, Liu D, Platt M, Smith DG, Sun B, Vallender EJ, Wang F, Wiseman RW, Chen R, Muzny DM, Gibbs RA, Yu F, Rogers J. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res. 2016 ;26(12):1651-1662.
2015
Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics. 2015 ;16(1):143.
Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics. 2015 ;16(1):214.
Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, L Cupples A, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E. Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One. 2015 ;10(3):e0121644.
2014
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics. 2014 ;15:30.
Zhou Z, Yu F, Buchanan A, Fu Y, Campos M, Wu KK, Chambless LE, Folsom AR, Boerwinkle E, Dong J-fei. Possible race and gender divergence in association of genetic variations with plasma von Willebrand factor: a study of ARIC and 1000 genome cohorts. PLoS One. 2014 ;9(1):e84810.
2013
Gibson IB, Jiang R, Yu F. The 1000 Genomes Project: paving the way for personalized genomic medicine. Per Med. 2013 ;10(4):321-324.
Khurana E, Fu Y, Colonna V, Mu XJasmine, Kang HMin, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs RA, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny DM, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 ;342(6154):1235587.
Wang Y, Lu J, Yu J, Gibbs RA, Yu F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res. 2013 ;23(5):833-42.
Morrison AC, Voorman A, Johnson AD, Liu X, Yu J, Li A, Muzny D, Yu F, Rice K, Zhu C, Bis J, Heiss G, O'Donnell CJ, Psaty BM, L Cupples A, Gibbs R, Boerwinkle E. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet. 2013 ;45(8):899-901.