Peer-reviewed Articles 

Population Genetics

  1. Naseri A, Tang K, Geng X, Shi J, Zhang J, Shakya P, Liu X, Zhang S, Zhi D. (2021) Personalized genealogical history of UK individuals inferred from biobank-scale IBD segments. BMC Biology. 19:32. [PDF]
  2. Liu X* and Fu YX. (2020) Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biology 21:280. [PDF] *corresponding author
  3. Xue C, Rustagi N, Liu X, Raveendran M, Harris RA, Venkata MG, Rogers J, Yu F. (2020) Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS ONE 15(8): e0236285. [PDF]
  4. Liu X. (2020) Human prehistoric demography revealed by the polymorphic pattern of CpG transitions. Molecular Biology and Evolution 37(9):2691-2698. [PDF] 
  5. Li Y, Hu Y, Zhao Y, Wang Q, Mbenda HGN, Kittichai V, Lawpoolsri S, Sattabongkot J, Menezes L, Liu X, Cui L, Cao Y. (2020) Dynamics of Plasmodium Vivax Populations in Border Areas of the Greater Mekong Sub-Region During Malaria Elimination. Malaria Journal 19:145. 
  6. Naseri A, Liu X, Tang K, Zhang S, Zhi D. (2019) Ultra-fast, powerful and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts. Genome Biology 20:143. [PDF]
  7. Cristofari R, Liu X, Bonadonna F, Cherel Y, Pistorius P, Le Maho Y, Raybaud V, Stenseth N, Le Bohec C, Trucchi E. (2018) Climate-driven range shifts of the king penguin in a fragmented ecosystem. Nature Climate Change 8:245–251. [PDF]
  8. Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X, White S, Dahdouli M, Rio Deiros D, Below JE, Salerno W, Cox L, Fan D, Ferguson B, Horvath J, Johnson Z, Kanthaswamy S, Kubisch HM, Liu D, Platt M, Smith DG, Sun B, Vallender EJ, Wang F, Wiseman R, Chen R, Muzny DM, Gibbs RA, Yu F and Rogers J. (2016) ​The population genomics of rhesus macaques (Macaca mulatta) based on whole genome sequences. Genome Research 26(12):1651-1662. [PDF]
  9. Liu X* and Fu YX. (2015) Exploring population size changes using SNP frequency spectra. Nature Genetics. 47(5):555-559. [PDF] *corresponding author
  10. 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, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E. (2015) Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One. 10(3):e0121644. [PDF] *contributed equally 
  11. Xue C, Liu X, Gong Y, Zhao Y, Fu YX. (2013) Significantly fewer protein functional changing variants for lipid metabolism in Africans than in Europeans. Journal of Translational Medicine 11:67. [PDF]
  12. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM; Broad GO; Seattle GO; on behalf of the NHLBI Exome Sequencing Project (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69. [PDF]
  13. Liu X (2012) jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors. Methods in Ecology and Evolution 3:624-627. [PDF]
  14. Xue C, Fu YX, Zhao Y, Gong Y, Liu X. (2011) Smaller genetic risk in catabolic process explains lower energy expenditure, more athletic capability and higher prevalence of obesity in Africans. PLoS One 6(10):e26027. [PDF]
  15. Peng B and Liu X (2010) Simulating sequences of the human genome with rare variants. Human Heredity 70:287-291. [PDF]
  16. Coventry A, Bull-Otterson L, Liu X, Clark AG, Maxwell TJ, Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, Gross S, Joshi V, Santibanez J, Morgan M, Chang K, Hale W, Templeton AR, Boerwinkle E, Gibbs R and Sing CF (2010) Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nature Communications 1: 131. [PDF]
  17. Liu X*, Fu YX, Maxwell TJ, and Boerwinkle E (2010) Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Research 20:101-109. [PDF] *corresponding author
  18. Liu X, Maxwell TJ, Boerwinkle E, and Fu YX (2009) Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences. Molecular Biology and Evolution 26: 1479-1490. [PDF]
  19. Liu X, Fu YX. (2008) Summary statistics of neutral mutations in longitudinal DNA samples. Theoretical Population Biology 74: 56-67. [PDF]
  20. Liu X, Fu YX. (2008) Algorithms to estimate lower bounds of recombination with or without recurrent mutations. BMC Genomics 9 (Suppl. I):S24. [PDF]
  21. Liu X, Fu YX (2007) Test of genetical isochronism for longitudinal samples of DNA sequences. Genetics 176(1):327-342. [PDF]
  22. Liu X, Gutacker MM, Musser JM, Fu YX. (2006) Evidence for recombination in Mycobacterium tuberculosis. Journal of Bacteriology 188(23):8169-8177. [PDF]
  23. 陶士珩, 储建华, 刘晓明, 张荣梅, 张镇, 罗泽伟. (2001) 应用混合群体的连锁不平衡信息实现基因定位的解析率分析. 科学通报 46(16):1356-1358.
  24. 陶士珩, 刘晓明, 储建华, 张荣梅, 杜丽萍, 罗泽伟. (2000) 混合群体连锁不平衡的衰减速率与基因定位. 科学通报 45(21):2274-2280.
  25. 陶士珩, 张荣梅, 储建华, 刘晓明, 杜丽萍, 齐庆远, 罗泽伟. (2000) 混合群体连锁不平衡的群体遗传学模型. 科学通报 45(19):2041-2047.​ 

Bioinformatics

  1. Wang C*, Dong Y, Li C, Oberstaller J, Zhang M, Gibbons J, Pires CV, Xiao M, Zhu L, Jiang RH, Kim K, Miao J, Otto TD, Cui L, Adams JH, Liu X. (2023) MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites. Genome Biology. 24:231. [PDF] *corresponding author
  2. Li C*, Hou I, Ma M, Wang G, Bai Y*, Liu X*. (2023) Orthogonal analysis of variants in APOE gene using in-silico approaches reveals novel disrupting variants. Frontiers in Bioinformatics. 3:1122559. [PDF] *corresponding authors
  3. Li C, Zhi D, Wang K, Liu X. (2022) MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning. Genome Medicine. 14:115. [PDF]
  4. Li C, Ma K, Xu N, Fu C, He A, Liu X*, Bai Y*. (2022) SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data. Frontiers in Artificial Intelligence. 5:991733. [PDF] *corresponding authors
  5. Dong Y*, Li C, Kim K, Cui L, Liu X*. (2021) Genome annotation of disease-causing microorganisms. Briefings in Bioinformatics 22(2):845–854. [PDF] *corresponding authors 
  6. Liu X*, Li C, Mou C, Dong Y, Tu Y. (2020) dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Medicine 12:103. [PDF] *corresponding author ​
  7. Li C, Wu B, Han H, Zhao J, Bai Y*, Liu X*. (2020) Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data. Genes 11(9): 953. [PDF] *corresponding authors
  8. Bai Y, Baker S, Exoo K, Dai X, Ding L, Khattak NA, Li H, Liu H, Liu X. (2020) MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network. BMC Bioinformatics 21(Suppl 4):247. [PDF]
  9. Li C, Mou C, Swartz MD, Yu B, Bai Y, Tu Y, Liu X. (2020) dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions. Human Mutation 41(6):1123–1130. [PDF]
  10. Djotsa A, Chen K and Liu X. (2019) Comparison of different functional prediction scores using a gene-based permutation model for identifying cancer driver genes. BMC Medical Genomics 12(Suppl 1):22. [PDF]
  11. Liu X*, Li C and Boerwinkle E. (2017) The performance of deleteriousness prediction scores for rare non-protein-changing single nucleotide variants in human genes. Journal of Medical Genetics 54:134-144. [PDF] *corresponding author
  12. Dong C, Guo Y, He Z, Yang H, Liu X, Wang K. (2016) iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. Genome Medicine 8:135. [PDF]
  13. Liu X*, Wu C, Li C and Boerwinkle E. (2016) dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutation 37(3):235-241. [PDF] *corresponding author
  14. Liu X*, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ and Boerwinkle E. (2016) WGSA: an annotation pipeline for human genome sequencing studies. Journal of Medical Genetics 53:111-112. [PDF] *corresponding author
  15. Dong C*, Wei P*, Jian X, Gibbs R, Boerwinkle E, Wang K^ and Liu X^. (2015) Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Human Molecular Genetics 24(8):2125-2137. [PDF] ^corresponding authors; *contributed equally
  16. Jian X, Boerwinkle E and Liu X. (2014) In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Research 42(22):13534-13544. [PDF]
  17. Li Q, Liu X*, Gibbs RA, Boerwinkle E, Polychronakos C, Qu HQ* (2014) Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes. PLoS One 9(8):e104452. [PDF] *corresponding authors
  18. Jian X, Boerwinkle E and Liu X. (2014) In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genetics in Medicine 16(7):497–503. [PDF]
  19. Liu X*, Jian X, Boerwinkle E. (2013) dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Human Mutation. 34:E2393-E2402. [PDF] *corresponding author
  20. Line SR, Liu X, de Souza AP, Yu F. (2013) Translational signatures and mRNA levels are highly correlated in human stably expressed genes. BMC Genomics 14(1):268. [PDF]
  21. Yao J, Zhao Q, Yuan Y, Zhang L, Liu X, Yung WK, Weinstein JN. (2012) Identification of common prognostic gene expression signatures with biological meanings from microarray gene expression datasets. PLoS One 7(9):e45894. [PDF]
  22. Liu X*, Jian X and Boerwinkle E (2011) dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation 32:894-899. (recommended by Faculty of 1000) [PDF] *corresponding author

Genetic Epidemiology and medical genetics

  1. Li C*, Wang R, Wu A, Yuan T, Song K, Bai Y*, Liu X*. (2022) SARS-COV-2 as potential microRNA sponge in COVID-19 patients. BMC Medical Genomics. 15:94. *corresponding authors [PDF]
  2. Li C*, Wu A, Song K, Gao J, Huang E, Bai Y*, Liu X*. (2021) Identifying Putative Causal Links between MicroRNAs and Severe COVID-19 Using Mendelian Randomization. Cells. 10(12): 3504. *Corresponding authors. [PDF]
  3. Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee S, Tian X, Browning BL, Das S, Emde A, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, Andrade MD, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin K, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O’Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo J, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng L, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O’Connor TD, Abecasis GR. (2021) Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature. 590: 290-299. [PDF]
  4. Lin BM, Grinde KE, Brody JA, Breeze CE, Raffield LM, Mychaleckyj JC, Thornton TA, Perry JA, Baier LJ, de las Fuentes L, Guo X, Heavner BD, Hanson RL, Hung YJ, Qian H, Hsiung CA, Hwang SJ, Irvin MR, Jain D, Kelly TN, Kobes S, Lange L, Lash JP, Li Y, Liu X, Mi X, Musani SK, Papanicolaou GJ, Parsa A, Reiner AP, Salimi S, Sheu WHH, Shuldiner AR, Taylor KD, Smith AV, Smith JA, Tin A, Vaidya D, Wallace RB, Yamamoto K, Sakaue S, Matsuda K, Kamatani Y, Momozawa Y, Yanek LR, Young BA, Zhao W, Okada Y, Abecasis G, Psaty BM, Arnett DK, Boerwinkle E, Cai J, Chen IYD, Correa A, Cupples LA, He J, Kardia SLR, Kooperberg C, Mathias RA, Mitchell BD, Nickerson D, Turner ST, Ramachandran VS, Rotter JI, Levy D, Kramer H, Kottgen A, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Kidney Working Group, Rich SS, Lin DY, Browning SR, Franceschini N. (2021) Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium. EBioMedicine 63:1031573. [PDF]
  5. Liu X*^, Cragun D*, Pang J, Adapa SR, Fonseca R, Jiang RHY. (2020) False Alarms in Consumer Genomics Add to Public Fear and Potential Health Care Burden. Journal of Personalized Medicine 10(4): 187. ^corresponding author; *contributed equally [PDF]
  6. Pei G, Sun H, Dai Y, Liu X, Zhao Z, Jia P. (2019) Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics. BMC Genomics 20(Suppl 1):79. [PDF]
  7. Chen H, Huffman JE, Brody JA, Wang C, Lee S, Li Z, Gogarten SM, Sofer T, Bielak LF, Bis JC, Blangero J, Bowler RP, Cade BE, Cho MH, Correa A, Curran JE, de Vries PS, Glahn DC, Guo X, Johnson AD, Kardia S, Kooperberg C, Lewis JP, Liu X, Mathias RA, Mitchell BD, O'Connell JR, Peyser PA, Post WS, Reiner AP, Rich SS, Rotter JI, Silverman EK, Smith JA, Vasan RS, Wilson JG, Yanek LR; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Hematology and Hemostasis Working Group, Redline S, Smith NL, Boerwinkle E, Borecki IB, Cupples LA, Laurie CC, Morrison AC, Rice KM, Lin X. (2019) Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies. American Journal of Human Genetics 104(2):260-274. [PDF]
  8. Floyd JS, Bloch KM, Brody JA, Maroteau C, Siddiqui MK, Gregory R, Carr DF, Molokhia M, Liu X, Bis JC, Ahmed A, Liu X, Hallberg P, Yue Q, Magnusson PKE, Brisson D, Wiggins KL, Morrison AC, Khoury E, McKeigue P, Stricker BH, Lapeyre-Mestre M, Heckbert SR, Gallagher A, Chinoy H, Gibbs RA, Bondon-Guitton E, Tracy R, Boerwinkle E, Gaudet D, Conforti A, van Staa T, Sitlani CM, Rice KM, van der Zee AHM, Wadelius M, Morris AP, Pirmohamed M, Palmer CAN Psaty BM, Alfirevic A on beharf of the PREDICTION-ADR Consortium and EUDRAGENE. (2019) Pharmacogenomics of statin-related myopathy: meta-analysis of rare variants from whole-exome sequencing. PLoS ONE 14(6): e0218115. [PDF]
  9. Feofanova E, Yu B, Metcalf G, Liu X, Muzny D, Below J, Wagenknecht L, Gibbs R, Morrison A, Boerwinkle E. (2018) Sequence-Based Analysis of Lipid-Related Metabolites in a Multiethnic Study. Genetics 209(2):607-616. [PDF]
  10. Williams M, Biguetti C, Romero-Bustillos M, Maheshwari K, Dinckan N, Cavalla F, Liu X, Silva R, Akyalcin S, Uyguner ZO, Vieira A, Amendt B, Fakhouri W, and Letra A (2018) Colorectal Cancer-Associated Genes Are Associated with Tooth Agenesis and May Have a Role in Tooth Development. Scientific Reports 8:2979. [PDF]
  11. Li C, Grove ML, Yu B, Jones BC, Morrison A, Boerwinkle E*, Liu X*. (2018) Genetic variants in microRNA genes and targets associated with cardiovascular disease risk factors in the African-American population. Human Genetics 137(1):85–94. *Corresponding authors. [PDF]
  12. Hwang JL, Park S-Y, Ye H, Sanyoura M, Pastore AN, Carmody D, del Gaudio D, Wilson JF, Hanis CL, Liu X, Atzmon G, Glaser B, Philipson LH, Greeley SAW, T2D-Genes Consortium. (2017) FOXP3 mutations causing early-onset insulin-requiring diabetes but without other features of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome. Pediatric Diabetes 19(3):388-392. [PDF]
  13. Yuan Q, Zhao M, Liu Q, Tandon B, Maili L, Liu X, Zhang A, Baugh EH, Tran T, Silva RM, Hecht JT, Swindell EC, Wagner DS, Letra A. (2017) Role of WNT10A in failure of tooth development in humans and zebrafish. Molecular Genetics and Genomic Medicine 5(6):730-741. [PDF]
  14. Andersen AM, Pietrzak RH, Kranzler HR, Ma L, Zhou H, Liu X, Kramer J, Kuperman S, Edenberg HJ, Nurnberger JI Jr, Rice JP, Tischfield JA, Goate A, Foroud TM, Meyers JL, Porjesz B, Dick DM, Hesselbrock V, Boerwinkle E, Southwick SM, Krystal JH, Weissman MM, Levinson DF, Potash JB, Gelernter J, Han S (2017) Polygenic Scores for Major Depressive Disorder and Risk of Alcohol Dependence. JAMA Psychiatry 74(11):1153-1160. [PDF]
  15. Brody JA, Morrison AC, Bis JC, O’Connell JR, Brown MR, Huffman JE, Ames DC, Carroll A, Conomos MP, Gabriel S, Gibbs RA, Gogarten SM, Gupta N, Jaquish CE, Johnson AD, Lewis JP, Liu X, Manning AK, Papanicolaou GJ, Pitsillides AN, Rice KM, Salerno W, Sitlani CM, Smith NL, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, TOPMed Hematology and Hemostasis Working Group, CHARGE Analysis and Bioinformatics Working Group, Heckbert SR, Laurie CC, Mitchell BD, Vasan RS, Rich SS, Rotter JI, Wilson JG, Boerwinkle E, Psaty BM, Cupples LA. (2017) Analysis Commons, A Team Approach to Discovery in a Big-Data Environment for Genetic Epidemiology. Nature Genetics 49(11):1560-1563. [PDF]
  16. de Vries PS, Yu B, Feofanova EV, Metcalf GA, Brown MR, Zeighami AL, Liu X, Muzny DM, Gibbs RA, Boerwinkle E, Morrison AC. (2017) Whole-genome sequencing study of serum peptide levels: the Atherosclerosis Risk in Communities study. Human Molecular Genetics. 26(17):3442-3450. [PDF]
  17. Feng Y, Ge X, Meng L, Scull J, Li J, Tian X, Zhang T, Jin W, Cheng H, Wang X, Tokita M, Liu P, Mei H, Wang Y, Li F, Schmitt ES, Zhang WV, Muzny D, Wen S, Chen Z, Yang Y, Beaudet AL, Liu X, Eng CM, Xia F, Wong L-J, Zhang J. (2017) The Next-Generation of Spinal Muscular Atrophy Carrier Screening: Comprehensive Pan-ethnic SMN1 Copy Number and Sequence Variant Analysis by Massively Parallel Sequencing. Genetics in Medicine 19(8):936-944. [PDF]
  18. 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. (2017) Practical Approaches for Whole Genome Sequence Analysis of Complex Traits. American Journal of Human Genetics 100:205–215. [PDF]
  19. Yu B, de Vries P, Metcalf G, Wang Z, Feofanova E, Liu X, Muzny D, Wagenknecht L, Gibbs R, Morrison A, Boerwinkle E. (2016) Whole genome sequence analysis of serum amino acid levels. Genome Biology 17:237. [PDF]
  20. Yazdani A, Yazdani A, Liu X, Boerwinkle E. (2016) Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis. Genetic Epidemiology. 40(6):486-91. [PDF]
  21. Huang J, Wang K, Wei P, Liu X, Liu X, Tan K, Boerwinkle E, Potash JB and Han S. (2016) FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics. Genetics. 202(3):919-29. [PDF]
  22. Li AH, Morrison AC, Kovar C, Cupples LA, Brody JA, Polfus LM, Yu B, Metcalf G, Muzny D, Veeraraghavan N, Liu X, Lumley T, Mosley TH, Gibbs RA, Boerwinkle E. (2015) Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease. Nature Genetics. 47(6):640-2. [PDF]
  23. Bis JC, DeStefano A, Liu X, Brody JA, Choi SH, Verhaaren BF, Debette S, Ikram MA, Shahar E, Butler KR Jr, Gottesman RF, Muzny D, Kovar CL, Psaty BM, Hofman A, Lumley T, Gupta M, Wolf PA, van Duijn C, Gibbs RA, Mosley TH, Longstreth WT Jr, Boerwinkle E, Seshadri S, Fornage M. (2014) Associations of NINJ2 Sequence Variants with Incident Ischemic Stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) Consortium. PLoS One 9(6):e99798. [PDF]
  24. Bis JC, White CC, Franceschini N, Brody J, Zhang X, Muzny D, Santibanez J, Gibbs R, Liu X, Lin H, Boerwinkle E, Psaty BM, North KE, Cupples LA, O'Donnell CJ; CHARGE Subclinical Atherosclerosis Working Group. (2014) Sequencing of 2 Subclinical Atherosclerosis Candidate Regions in 3669 Individuals: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. Circulation: Cardiovascular Genetics 7(3):359-64. [PDF]
  25. Lin H, Wang M, Brody JA, Bis JC, Dupuis J, Lumley T, McKnight B, Rice KM, Sitlani CM, Reid JG, Bressler J, Liu X, Davis BC, Johnson AD, O'Donnell CJ, Kovar CL, Dinh H, Wu Y, Newsham I, Chen H, Broka A, DeStefano AL, Gupta M, Lunetta KL, Liu CT, White CC, Xing C, Zhou Y, Benjamin EJ, Schnabel RB, Heckbert SR, Psaty BM, Muzny DM, Cupples LA, Morrison AC, Boerwinkle E.(2014) Strategies to Design and Analyze Targeted Sequencing Data: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. Circulation: Cardiovascular Genetics 7(3):335-43. [PDF]
  26. Concepcion JP, Reh CS, Daniels M, Liu X, Paz VP, Ye H, Highland HM, Hanis CL, Greeley SA. (2014) Neonatal diabetes, gallbladder agenesis, duodenal atresia, and intestinal malrotation caused by a novel homozygous mutation in RFX6.Pediatric Diabetes 15(1):67-72. [PDF]
  27. Han S, Yang B-Z, Kranzler HR, Liu X, Zhao H, Farrer LA, Boerwinkle E, Potash JB and Gelernter J. (2013) Integrating GWASs and Human Protein Interaction Networks Identifies a Gene Subnetwork Underlying Alcohol Dependence.American Journal of Human Genetics 93(6):1027-1034. [PDF]
  28. 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, Cupples LA, Gibbs R, Boerwinkle E; the Cohorts for Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium. (2013) Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nature Genetics 45:899–901 [PDF] *contributed equally
  29. Wei P, Liu X and Fu YX (2011) Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study. BMC Proceedings 5(Suppl 9):S20. [PDF]
  30. Daw EW, Liu X, Wu CC. (2003) Age-of-onset of hypertension vs. a single measurement of systolic blood pressure in a combined linkage and segregation analysis. BMC Genetics 4 (Suppl. 1):S80. [PDF]
  31. Feng BJ, Huang W, Shugart YY, Lee MK, Zhang F, Xia JC, Wang HY, Huang TB, Jian SW, Huang P, Feng QS, Huang LX, Yu XJ, Li D, Chen LZ, Jia WH, Fang Y, Huang HM, Zhu JL, Liu XM, Zhao Y, Liu WQ, Deng MQ, Hu WH, Wu SX, Mo HY, Hong MF, King MC, Chen Z, Zeng YX. (2002) Genome-wide scan for familial nasopharyngeal carcinoma reveals evidence of linkage to chromosome 4. Nature Genetics 31(4):395-99. [PDF]
  32. Chu J, Zhang R, Zhao Z, Zou W, Han Y, Qi Q, Zhang H, Wang JC, Tao S, Liu X, Luo Z. (2002) Male fertility is compatible with an Arg(840)Cys substitution in the AR in a large chinese family affected with divergent phenotypes of AR insensitivity syndrome. Journal of Clinical Endocrinology and Metabolism 87(1):347-51.
  33. He X, Zhu DL, Chu SL, Jin L, Xiong MM, Wang GL, Zhang WZ, Zhou HF, Mao SY, Zhan YM, Zhuang QN, Liu XM, Zhao Y, Huang W. (2001) Alpha-adducin gene and essential hypertension in China. Clinical and Experimental Hypertension 23(7):579-589. [PDF]
  34. Wang G*, Zhao Y*, Liu X*, Wang L*, Wu C, Zhang W, Liu W, Zhang P, Cong W, Zhu Y, Zhang L, Chen S, Wan D, Zhao X, Huang W, Gu J. (2001) Allelic loss and gain, but not genomic instability, as the major somatic mutation in primary hepatocellular carcinoma. Genes Chromosomes and Cancer 31(3):221-227. [PDF] *contributed equally
  35. 何鑫, 朱鼎良, 韩战营, 刘晓明, 王谷亮, 初少莉, 张伟忠, 周怀发, 茅守玉, 庄启南, 赵彦, 黄薇. (2001) 应用微卫星DNA 基因分型技术进行双生子卵型鉴定. 中华医学遗传学杂志 18: 421-425. [PDF]
  36. 张荣梅, 杜丽萍, 彭志海, 储建华, 刘晓明, 陶士珩, 罗泽伟. (2000) 多结节性甲状腺肿的分子遗传学研究进展. 中华医学遗传学杂志 17: 359-361. 
BIOLOGICAL ANTHROPOLOGY
  1. Pang J, Dong Y, Turner C, Li C, Liu X. (2022) Analysis of data consistency identifies measurement abnormality in Howells' craniometric test data set. American Journal of Biological Anthropology. 179(4):687-692. [PDF]
  2. Pang J, Liu X. (2023) Evaluation of missing data imputation methods for human osteometric measurements. American Journal of Biological Anthropology. 181(4):666-676. [PDF]

Book Chapters

  1. Jian X and Liu X. (2016) In Silico Prediction of Deleteriousness for Nonsynonymous and Splice-Altering Single Nucleotide Variants in the Human Genome. In: In Vitro Mutagenesis. (Reeves A ed.) New York: Springer Nature pp. 191-198.
  2. Djotsa Nono AB, Chen K, Liu X. (2016) Computational Prediction of Genetic Drivers in Cancer. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0025331. [PDF] [preprint]
  3. Fu YX., Liu X. (2010) Statistical methods for detecting the presence of natural selection in bacterial populations. In: Bacterial Population Genetics in Infectious Disease. (Robinson A., Feil E., Falush D. ed.) Hoboken, New Jersey: Wiley-Blackwell pp. 87-101. [PDF]
  4. 罗泽伟, 张荣梅, 陶士珩, 刘晓明, 方福德. (2002) 复杂性遗传病基因定位与分离的理论和方法. In: 基因组科学与人类疾病. (陈竺, 强伯勤, 方福德 主编) 北京: 科学出版社 pp. 137-165.
  5. 刘晓明, 张荣梅, 罗泽伟. (2000) 生物信息学及其在基因组研究中的应用. In: 解码生命-人类基因组计划和后基因组计划. (贺林 主编) 北京: 科学出版社 pp. 333-351. [PDF]
Full Publication List (including team science papers) @ Google Scholar