Yingrui Li

Yingrui Li



Research interests

Indicators of esteem

  • Guangdong Provincial Special Support Program on Elite Youth Scientist (2015)

  • Top 10 Scientific Achievements in China (for BGI’s giant panda genome sequence) (2010)

  • National Elitist in Shenzhen (2009-2019)

  • Top 10 Scientific Achievements in China (for BGI’s first Asian genome sequence) (2008)

My publications


*Corresponding author; # first-author or equal first-author 

1. Laurent C Francioli, Mircea Cretu-Stancu, …, Yingrui Li, et al. A framework for the detection of denovo mutations in family-based sequencing data. European Journal of Human Genetics 25(2), 227, 2017

2. Yuen RKC, Merico D, …, Yingrui Li, et al. Genome-wide characteristics of de novomutations in autism. NPJ genomic medicine. 2016;1:16027-1-16027-10. doi:10.1038/npjgenmed.2016.27

3. Demontis, Ditte, Østergaard, Søren, Yingrui Li, et al. Whole-Exome Sequencing Reveals Increased Burden of Rare Functional and Disruptive Variants in Candidate Risk Genes in Individuals With Persistent Attention-Deficit/Hyperactivity Disorder. Journal of the American Academy of Child & Adolescent Psychiatry, Volume 55 , Issue 6 , 521 - 523

4. Fusheng Zhou, Hongzhi Cao, …, Yingrui Li, et al. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease. Nature Genetics 48, 740–746 (2016) doi:10.1038/ng.3576

5. Yue Shen, Giovanni Stracquadanio, …, Yingrui Li, et al. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res. 2016. 26: 36-49

6. Aifa Tang, Yi Huang, …, Yingrui Li, et al. Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells. Sci Rep. 2016; 6: 19260.

7. Chenguang Li, Zhibo Gao, …, Yingrui Li, et al. Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma. SciRep. 2015; 5: 14237.

8. Yong Hou, Kui, Wu, …, Yingrui Li, et al. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing. GigaScience 2015 4:37. DOI: 10.1186/s13742-015-0068-3

9. Ling Zhao, Xiang-Jun Chen, …, Yingrui Li, et al. Lanosterol reverses protein aggregation in cataracts. Nature 523, 607–611 (30 July 2015) doi:10.1038/nature14650

10. Xuan Zhang, Dongya Zhang, …, Yingrui Li*, ,et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nature Medicine 21, 895–905 (2015) doi:10.1038/nm.3914

11. Francioli LC, Polak PP,…, Yingrui Li, et al. Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics, 2015 May 18, doi: 10.1038/ng.3292. (IF: 29.352) 12. Hongzhi Cao, Honglong Wu, …, Yingrui Li*, ,et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology 33, 617–622 (2015) doi:10.1038/nbt.3200

13. Na Cai, Simon Chang, …, Yingrui Li, et al. Molecular Signatures of Major Depression. Current Biology, Volume 25, Issue 9, p1146–1156, 4 May 2015. DOI: 10.1016/j.cub.2015.03.008 

14. Thomas Bataillon, Jinjie Duan, …, Yingrui Li, et al. Inference of Purifying and Positive Selection in Three Subspecies of Chimpanzees (Pan troglodytes) from Exome Sequencing. Genome Biol Evol (2015) 7 (4): 1122-1132. doi: 10.1093/gbe/evv058

15. Ling Zhang, Yong Zhou, Yingrui Li, et al. Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma. The American Journal of Human Genetics , Volume 96 , Issue 4 , 597 - 611 DOI: 10.1016/j.ajhg.2015.02.017

16. Zesong Li, Yi Huang, Yingrui Li, et al. Excess of Rare Variants in Genes that are Key Epigenetic Regulators of Spermatogenesis in the Patients with Non-Obstructive Azoospermia. Scientific Reports 5, Article number: 8785 (2015) doi:10.1038/srep08785

17. Bernhard Misof, Shanlin Liu, …, Yingrui Li, et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 07 Nov 2014: Vol. 346, Issue 6210, pp. 763-767 DOI: 10.1126/science.1257570

18. Ruibang Luo, Jeanno Cheung, …, Yingrui Li, et al. MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC) BMC Bioinformatics 2015 16 (Suppl 7):S10 DOI: 10.1186/1471-2105-16-S7-S10

19. Lin Kang, Xiaoqiao Liu, Yingrui Li, et al. Genome-wide identification of RNA editing in hepatocellular carcinoma. Genomics. Volume 105, Issue 2, February 2015, Pages 76–82

20. John C. Chambers, James Abbott, …,Yingrui Li, et al. The South Asian Genome .PLoS One, 2014 Aug 12,9(8):e102645.

21. Ganeshkumar Ganapathy, Jason T Howard, …,Yingrui Li, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Giga science,2014 Jul 8,3:11.

22. Emilia Huerta-Sa´nchez, Xin Jin, …,Yingrui Li, et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature, 2014 Jul 2,doi: 10.1038/nature13408.

23. Patrick Deelen, Androniki Menelaou, Yingrui Li, et al. Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’. European Journal of Human Genetics (2014) 22, 1321–1326; doi:10.1038/ejhg.2014.19

24. Jun Yu, William K K Wu, …, Yingrui Li, et al. Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer. Gut doi:10.1136/gutjnl-2013-306620

25. Keith R Bradnam, Joseph N Fass, …,Yingrui Li, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2013 Jul 22,2(1):10.

26. Yujun Sheng, Xin Jin, …,Yingrui Li, et al. Sequencing-based approach identified three new susceptibility loci for psoriasis. Nat Commun, 2014 Jul 9,5:4331.

27. Linhai Wang, Sheng Yu, …,Yingrui Li, et al. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol, 2014 Feb 27,15(2):R39.

28. Laurent C Francioli, Androniki Menelaou, …,Yingrui Li, et al. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet, 2014 Jun 29,doi: 10.1038/ng.3021.

29. Jeffrey M Kidd, Thomas J Sharpton, …,Yingrui Li, et al. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genetics. 2014,15(1):262.

30. Cheng Qin, Changshui Yu, …,Yingrui Li, et al. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Science, 2014, 111(14):5135-40.

31. Zhenxing Yang, Yu Xu, …,Yingrui Li, et al. Whole-exome sequencing for the identification of susceptibility genes of kashin-beck disease. PLoS One, 2014, 9(4):e92298.

32. Chang Yu, Jun Yu, …, Yingrui Li*, et al. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Research, 2014, doi: 10.1038/cr.2014.43.

33. Yanan Cao, Minghui He, …,Yingrui Li, et al. Activating Hotspot L205R Mutation in PRKACA and Adrenal Cushing's Syndrome. Science, 2014

34. Limei Ouyang, Jeeyun Lee, …,Yingrui Li, et al. Whole-genome sequencing of matched primary and metastatic hepatocellular carcinomas. BMC Med Genomics, 2014, 7:2.

35. Yongmei Song, Lin Li,…,Yingrui Li, et al. Identification of genomic alterations in oesophageal squamous cell cancer. Nature, 2014, doi:10.1038/nature13176.

36. Yinlong Xie, Gengxiong Wu,…,Yingrui Li, et al. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, 2014. 

37. Qingle Cai, Xiaoju Qian,…,Yingrui Li, et al. Correction: The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude. Genome Biol., 2014, 15(2):R33.

38. Kirk E. Lohmueller, Thomas Sparsø, Yingrui Li, et al. Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes. Am J Hum Genet., 2013, 93(6) :1072-1086.

39. Shengting Li, Soren Besenbacher, Yingrui Li, et al. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. Eur J Hum Genet., 2014, doi: 10.1038/ejhg.2013.282.

40. Dorret I Boomsma, Cisca Wijmenga,…,Yingrui Li, et al. The Genome of the Netherlands: design, and project goals. Eur J Hum Genet., 2014, 22(2):221-7. 

41. Yanfeng Yan, Hu Wang,…,Yingrui Li, et al. Two-Step Source Tracing Strategy of Yersinia pestis and Its Historical Epidemiology in a Specific Region. PLOS One, 2014, 9(1):e85374. 

42. Xianhui Wang, Xiaodong Fang,…,Yingrui Li, et al. The locust genome provides insight into swarm formation and long-distance flight. Nat Communications, 2014, 5:2957.

43. Adam Auton, Yingrui Li, Jeffrey Kidd, et al. Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs. PLoS Genet., 2013, 9(12):e1003984. 

44. Meredith L. Carpenter, Jason D. Buenrostro,…,Yingrui Li, et al. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. The American Journal of Human Genetics, 2013, 93:852–864.

45. Yanan Cao, Zhibo Gao,…,Yingrui Li, et al. Whole exome sequencing of insulinoma reveals recurrent T372R mutations in YY1. Nature Communications, 2013, 4:2810.

46. Ekta Khurana, Yao Fu,…,Yingrui Li, et al. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science, 2013, 342(6154):1235587.

47. Huayang Tang, Xin Jin, …, Yingrui Li, et al. A large-scale screen for coding variants predisposing to psoriasis. Nat Genet, 2013, doi: 10.1038/ng.2827.

48. Anu Tammiste, Tao Jiang, …, Yingrui Li, et al. Whole-exome sequencing identifies a polymorphism in the BMP5 gene associated with SSRI treatment response in major depression. J Psychopharmacol., 2013, 27(10):915-20.

49. Fan Zhang, Ruoyan Chen, …, Yingrui Li*, et al. YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data. BMC Bioinformatics, 2013, 14(1):331. 

50. Guangwu Guo, Xiaojuan Sun, …, Yingrui Li, et al.Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nature Genetics, 2013, doi: 10.1038/ng.2798.

51. Niels Grarup, Patrick Sulem, …, Yingrui Li, et al. Genetic Architecture of Vitamin B-12 and Folate Levels Uncovered Applying Deeply Sequenced Large Datasets. PLoS Genetics, 2013, 9(6):e1003530.

52. Zhengyan Kan, Hancheng Zheng, …, Yingrui Li*,et al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Research, 2013,23(9):1422-33.

53. Yali Zhao, Feifan Zhao, …, Yingrui Li, et al. Exome Sequencing and Linkage Analysis Identified Tenascin-C (TNC) as a Novel Causative Gene in Nonsyndromic Hearing Loss. PLOS One, 2013, 8(7):e69549.

54. Hongzhi Cao, Yu Wang, …, Yingrui Li, et al. A Short-Read Multiplex Sequencing Method for Reliable, Cost-Effective and High-Throughput Genotyping in Large-Scale Studies. Human Mutation, 2013, doi: 10.1002/humu.22439.

55. Yong-hui Jiang,Ryan K.C. Yuen, …, Yingrui Li*,et al.Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing. The American Journal of Human Genetics, 2013,93:249-263.

56. Xiaosen Guo, Max Brenner, …, Yingrui Li, et al. Whole-genome sequences of da and f344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer. Genetics, 2013, 194(4):1017-28.

57. Hongzhi Cao, Jinghua Wu, …, Yingrui Li*. An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing. PLOS One, 2013, 8(7):e69388.

58. Weiyang Li, Xi Zeng, …, Yingrui Li, et al. HIVID: An efficient method to detect HBV integration using low coverage sequencing. Genomics, 2013, pii: S0888-7543(13)00130-4. doi: 10.1016/j.ygeno.2013.07.002.

59. Shengpei Chen, Huijuan Ge, …, Yingrui Li*, et al. Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing. Genome Med, 2013, 5(2):18. 60. Yinhua Huang, Yingrui Li#, David W Burt, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nature Genetics, 2013, doi: 10.1038/ng.2657.

61. Ruibang Luo, Thomas Wong, …, Yingrui Li*, et al. SOAP3-dp: Fast, Accurate and Sensitive GPUBased Short Read Aligner. PLoS One, 2013, 8(5):e65632. 

62. Wenlong Jia, Kunlong Qiu, …, Yingrui Li, et al. et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biology, 2013, 14(2):R12. 

63. Chen S, Lau TK, …, Yingrui Li, et al.A method for non-invasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenatal Diagnosis, 2013,33(6):584-90.

64. Jizeng Jia, Shancen Zhao, …, Yingrui Li#, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 2013, doi:10.1038/nature12028 

65. Chunlei Zhang, Chunsheng Zhang, …, Yingrui Li, et al. A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing. Plos one, 2013, 8(1): e54236.

66. Yujun Cui, Chang Yu, …, Yingrui Li, et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. PNAS. 2013, 110:577-82.

67. Fuman Jiang, Jinghui Ren, Fang Chen,… Yingrui Li,…, et al.Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies. BMC Medical Genomics. 2012,5:57.

68. Jacob J. Michaelson, Yujian Shi, Madhusudan Gujral, …Yingrui Li,…, et al. Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation. Cell, 2012, 151(7): 1431-42.

69. Haojing Shao, Evangelos Bellos, Hanjiudai Yin, …Yingrui Li,…, et al. A population model for genotyping indels from next-generation sequence data. Nucleic Acids Res. 2012, doi: 10.1093/nar/gks1143.

70. Xiaodong Fang, Yulian Mou, Zhiyong Huang, …Yingrui Li,…, et al. The sequence and analysis of a Chinese pig genome. GigaScience, 2012, 1:16.

71. Martien A. M. Groenen, Alan L. Archibald, Hirohide Uenishi, …Yingrui Li,…, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 2012, 491(7424): 393–8.

72. Shan Dan, Wei Wang, Jinghui Ren, …Yingrui Li,…,et al. Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11 105 pregnancies with mixed risk factors. Prenatal Diagnosis, 2012, 32: 1-8.

73. Yingrui Li,as one authors of the The 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422):56–65.

74. Xin Zhang, Birong Guo, Liqiong Cai, …Yingrui Li,…,et al. Exome sequencing identified a missense mutation of EPS8L3 in Marie Unna hereditary hypotrichosis. J Med Genet, 2012, 49(12):727-30.

75. Binghang Liu, Jianying Yuan, Siu-Ming Yiu, …Yingrui Li,…,et al. COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly. Bioinformatics, 2012, doi: 10.1093/bioinformatics/bts563.

76. Junjie Qin, Yingrui Li#, Zhiming Cai, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 2012, 490(7418):55-60. 

77. Guofan Zhang,Xiaodong Fang, Ximing Guo, …Yingrui Li,…,et al.The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 2012,490(7418):49-54.

78. Lachlan J.M. Coin, Dandan Cao, Jingjing Ren, …Yingrui Li,…,et al.An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinformatics. 2012.28(18):i370-4.

79. Shengting Li, Ruiqiang Li, Heng Li, …Yingrui Li,…, et al. SOAPindel: Efficient identification of indels from short paired reads. Genome Res, 2012, doi: 10.1101/gr.132480.111.

80. Yingrui Li#, Xun Xu, Luting Song,…, et al. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Giga Science, 2012, doi:10.1186/2047-217X-1-12.

81. Rasmus Nielsen, Thorfinn Korneliussen, Anders Albrechtsen…Yingrui Li,…, et al. SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data. PLoS ONE, 2012, 7(7): e37558.

82. Chang Fu Tian, Yuan Jie Zhou, Yan Ming Zhang, …Yingrui Li*, et al.Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. PNAS, 2012, vol.109 no.22:8629-8634.

83. Wing-Kin Sung, Hancheng Zheng, Shuyu Li, …Yingrui Li,…,et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature Genetics, 2012, doi:10.1038/ng.2295.

84. Mingzhou Li, Honglong Wu, Zonggang Luo, …Yingrui Li,…,et al. An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun, 2012, doi:10.1038/ncomms1854.

85. Gengyun Zhang, Xin Liu, Zhiwu Quan,…Yingrui Li,…,et al .Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 2012, doi:10.1038/nbt.2195.

86. Xun Xu, Yong Hou, Xuyang Yin, …Yingrui Li*,…, et al. Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor. Cell, 2012, 148(5): 886-895.

87. Yong Hou, Luting Song, Ping Zhu,…Yingrui Li*,…,et al. Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm. Cell, 2012, 148(5): 873-885.

88. Daniel G. MacArthur,Suganthi Balasubramanian, Adam Frankish, …Yingrui Li,…,et al .A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes. Scicence, 2012,Feb 17,Vol. 335 no. 6070 pp. 823-828

89. Xu Yang, Rui Jiao, Lin Yang, …Yingrui Li,…, et al. New-generation high-throughput technologies based 'omics' research strategy in human disease(Article in Chinese). Yi chuan, 2011, 33(8):829-46.

90. Chi-Man Liu, Thomas Wong, Edward Wu, …Yingrui Li,…,et al. SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 2012, doi: 10.1093/bioinformatics/bts061.

91. Christina Hvilsom, Yu Qian, Thomas Bataillon,…Yingrui Li#,…et al. Extensive X-linked adaptive evolution in central chimpanzees. PNAS, 2012, doi: 10.1073/pnas.1106877109.

92. Neil D Young, Aaron R Jex, Bo Li,…, Yingrui Li,...,et al. Whole-genome sequence of Schistosoma haematobium. Nature Genetics, 2012, 44(2):221-5.

93. Xun Xu, Xin Liu, Song Ge, …, Yingrui Li, … et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 2011, 30(1):105-11.

94. Guangwu Guo, Yaoting Gui, Shengjie Gao,…Yingrui Li, …,et al. Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nature Genetics, 2011, 44(1):17-9. 

95. Kirk E. Lohmueller, Anders Albrechtsen, Yingrui Li, et al. Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome. PLoS Genet, 2011, 7(10):e1002326.

96. Dent Earl, Keith Bradnam, John St. John, …Yingrui Li,…, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res, 2011, 21(12):2224-41.

97. Aaron R. Jex, Shiping Liu, Bo Li, …Yingrui Li,…,et al. Ascaris suum draft genome. Nature, 2011, doi:10.1038/nature10553

98. Guangmei Yan, Guojie Zhang, Xiaodong Fang, …Yingrui Li,…,et al. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nature Biotechnology, 2011, doi:10.1038/nbt.1992. 

99. Yingrui Li,as one authors of the Brassica rapa Genome Sequencing Project Consortium. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics, 2011, doi:10.1038/ng.919

100. Yaoting Gui, Guangwu Guo, Yi Huang,…Yingrui Li,…, et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nature Genetics, 2011, 43(9):875-8.

101. Holger Rohde, Junjie Qin, Yujun Cui,…Yingrui Li,…,et al. Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4. The New England Journal of Medicine, 2011, 365(8):718-24.

102. Yingrui Li#, Hancheng Zheng, Ruibang Luo, et al. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology, 2011, 29(8):723-30.

103. Donald F. Conrad, Jonathan E. Keebler, Mark A. DePristo,…Yingrui Li,…, et al. Variation in genome-wide mutation rates within and between human families. Nature Genetics, 2011, 43(7):712-4. 

104. Su Yeon Kim, Kirk E Lohmueller, Anders Albrechtsen,…Yingrui Li,…, et al. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics,2011.

105. Shi Y, Yingrui Li#, Zhang D, et al. Exome Sequencing Identifies ZNF644 Mutations in High Myopia . PLoS Genet, 2011, 7(6): e1002084.

106. Yuan Liu, Min Gao, Yong-mei Lv,…Yingrui Li,…,et al. Confirmation by Exome Sequencing of the Pathogenic Role of NCSTN Mutations in Acne Inversa (Hidradenitis Suppurativa). Journal of Investigative Dermatology, 2011. 131(7):1570-2. 

107. Ryan E. Mills, Klaudia Walter, Chip Stewart,…Yingrui Li,…, et al. Mapping copy number variation by population-scale genome sequencing. Nature, 2011, 470:59-65.

108. Junling Wang, Xu Yang, Kun Xia, …Yingrui Li,…, et al. TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain, 2010, 133:3510-8.

109. Yingrui Li#, Jingde Zhu, Geng Tian,et al. The DNA Methylome of Human Peripheral Blood Mononuclear Cells. PLoS Biol, 2010, 8(11):e1000533.

110. Peter H. Sudmant, Jacob O. Kitzman, Francesca Antonacci,…Yingrui Li,…,et al. Diversity of Human Copy Number Variation and Multicopy Genes. Science, 2010, 330: 641-6. 

111. Yingrui Li,as one authors of the 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature, 2010, 467(7319):1061-73.

112. Yingrui Li#, Nicolas Vinckenbosch, Geng Tian,et al.Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet, 2010, 42(11): 969-72.

113. Xin Yi, Yu Liang, Emilia Huerta-Sanchez,…Yingrui Li,…, et al. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude. Science, 2010, 329(5987): 75-78.

114. Su Yeon Kim, Yingrui Li, Yiran Guo, et al. Design of Association Studies with Pooled and Unpooled Next-Generation Sequencing Data. Genet Epidemiol, 2010, 34(5):479-91. 

115. Hui Xiang, Jingde Zhu, Quan Chen,…Yingrui Li,…,et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol, 2010, 28(5):516-20.

116. Ning Li ,Mingzhi Ye , Yingrui Li#, et al.Whole genome DNA Methylation analysis based on high throughput sequencing technology. Methods. 2010, 52(3):203-12.

117. Yingrui Li#, Yujie Hu , Lars Bolund ,et al. State of the art de novo assembly of human genomes from massively parallel sequencing data. Human Genomics, 2010, 4(4): 271 -7.

118. Junjie Qin, Ruiqiang Li,Jeroen Raes,…Yingrui Li,…,et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010, 464(7285):59-65.

119. Morten Rasmussen,Yingrui Li#, Stinus Lindgreen, et al.Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 2010, 463(7282):757-62.

120. Ruiqiang Li, Hongmei Zhu,Jue Ruan,…Yingrui Li,…,et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res, 2010, 20(2): 265-72.

121. Aihua Sun, Ying Jiang, Xue Wang,…Yingrui Li,…,et al.The sequence and de novo assembly of the giant panda genome. Nature, 2010, 463(7279):311-7.

122. Ruiqiang Li, Yingrui Li#, Hancheng Zheng,et al.Building the sequence map of the human pangenome. Nat Biotechnol, 2009,28(1):57-63.

123. Sanwen Huang, Ruiqiang Li, Zhonghua Zhang,…Yingrui Li,…,et al.The genome of the cucumber, Cucumis sativus L. Nature Genetics, 2009, 41(12): 1275-81.

124. Qingyou Xia, Yiran Guo,Ze Zhang,…Yingrui Li,…,et al.Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx). Science, 2009, 326(5951):433-6.

125. Yingrui Li# , Jun Wang.Faster human genome sequencing. Nature biotechnology, 2009, 27(9): 820-1.

126. Ruiqiang Li, Chang Yu, Yingrui Li, et al.SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 2009, 25(15): 1966-7.

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