Xiaoxu Yang

Xiaoxu Yang, PhD

Languages spoken: Chinese, English

Academic Information

Departments Primary - Human Genetics

Lab

Education History

Postdoctoral Training University of California, San Diego, Rady Children’s Institute for Genomic Medicine
 Postdoctoral Researcher
Center for Bioinformatics, School of Life Sciences, Peking University
 PhD
Undergraduate College of Life Sciences, Beijing Normal University
 BS
Undergraduate College of Information Science and Technology, Beijing Normal University

Selected Publications

Journal Article

  1. Maury EA, Jones A, Seplyarskiy V, Nguyen TTL, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Brain Somatic Mosaicism Network, Park PJ, Akbarian S, Brennand K, Reilly S, Lee EA, Sunyaev SR, Walsh CA, Chess A (2024). Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science, 386(6718), 217-224. (Read full article)
  2. Vong KI, Alvarez YD, Noel G, Barton ST, Chung C, Howarth R, Meave N, Zhang Q, Jiwani F, Barrows C, Patel A, Wang JX, Chi N, Kingsmore SF, White MD, Yang X, Gleeson JG (2024). Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia. bioRxiv. (Read full article)
  3. Schlachetzki JC, Gianella S, Ouyang Z, Lana AJ, Yang X, OBrien S, Challacombe JF, Gaskill PJ, Jordan-Sciutto KL, Chaillon A, Moore D, Achim CL, Ellis RJ, Smith DM, Glass CK (2024). Gene expression and chromatin conformation of microglia in virally suppressed people with HIV. Life Sci Alliance, 7(10). (Read full article)
  4. Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Brain Somatic Mosaicism Network, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ (2024). Mapping recurrent mosaic copy number variation in human neurons. Nat Commun, 15(1), 4220. (Read full article)
  5. Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A, BSMN Consortium (2023). Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data, 10(1), 813. (Read full article)
  6. Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Gleeson JG (2023). Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain. bioRxiv. (Read full article)
  7. Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, Burris SJ, Rajarajan P, Flaherty E, Akbarian S, Chess A, McCarroll SA, Loh PR, Phillips-Cremins JE, Brennand KJ, Macosko EZ, Walters JTR, ODonovan M, Sullivan P, Psychiatric Genomic Consortium Schizophrenia and CNV workgroup, Brain Somatic Mosaicism Network, Sebat J, Lee EA, Walsh CA (2023). Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions. Cell Genom, 3(8), 100356. (Read full article)
  8. Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL, NIMH Brain Somatic Mosaicism Network, Gleeson JG (2023). Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol, 41(6), 870-877. (Read full article)
  9. Wen Y, Wang J, Zhang Q, Yang X, Wei L, Bao X (2023). MECP2 germline mosaicism plays an important part in the inheritance of Rett syndrome: a study of MECP2 germline mosaicism in males. BMC Med, 21(1), 155. (Read full article)
  10. Chen J, Chen Y, Yang Y, Niu X, Zhang J, Zeng Q, Liu A, Xu X, Yang X, Li S, Yang X, Wang Y, Zhang Y (2022). Detecting genomic mosaicism in "de novo" genetic epilepsy by amplicon-based deep sequencing. J Hum Genet, 68(2), 73-80. (Read full article)
  11. Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Focal Cortical Dysplasia Neurogenetics Consortium, Brain Somatic Mosaicism Network, Gleeson JG (2023). Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet, 55(2), 209-220. (Read full article)
  12. Zhang J, Li Z, Wu Y, Ye AY, Chen L, Yang X, Wu Q, Wei L (2022). RJAfinder: An automated tool for quantification of responding to joint attention behaviors in autism spectrum disorder using eye tracking data. Front Neurosci, 16, 915464. (Read full article)
  13. Chen Y, Yang X, Chen J, Yang X, Yang Y, Liu A, Zhang X, Wu W, Sun D, Yang Z, Jiang Y, Zhang Y (2022). PCDH19-related epilepsy in mosaic males: The phenotypic implication of genotype and variant allele frequency. Front Neurol, 13, 1041509. (Read full article)
  14. Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Brain Somatic Mosaicism Network, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A (2022). Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science, 377(6605), 511-517. (Read full article)
  15. Breuss MW, Yang X, Stanley V, McEvoy-Venneri J, Xu X, Morales AJ, Gleeson JG (2022). Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission. Elife, 11. (Read full article)
  16. von Elsner L, Chai G, Schneeberger PE, Harms FL, Casar C, Qi M, Alawi M, Abdel-Salam GMH, Zaki MS, Arndt F, Yang X, Stanley V, Hempel M, Gleeson JG, Kutsche K (2021). Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation. Brain, 145(4), 1551-1563. (Read full article)
  17. Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, OBrien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y, NIMH Brain Somatic Mosaicism Network, Glass CK, Gleeson JG (2022). Somatic mosaicism reveals clonal distributions of neocortical development. Nature, 604(7907), 689-696. (Read full article)
  18. Chai G, Szenker-Ravi E, Chung C, Li Z, Wang L, Khatoo M, Marshall T, Jiang N, Yang X, McEvoy-Venneri J, Stanley V, Anzenberg P, Lang N, Wazny V, Yu J, Virshup DM, Nygaard R, Mancia F, Merdzanic R, Toralles MBP, Pitanga PML, Puri RD, Hernan R, Chung WK, Bertoli-Avella AM, Al-Sannaa N, Zaki MS, Willert K, Reversade B, Gleeson JG (2021). A Human Pleiotropic Multiorgan Condition Caused by Deficient Wnt Secretion. N Engl J Med, 385(14), 1292-1301. (Read full article)
  19. Yang X, Breuss MW, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, Chai G, Nahas S, Van Der Kraan L, Ding Y, Sebat J, Gleeson JG (2021). Developmental and temporal characteristics of clonal sperm mosaicism. Cell, 184(18), 4772-4783.e15. (Read full article)
  20. Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marqus-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Brain Somatic Mosaicism Network, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A (2021). Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol, 22(1), 92. (Read full article)
  21. Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, NIMH Brain Somatic Mosaicism Network, Park PJ, Walsh CA (2020). Landmarks of human embryonic development inscribed in somatic mutations. Science, 371(6535), 1249-1253. (Read full article)
  22. Ghosh SG, Scala M, Beetz C, Helman G, Stanley V, Yang X, Breuss MW, Mazaheri N, Selim L, Hadipour F, Pais L, Stutterd CA, Karageorgou V, Begtrup A, Crunk A, Juusola J, Willaert R, Flore LA, Kennelly K, Spencer C, Brown M, Trapane P, Hurst ACE, Lane Rutledge S, Goodloe DH, McDonald MT, Shashi V, Schoch K, Undiagnosed Diseases Network, Tomoum H, Zaitoun R, Hadipour Z, Galehdari H, Pagnamenta AT, Mojarrad M, Sedaghat A, Dias P, Quintas S, Eslahi A, Shariati G, Bauer P, Simons C, Houlden H, Issa MY, Zaki MS, Maroofian R, Gleeson JG (2020). A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. Eur J Hum Genet, 29(2), 271-279. (Read full article)
  23. Chai G, Webb A, Li C, Antaki D, Lee S, Breuss MW, Lang N, Stanley V, Anzenberg P, Yang X, Marshall T, Gaffney P, Wierenga KJ, Chung BH, Tsang MH, Pais LS, Lovgren AK, VanNoy GE, Rehm HL, Mirzaa G, Leon E, Diaz J, Neumann A, Kalverda AP, Manfield IW, Parry DA, Logan CV, Johnson CA, Bonthron DT, Valleley EMA, Issa MY, Abdel-Ghafar SF, Abdel-Hamid MS, Jennings P, Zaki MS, Sheridan E, Gleeson JG (2020). Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Neuron, 109(2), 241-256.e9. (Read full article)
  24. Ghosh SG, Wang L, Breuss MW, Green JD, Stanley V, Yang X, Ross D, Traynor BJ, Alhashem AM, Azam M, Selim L, Bastaki L, Elbastawisy HI, Temtamy S, Zaki M, Gleeson JG (2019). Recurrent homozygous damaging mutation in TMX2, encoding a protein disulfide isomerase, in four families with microlissencephaly. J Med Genet, 57(4), 274-282. (Read full article)
  25. Yang X, Yang C, Zheng X, Xiong L, Tao Y, Wang M, Ye AY, Wu Q, Dou Y, Luo J, Wei L, Huang AY (2020). MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals. Genomics Proteomics Bioinformatics, 18(2), 140-149. (Read full article)
  26. Garcia CAB, Carvalho SCS, Yang X, Ball LL, George RD, James KN, Stanley V, Breuss MW, Thom U, Santos MV, Saggioro FP, Neder Serafini L, Silva WA Jr, Gleeson JG, Machado HR (2020). mTOR pathway somatic variants and the molecular pathogenesis of hemimegalencephaly. Epilepsia Open, 5(1), 97-106. (Read full article)
  27. Breuss MW, Antaki D, George RD, Kleiber M, James KN, Ball LL, Hong O, Mitra I, Yang X, Wirth SA, Gu J, Garcia CAB, Gujral M, Brandler WM, Musaev D, Nguyen A, McEvoy-Venneri J, Knox R, Sticca E, Botello MCC, Uribe Fenner J, Prez MC, Arranz M, Moffitt AB, Wang Z, Hervs A, Devinsky O, Gymrek M, Sebat J, Gleeson JG (2019). Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nat Med, 26(1), 143-150. (Read full article)
  28. Pelorosso C, Watrin F, Conti V, Buhler E, Gelot A, Yang X, Mei D, McEvoy-Venneri J, Manent JB, Cetica V, Ball LL, Buccoliero AM, Vinck A, Barba C, Gleeson JG, Guerrini R, Represa A (2019). Somatic double-hit in MTOR and RPS6 in hemimegalencephaly with intractable epilepsy. Hum Mol Genet, 28(22), 3755-3765. (Read full article)
  29. Jiang S, Cheng SJ, Ren LC, Wang Q, Kang YJ, Ding Y, Hou M, Yang XX, Lin Y, Liang N, Gao G (2019). An expanded landscape of human long noncoding RNA. Nucleic Acids Res, 47(15), 7842-7856. (Read full article)
  30. Yang X, Yang X, Chen J, Li S, Zeng Q, Huang AY, Ye AY, Yu Z, Wang S, Jiang Y, Wu X, Wu Q, Wei L, Zhang Y (2019). ATP1A3 mosaicism in families with alternating hemiplegia of childhood. Clin Genet, 96(1), 43-52. (Read full article)
  31. Zhang Q, Yang X, Wang J, Li J, Wu Q, Wen Y, Zhao Y, Zhang X, Yao H, Wu X, Yu S, Wei L, Bao X (2018). Genomic mosaicism in the pathogenesis and inheritance of a Rett syndrome cohort. Genet Med, 21(6), 1330-1338. (Read full article)
  32. Zhao B, Wu Q, Ye AY, Guo J, Zheng X, Yang X, Yan L, Liu QR, Hyde TM, Wei L, Huang AY (2019). Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals. PLoS Genet, 15(4), e1008043. (Read full article)
  33. Liu A, Yang X, Yang X, Wu Q, Zhang J, Sun D, Yang Z, Jiang Y, Wu X, Wei L, Zhang Y (2018). Mosaicism and incomplete penetrance of PCDH19 mutations. J Med Genet, 56(2), 81-88. (Read full article)
  34. Ye AY, Dou Y, Yang X, Wang S, Huang AY, Wei L (2018). A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations. Genome Res, 28(7), 943-951. (Read full article)
  35. Huang AY, Yang X, Wang S, Zheng X, Wu Q, Ye AY, Wei L (2018). Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs. PLoS Genet, 14(5), e1007395. (Read full article)
  36. Yang C, Li J, Wu Q, Yang X, Huang AY, Zhang J, Ye AY, Dou Y, Yan L, Zhou WZ, Kong L, Wang M, Ai C, Yang D, Wei L (2018). AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder. Database (Oxford), 2018. (Read full article)
  37. Yang X, Liu A, Xu X, Yang X, Zeng Q, Ye AY, Yu Z, Wang S, Huang AY, Wu X, Wu Q, Wei L, Zhang Y (2017). Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort. Sci Rep, 7(1), 15677. (Read full article)
  38. Liu AJ, Yang XX, Xu XJ, Wu QX, Tian XJ, Yang XL, Wu XR, Wei LP, Zhang YH (2017). [Study on mosaicism of SCN1A gene mutation in parents of children with Dravet syndrome]. Zhonghua Er Ke Za Zhi, 55(11), 818-823. (Read full article)
  39. Dou Y, Yang X, Li Z, Wang S, Zhang Z, Ye AY, Yan L, Yang C, Wu Q, Li J, Zhao B, Huang AY, Wei L (2017). Postzygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. Hum Mutat, 38(8), 1002-1013. (Read full article)
  40. Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L (2016). MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Res, 45(10), e76. (Read full article)
  41. Wang K, Lai S, Yang X, Zhu T, Lu X, Wu CI, Ruan J (2017). Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq. Nat Commun, 8, 15335. (Read full article)
  42. Xu X, Yang X, Wu Q, Liu A, Yang X, Ye AY, Huang AY, Li J, Wang M, Yu Z, Wang S, Zhang Z, Wu X, Wei L, Zhang Y (2015). Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome. Hum Mutat, 36(9), 861-72. (Read full article)
  43. Ding Y, Wang M, He Y, Ye AY, Yang X, Liu F, Meng Y, Gao G, Wei L (2014). "Bioinformatics: introduction and methods," a bilingual Massive Open Online Course (MOOC) as a new example for global bioinformatics education. PLoS Comput Biol, 10(12), e1003955. (Read full article)
  44. Huang AY, Xu X, Ye AY, Wu Q, Yan L, Zhao B, Yang X, He Y, Wang S, Zhang Z, Gu B, Zhao HQ, Wang M, Gao H, Gao G, Zhang Z, Yang X, Wu X, Zhang Y, Wei L (2014). Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. Cell Res, 24(11), 1311-27. (Read full article)

Review

  1. Graham JH, Schlachetzki JCM, Yang X, Breuss MW (2023). Genomic Mosaicism of the Brain: Origin, Impact, and Utility. [Review]. Neurosci Bull, 40(6), 759-776. (Read full article)
  2. Yang X (2024). [Sperm Mosaic Variants and Their Influence on the Offspring]. [Review]. Sichuan Da Xue Xue Bao Yi Xue Ban, 55(3), 535-541. (Read full article)
  3. Chung C, Yang X, Gleeson JG (2023). Post-zygotic brain mosaicism as a result of partial reversion of pre-zygotic aneuploidy. [Review]. Nat Genet, 55(11), 1784-1785. (Read full article)
  4. Breuss MW, Yang X, Gleeson JG (2021). Sperm mosaicism: implications for genomic diversity and disease. [Review]. Trends Genet, 37(10), 890-902. (Read full article)