Tools and Publications

SELECTED Tools

2023

High-resolution dissection of human cell type-specific enhancers in cis and trans activities, Meng Wang#, Xiaoxu Yang, Qixi Wu#, 2023, bioRxiv, 2023.09. 23.559140. (doi: https://doi.org/10.1101/2023.09.23.559140)

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases, McKinzie A Garrison, Yeongjun Jang, Taejeong Bae, Adriana Cherskov, Sarah B Emery, Liana Fasching, Attila Jones, John B Moldovan, Cindy Molitor, Sirisha Pochareddy, Mette A Peters, Joo Heon Shin, Yifan Wang, Xiaoxu Yang, Schahram Akbarian, Andrew Chess, Fred H Gage, Joseph G Gleeson, Jeffrey M Kidd, Michael McConnell, Ryan E Mills, John V Moran, Peter J Park, Nenad Sestan, Alexander E Urban, Flora M Vaccarino, Christopher A Walsh, Daniel R Weinberger, Sarah J Wheelan, Alexej Abyzov, & BSMN Consortium, 2023, Scientific Data, 2023.10.24.563814. (PMID 37985666, Codes on GitHub)

MECP2 germline mosaicism plays an important part in the inheritance of Rett syndrome: a study of MECP2 germline mosaicism in males, Yongxin Wen*, Jiaping Wang*, Qingping Zhang, Xiaoxu Yang, Liping Wei, Xinhua Bao, 2023, BMC Medicine, 21(155), 1-10. (PMID 37081442)

2022

Detecting genomic mosaicism in "de novo" genetic epilepsy by amplicon-based deep sequencing, Jiaoyang Chen*, Yi Chen*, Ying Yang, Xueyang Niu, Jing Zhang, Qi Zeng, Aijie Liu, Xiaojiang Xu, Xiaoxu Yang, Shupin Li, Xiaoling Yang, Yi Wang, Yuehua Zhang, 2022, Journal of Human Genetics, 68(2), 73-80. (PMID 36482122)

RJAfinder: an automated tool for quantification of responding to joint attention behaviors in autism spectrum disorder using eye tracking data, Jie Zhang*, Ziyi Li*, Yige Wu, Adam Yongxin Ye, Lei Chen, Xiaoxu Yang, Qixi Wu, Liping Wei, 2022, Frontiers in Neurosciences, 16(915464), 1-13. (PMID 36466175)

PCDH19-related epilepsy in mosaic males: The phenotypic implication of genotype and variant allele frequency, Yi Chen, Xiaoxu Yang, Jiaoyang Chen, Xiaoling Yang, Ying Yang, Aijie Liu, Xiaoli Zhang, Wenjuan Wu, Dan Sun, Zhixian Yang, Yuwu Jiang, Zhang Yuehua, 2022, Frontiers in Neurology, 13(1041509), 1-13. (PMID 36408521)

2021

Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation, Leonie von Elsner*, Guoliang Chai*, Pauline E Schneeberger*, Frederike L Harms, Christian Casar, Minyue Qi, Malik Alawi, Ghada MH Abdel-Salam, Maha S Zaki, Florian Arndt, Xiaoxu Yang, Valentina Stanley, Maja Hempel, Joseph G Gleeson, Kerstin Kutsche, 2021, Brain, 145(4),1551-1563. (PMID 34694367)

A human pleiotropic multiorgan condition caused by deficient Wnt secretion, Guoliang Chai, Emmanuelle Szenker-Ravi, Changuk Chung, Zhen Li, Lu Wang, Muznah Khatoo, Trevor Marshall, Nan Jiang, Xiaoxu Yang, Jennifer McEvoy-Venneri, Valentina Stanley, Paula Anzenberg, Nhi Lang, Vanessa Wazny, Jia Yu, David M Virshup, Rie Nygaard, Filippo Mancia, Rijad Merdzanic, Maria BP Toralles, Paula ML Pitanga, Ratna D Puri, Rebecca Hernan, Wendy K Chung, Aida M Bertoli-Avella, Nouriya Al-Sannaa, Maha S Zaki, Karl Willert, Bruno Reversade#, Joseph G Gleeson#, 2021, New England Journal of Medicine, 385(14), 1292-1301. (PMID 34587386)

Comprehensive identification of somatic nucleotide variants in human brain tissue, Yifan Wang*, Taejeong Bae*, Jeremy Thorpe*, Maxwell A Sherman*, Attila G Jones*, Sean Cho, Kenneth Daily, Yanmei Dou, Javier Ganz, Alon Galor, Irene Lobon, Reenal Pattni, Chaggai Rosenbluh, Simone Tomasi, Livia Tomasini, Xiaoxu Yang, Bo Zhou, Schahram Akbarian, Laurel L Ball, Sara Bizzotto, Sarah B Emery, Ryan Doan, Liana Fasching, Yeongjun Jang, David Juan, Esther Lizano, Lovelace J Luquette, John B Moldovan, Rujuta Narurkar, Matthew T Oetjens, Rachel E Rodin, Shobana Sekar, Joo Heon Shin, Eduardo Soriano, Richard E Straub, Weichen Zhou, Andrew Chess, Joseph G Gleeson, Tomas Marquès-Bonet, Peter J Park, Mette A Peters, Jonathan Pevsner, Christopher A Walsh, Daniel R Weinberger, Flora M Vaccarino, John V Moran, Alexander E Urban, Jeffrey M Kidd, Ryan E Mills, Alexej Abyzov, 2021, Genome Biology, 22(92), 1-23. (PMID 33781308, Codes on GitHub)

2020

Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly, Guoliang Chai*, Alice Webb*, Chen Li, Danny Antaki, Sangmoon Lee, Martin W Breuss, Nhi Lang, Valentina Stanley, Paula Anzenberg, Xiaoxu Yang, Trevor Marshall, Patrick Gaffney, Klaas J Wierenga, Brian Hon-Yin Chung, Mandy Ho-Yin Tsang, Lynn S Pais, Alysia Kern Lovgren, Grace E VanNoy, Heidi L Rehm, Ghayda Mirzaa, Eyby Leon, Julianne Diaz, Alexander Neumann, Arnout P Kalverda, Iain W Manfield, David A Parry, Clare V Logan, Colin A Johnson, David T Bonthron, Elizabeth MA Valleley, Mahmoud Y Issa, Sherif F Abdel-Ghafar, Mohamed S Abdel-Hamid, Patricia Jennings, Maha S Zaki, Eamonn Sheridan#, Joseph G Gleeson#, 2020, Neuron, 109(2), 241-256 e9. (PMID 33220177, Data on SRA)

A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome, Shereen G Ghosh*, Marcello Scala*, Christian Beetz, Guy Helman, Valentina Stanley, Xiaoxu Yang, Martin W Breuss, Neda Mazaheri, Laila Selim, Fatemeh Hadipour, Lynn Pais, Chloe A Stutterd, Vasiliki Karageorgou, Amber Begtrup, Amy Crunk, Jane Juusola, Rebecca Willaert, Leigh A Flore, Kelly Kennelly, Christopher Spencer, Martha Brown, Pamela Trapane, Anna CE Hurst, S Lane Rutledge, Dana H Goodloe, Marie T McDonald, Vandana Shashi, Kelly Schoch, Hoda Tomoum, Raghda Zaitoun, Zahra Hadipour, Hamid Galehdari, Alistair T Pagnamenta, Majid Mojarrad, Alireza Sedaghat, Patrícia Dias, Sofia Quintas, Atiyeh Eslahi, Gholamreza Shariati, Peter Bauer, Cas Simons, Henry Houlden, Mahmoud Y Issa, Maha S Zaki, Reza Maroofian#, Joseph G Gleeson#, 2020, European Journal of Human Genetics, 29(2), 271-279. (PMID 32901138)

Recurrent homozygous damaging mutation in TMX2, encoding a protein disulfide isomerase, in four families with microlissencephaly, Shereen Georges Ghosh, Lu Wang, Martin W Breuss, Joshua D Green, Valentina Stanley, Xiaoxu Yang, Danica Ross, Bryan J Traynor, Amal M Alhashem, Matloob Azam, Laila Selim, Laila Bastaki, Hanan I Elbastawisy, Samia Temtamy, Maha Zaki, Joseph G Gleeson, 2020, Journal of Medical Genetics, 57(4), 274-282. (PMID 31586943)

mTOR pathway somatic variants and the molecular pathogenesis of hemimegalencephaly, Camila AB Garcia, Simone CS Carvalho, Xiaoxu Yang, Laurel L Ball, Renee D George, Kiely N James, Valentina Stanley, Martin W Breuss, Ursula Thomé, Marcelo V Santos, Fabiano P Saggioro, Luciano Neder Serafini, Wilson A Silva, Joseph G Gleeson, Hélio R Machado, 2020, Epilepsia Open, 2020(5), 97-106. (PMID 32140648)

Autism risk in offspring can be assessed through quantification of male sperm mosaicism, Martin W Breuss, Danny Antaki, Renee D George, Morgan Kleiber, Kiely N James, Laurel L Ball, Oanh Hong, Ileena Mitra, Xiaoxu Yang, Sara A Wirth, Jing Gu, Camila AB Garcia, Madhusudan Gujral, William M Brandler, Damir Musaev, An Nguyen, Jennifer McEvoy-Venneri, Renatta Knox, Evan Sticca, Martha Cristina Cancino Botello, Javiera Uribe Fenner, Maria Cárcel Pérez, Maria Arranz, Andrea B Moffitt, Zihua Wang, Amaia Hervás, Orrin Devinsky, Melissa Gymrek, Jonathan Sebat#, Joseph G Gleeson#, 2020, Nature Medicine, 26(1), 143-150. (PMID 31873310, Codes on GitHub)

2019

Somatic double-hit in MTOR and RPS6 in hemimegalencephaly with intractable epilepsy, Cristiana Pelorosso*, Françoise Watrin*, Valerio Conti*, Emmanuelle Buhler, Antoinette Gelot, Xiaoxu Yang, Davide Mei, Jennifer McEvoy-Venneri, Jean-Bernard Manent, Valentina Cetica, Laurel L Ball, Anna Maria Buccoliero, Antonin Vinck, Carmen Barba, Joseph G Gleeson, Renzo Guerrini, Alfonso Represa, 2019, Human Molecular Genetics, 28(22), 3755-3765. (PMID 31411685)

An expanded landscape of human long noncoding RNA, Shuai Jiang*, Si-Jin Cheng*, Li-Chen Ren, Qian Wang, Yu-Jian Kang, Yang Ding, Mei Hou, Xiao-Xu Yang, Yuan Lin, Nan Liang, Ge Gao, 2019, Nucleic Acids Research, 47(15), 7842-7856. (PMID 31350901)

Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals, Boxun Zhao, Qixi Wu, Adam Yongxin Ye, Jing Guo, Xianing Zheng, Xiaoxu Yang, Linlin Yan, Qing-Rong Liu, Thomas M Hyde, Liping Wei#, August Yue Huang#, 2019, PLoS Genetics, 15(4), e1008043. (PMID 30973874)

2018

AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder, Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei, 2018, Database, 2018(bay106), 1-8. (PMID 30339214)

A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations, Adam Yongxin Ye*, Yanmei Dou*, Xiaoxu Yang, Sheng Wang, August Yue Huang#, Liping Wei#, 2018, Genome Research, 28(7), 943-951. (PMID 29875290)

2017

Study on mosaicism of SCN1A gene mutation in parents of children with Dravet syndrome, AiJie Liu, Xiaoxu Yang, Xiaojing Xu, Qiqi Wu, Xiaojuan Tian, Xiaoling Yang, Xiru Wu, Liping Wei, Yuehua Zhang, 2017, Chinese Journal of Pediatrics, 55(11), 818-823. (PMID 29141311)

Postzygotic single‐nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations, Yanmei Dou, Xiaoxu Yang, Ziyi Li, Sheng Wang, Zheng Zhang, Adam Yongxin Ye, Linlin Yan, Changhong Yang, Qixi Wu, Jiarui Li, Boxun Zhao, August Yue Huang#, Liping Wei#, 2017, Human Mutation, 38(8), 1002-1013. (Cover Article, PMID 28503910)

MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples,  August Yue Huang*, Zheng Zhang*, Adam Yongxin Ye*, Yanmei Dou*, Linlin Yan, Xiaoxu Yang, Yuehua Zhang, Liping Wei, 2017, Nucleic Acids Research, 45(10), e76. (PMID 28132024)

Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq, Kaile Wang, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I Wu#, Jue Ruan#, 2017, Nature Communications, 8(1), 1-11. (PMID 28530222)

2014

“Bioinformatics: Introduction and Methods,” a bilingual Massive Open Online Course (MOOC) as a new example for global bioinformatics education, Yang Ding, Meng Wang, Yao He, Adam Yongxin Ye, Xiaoxu Yang, Fenglin Liu, Yuqi Meng, Ge Gao#, Liping Wei#, 2014, PLoS Computational Biology, 10(12), e1003955. (PMID 25503717, Course on Coursera)

Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals, August Y Huang*, Xiaojing Xu*, Adam Y Ye*, Qixi Wu*, Linlin Yan, Boxun Zhao, Xiaoxu Yang, Yao He, Sheng Wang, Zheng Zhang, Bowen Gu, Han-Qing Zhao, Meng Wang, Hua Gao, Ge Gao, Zhichao Zhang, Xiaoling Yang, Xiru Wu, Yuehua Zhang#, Liping Wei#, 2014, Cell Research, 24(11), 1311. (Cover Article, PMID 25312340)