王小滔

发布者：林佳丽发布时间：2023-02-22浏览次数：820

基本信息

姓名：

王小滔

职称：

青年研究员

专业：

生物信息学

研究方向：

三维基因组、基因组变异、基因转录调控

邮箱地址：

wangxiaotao@fudan.edu.cn

个人简介

王小滔，复旦大学生殖与发育研究院青年研究员，国家级海外高层次人才，国家自然科学基金优秀青年科学基金项目（海外）获得者。2017年12月毕业于华中农业大学，获得生物信息学博士学位。曾先后赴美国宾夕法尼亚州州立大学医学院和美国西北大学医学院从事博士后研究工作，期间参与美国国立卫生研究院（NIH）的ENCODE计划和4D核组计划。长期从事生物信息学算法和软件的开发工作，擅长通过结合多组学数据整合分析和深度学习等手段探索疾病发生机制，从而揭示发育和疾病发生过程三维基因组的动态变化规律及其与基因表达调控之间的关系。近年来在Nature Methods、Nature Communications、Science Advances以及Nucleic Acids Research等期刊发表多篇论文。代表性生物信息学软件包括NeoLoopFinder、EagleC、Peakachu、HiCLift、TADLib以及runHiC等，累计下载次数超过30万次（详见GitHub主页：https://github.com/XiaoTaoWang）。


主要科研项目

1.遗传代谢病产前筛查与诊断新技术与临床应用研究，国家重点研发计划，2022YFC2703400，课题骨干。



代表性论文（#第一作者，*通讯作者）

  1. Wang, Xiaotao#*; Yue, Feng*; HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies, Bioinformatics, 2023, 39(6): btad389

  2. Wang, Xiaotao#; Luan, Yu; Yue, Feng*; EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps, Science Advances, 2022, 8(24): eabn9215

  3. Wang, Xiaotao#; Xu, Jie; Zhang, Baozhen; Hou, Ye; Song, Fan; Lyu, Huijue; Yue, Feng*; Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes, Nature Methods, 2021, 18(6): 661-668

  4. Zhang, Haowen#; Song, Li#; Wang, Xiaotao; Cheng, Haoyu; Wang, Chenfei; Meyer, Clifford A.; Liu, Tao; Tang, Ming; Aluru, Srinivas; Yue, Feng; Liu, X. Shirley*; Li, Heng*; Fast alignment and preprocessing of chromatin profiles with Chromap, Nature Communications, 2021, 12(1): 6566

  5. Salameh, Tarik J.#; Wang, Xiaotao#*; Song, Fan; Zhang, Bo; Wright, Sage M.; Khunsriraksakul, Chachrit; Ruan, Yijun; Yue, Feng*; A supervised learning framework for chromatin loop detection in genome-wide contact maps, Nature Communications, 2020, 11(1): 3428

  6. Wang, Xiaotao#; Cui, Wang; Peng, Cheng*; HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions, Nucleic Acids Research, 2017, 45(19): e163

  7. Wang, Xiaotao#; Dong, Pengfei; Zhang, Hongyu; Peng, Cheng*; Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes, Nucleic Acids Research, 2015, 43(15): 7237-7246


其他论文（#第一作者，*通讯作者）

  1. Liu, Tingting#; Wang, Juan#; Yang, Hongbo; Wang, Xiaotao; Fu, Yihao; Luan, Yu; Wang, Qixuan; Youngblood, Mark; Lu, Xinyan; Casadei, Lucia; Pollock, Raphael; Yue, Feng*; Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma, Cancer Research, 2023, 83(9): 1517-1530

  2. Xu, Jie#; Song, Fan#; Lyu, Huijue; Kobayashi, Mikoto; Zhang, Baozhen; Zhao, Ziyu; Hou, Ye; Wang, Xiaotao; Luan, Yu; Jia, Bei; Stasiak, Lena; Wong, Josiah Hiu-Yuen; Wang, Qixuan; Jin, Qi; Jin, Qiushi; Fu, Yihao; Yang, Hongbo; Hardison, Ross C; Dovat, Sinisa; Platanias, Leonidas C; Diao, Yarui; Yang, Yue; Yamada, Tomoko; Viny, Aaron D; Levine, Ross L; Claxton, David; Broach, James R; Zheng, Hong; Yue, Feng*; Subtype-specific 3D genome alteration in acute myeloid leukaemia, Nature, 2022, 611(7935): 387-398

  3. Luo, Zaili#; Xia, Mingyang#; Shi, Wei#; Zhao, Chuntao#; Wang, Jiajia#; Xin, Dazhuan; Dong, Xinran; Xiong, Yu; Zhang, Feng; Berry, Kalen; Ogurek, Sean; Liu, Xuezhao; Rao, Rohit; Xing, Rui; Wu, Lai Man Natalie; Cui, Siying; Xu, Lingli; Lin, Yifeng; Ma, Wenkun; Tian, Shuaiwei; Xie, Qi; Zhang, Li; Xin, Mei; Wang, Xiaotao; Yue, Feng; Zheng, Haizi; Liu, Yaping; Stevenson, Charles B; Blank, Peter de; Perentesis, John P; Gilbertson, Richard J; Li, Hao*; Ma, Jie*; Zhou, Wenhao*; Taylor, Michael D; Lu, Q Richard*; Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis, Nature, 2022, 612(7941): 787-794

  4. Strom, Amy R#; Biggs, Ronald J#; Banigan, Edward J#; Wang, Xiaotao; Chiu, Katherine; Herman, Cameron; Collado, Jimena; Yue, Feng; Politz, Joan C Ritland; Tait, Leah J; Scalzo, David; Telling, Agnes; Groudine, Mark; Brangwynne, Clifford P; Marko, John F; Stephens, Andrew D*; HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics, Elife, 2021, 10: e63972

  5. Iyyanki, Tejaswi#; Zhang, Baozhen#; Wang, Qixuan#; Hou, Ye#; Jin, Qiushi; Xu, Jie; Yang, Hongbo; Liu, Tingting; Wang, Xiaotao; Song, Fan; Luan, Yu; Yamashita, Hironobu; Chien, Ruby; Lyu, Huijue; Zhang, Lijun; Wang, Lu; Warrick, Joshua; Raman, Jay D; Meeks, Joshua J; DeGraff, David J*; Yue, Feng*; Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer, Genome Biology, 2021, 22(1): 105

  6. Yang, Hongbo#; Luan, Yu#; Liu, Tingting#; Lee, Hyung Joo; Fang, Li; Wang, Yanli; Wang, Xiaotao; Zhang Bo; Jin, Qiushi; Ang, Khai Chung; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Sriranga, Iyyanki; Khunsriraksakul, Chachrit; Salameh, Tarik; Li, Daofeng; Choudhary, Mayank N K; Topczewski, Jacek; Wang, Kai; Gerhard, Glenn S; Hardison, Ross C; Wang, Ting; Cheng, Keith C; Yue, Feng*; A map of cis-regulatory elements and 3D genome structures in zebrafish, Nature, 2020, 588(7837): 337-343

  7. Xie, Ting#*; Zhang, Fugui; Zhang, Hongyu; Wang, Xiaotao; Hu, Jihong; Wu, Xiaoming; Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization, Nature Plants, 2019, 5(8):822-832

  8. Tao, Jingfen#; Zhou, Jinzhi; Xie, Ting; Wang, Xiaotao; Yang, Qingyong*; Zhang, Hongyu; Influence of Chromatin 3D Organization on Structural Variations of the Arabidopsis thaliana Genome; Molecular Plant, 2017, 10(2): 340-344

  9. Xie, Ting#; Yang, Qingyong#; Wang, Xiaotao; McLysaght, Aoife*; Zhang, Hongyu*; Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance, Molecular Biology and Evolution, 2016, 33(9): 2368-75

  10. Peng, Cheng#*; Fu, Liangyu#; Dong, Pengfei; Deng, Zhiluo; Li, Jianxin; Wang, Xiaotao; Zhang, Hongyu*; The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling, Nucleic Acids Research, 2013, 41(19): e183





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