王小滔，复旦大学生殖与发育研究院青年研究员，国家级海外高层次青年人才。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 基于人类染色质交互图谱的复杂疾病致病位点及其靶标基因的预测研究，国家自然科学基金委员会面上项目，32470698，项目负责人 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） 4D Nucleome Consortium, Job Dekker*, Betul Akgol Oksuz, Yang Zhang, Ye Wang, Miriam K. Minsk, Shuzhen Kuang, Liyan Yang, Johan H. Gibcus, Nils Krietenstein, Oliver J. Rando, Jie Xu, Derek H. Janssens, Steven Henikoff, Alexander Kukalev, Andréa Willemin, Warren Winick-Ng, Rieke Kempfer, Ana Pombo, Miao Yu, Pradeep Kumar, Liguo Zhang, Andrew S Belmont, Takayo Sasaki, Tom van Schaik, Laura Brueckner, Daan Peric-Hupkes, Bas van Steensel, Ping Wang, Haoxi Chai, Minji Kim, Yijun Ruan, Ran Zhang, Sofia A. Quinodoz, Prashant Bhat, Mitchell Guttman, Wenxin Zhao, Shu Chien, Yuan Liu, Sergey V. Venev, Dariusz Plewczynski, Ibai Irastorza Azcarate, Dominik Szabó, Christoph J. Thieme, Teresa Szczepińska, Mateusz Chiliński, Kaustav Sengupta, Mattia Conte, Andrea Esposito, Alex Abraham, Ruochi Zhang, Yuchuan Wang, Xingzhao Wen, Qiuyang Wu, Yang Yang, Jie Liu, Lorenzo Boninsegna, Asli Yildirim, Yuxiang Zhan, Andrea Maria Chiariello, Simona Bianco, Lindsay Lee, Ming Hu, Yun Li, R. Jordan Barnett, Ashley L. Cook, Daniel J. Emerson, Claire Marchal, Peiyao Zhao, Peter Park, Burak H. Alver, Andrew Schroeder, Rahi Navelkar, Clara Bakker, William Ronchetti, Shannon Ehmsen, Alexander Veit, Nils Gehlenborg, Ting Wang, Daofeng Li, Xiaotao Wang*, Mario Nicodemi*, Bing Ren*, Sheng Zhong*, Jennifer E. Phillips-Cremins*, David M. Gilbert*, Katherine S. Pollard*, Frank Alber*, Jian Ma*, William S. Noble*, Feng Yue*; An integrated view of the structure and function of the human 4D Nucleome, Biorxiv, 2024. Wang, Xiaotao#*; Yue, Feng*; Hijacked enhancer–promoter and silencer–promoter loops in cancer, Current Opinion in Genetics & Development, 2024, 86:102199 Wang, Xiaotao#*; Yue, Feng*; HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies, Bioinformatics, 2023, 39(6): btad389 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 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 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 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 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 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） Xie Ting#, Danieli-Mackay A, Buccarelli M, Barbieri M, Papadionysiou I, D'Alessandris QG, Robens C, Übelmesser N, Vinchure OS, Lauretti L, Fotia G, Schwarz RF, Wang X, Ricci-Vitiani L, Gopalakrishnan J, Pallini R, Papantonis A. Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs, Nature Communications, 2024, 15(1):3905 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 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 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 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 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 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 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 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 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 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
代表性著作 1. 《Computational Methods for 3D Genome Analysis》，Springer Nature，2024，负责编写章节《Supervised Chromatin Loop Detection Using Peakachu Version 2》 |
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