王小滔，复旦大学生殖与发育研究院青年研究员，博士生导师，国家级海外高层次青年人才。2017年获华中农业大学生物信息学博士学位，随后在美国宾夕法尼亚州立大学医学院及美国西北大学医学院从事博士后研究，期间深度参与美国国立卫生研究院（NIH）ENCODE计划与4D Nucleome（4DN）计划。2022年底全职加入复旦大学，开展独立研究工作。 王小滔研究员长期聚焦三维基因组计算生物学。围绕三维基因组数据处理、染色质结构特征解析以及结构–功能关系解码等关键问题，发展原创性的生物信息学方法，并结合多组学数据与机器学习技术，系统研究发育与疾病过程中染色质空间结构的动态变化及其调控作用。相关研究成果发表于Nature、Nature Methods、Nature Communications、Science Advances、Nucleic Acids Research、Bioinformatics等期刊，其中以第一作者或通讯作者身份发表论文10篇，累计发表SCI论文20余篇，并参与编写学术专著1部。 近年来，课题组作为国际4D Nucleome（4DN）联盟核心成员，深度参与多种三维基因组技术的跨平台整合与比较分析，相关成果发表于Nature，为系统理解染色质空间折叠、核内定位与细胞功能之间的关系提供了重要资源与方法学支撑。 课题组高度重视方法学创新、数据资源建设与可复用软件开发，围绕“三维基因组数据处理—染色质结构特征解析—调控机制解码”这一主线，课题组已主导发布十余个三维基因组相关生物信息学软件，包括 NeoLoopFinder、EagleC/EagleC2、Peakachu、Raichu、HiCLift、TADLib、runHiC等，累计下载量超过45万次，被广泛应用于基础研究与疾病机制研究，持续服务于国际科研社区。 课题组科研氛围开放，强调在扎实的方法学基础上开展问题驱动的研究，鼓励成员在导师指导下发展相对独立的研究方向，并产出高水平原创成果。
主要科研项目 三维基因组与基因表达调控，国家自然科学基金优秀青年科学基金（海外），2022hwyq38，项目负责人（2025.01—2027.12） 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（2025.01—2028.12） 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（2022.12—2025.11）
代表性论文（#第一作者，*通讯作者；完整论文列表请参见Google Scholar） 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, Nature, 2025 (共同通讯作者) Wang, Xiaotao#*; Yue, Feng*; Hijacked enhancer–promoter and silencer–promoter loops in cancer, Current Opinion in Genetics & Development, 2024, 86:102199 (第一作者兼共同通讯作者) Wang, Xiaotao#*; Yue, Feng*; HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies, Bioinformatics, 2023, 39(6): btad389 (第一作者兼共同通讯作者) 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 (第一作者) 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 (第一作者) 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 (共同第一兼共同通讯作者) 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 (第一作者) 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 (第一作者)
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 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 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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