基本信息
万晓华  女  硕导  中国科学院计算技术研究所
电子邮件: wanxiaohua@ict.ac.cn
通信地址: 北京市海淀区科学院南路6号
邮政编码:

研究领域

生物信息学、高性能计算、图像处理

招生信息

   
招生专业
081201-计算机系统结构
081203-计算机应用技术
招生方向
生物信息学
高性能计算
图像处理

教育背景

2008-09--2012-06   中国科学院计算技术研究所   博士

工作经历

   
工作简历
2015-09~现在, 中国科学院计算技术研究所, 副研究员
2012-12~2014-09,美国加州大学圣地亚哥分校UCSD, 博士后访问学者
2012-07~2015-08,中国科学院计算技术研究所, 助理研究员
社会兼职
2020-11-01-今,CAAI生物信息学与人工生命专委会, 委员
2016-10-10-今,CCF生物信息专委会, 委员

专利与奖励

   
奖励信息
(1) 中科院青年创新促进会成员, 一等奖, 院级, 2015
(2) 中科院计算技术研究所优秀研究人员, 一等奖, 研究所(学校), 2014
(3) 中科院计算技术研究所“学术百星”, 一等奖, 研究所(学校), 2013
(4) 中科院院长奖学金, 一等奖, 院级, 2012
(5) 中科院计算技术研究所优秀论文, 二等奖, 研究所(学校), 2011
(6) 中科院计算技术研究所所长奖学金, 特等奖, 研究所(学校), 2011
专利成果
[1] 万晓华, 赵方圆, 张法, 刘新宇. 一种基于异步数据传输的GPU调度方法及系统. CN: CN112346866A, 2021-02-09.
[2] 张法, 郝语, 万晓华, 刘志勇, 李锦涛. 一种基于卷积神经网络的三维颗粒类别检测方法及系统. CN: CN112001218A, 2020-11-27.
[3] 万晓华, 吕智龙, 张法, 王醒策, 刘新宇. 一种基于磁共振血管造影图像的脑血管分割方法和系统. CN: CN111126403A, 2020-05-08.
[4] 万晓华, 张恩泽, 张法. 基于卷积神经网络的ET细胞图像自动分割方法及系统. CN: CN110580704A, 2019-12-17.
[5] 万晓华, 申泽南, 张法, 张金智, 甘志猛. 芸香科多物种密码子使用模式分析方法和系统. CN: CN110400604A, 2019-11-01.

出版信息

   
发表论文
[1] Penglei Song, Ce Chi, Kaixuan Ji, Zhiyong Liu, Fa Zhang, Shikui Zhang, Dehui Qiu, Xiaohua Wan. A deep reinforcement learning-based task scheduling algorithm for energy efficiency in data centers. 2021 International Conference on Computer Communications and Networks(ICCCN)null. 2021, [2] Zhang, Enze, Zhang, Boheng, Hu, Shaohan, Zhang, Fa, Liu, Zhiyong, Wan, Xiaohua. Multi-labelled proteins recognition for high-throughput microscopy images using deep convolutional neural networks. BMC BIOINFORMATICS[J]. 2021, 22(SUPPL 3): 1-15, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8207617/.
[3] Chi Zhang, Hongjia Li, Xiaohua Wan, Xuemei Chen, Zhenghe Yang, Jieqing Feng, Fa Zhang. TransPicker: a Transformer-based Framework for Particle Picking in cryoEM Micscrographs. IEEE International Conference on Bioinformatics & Biomedicine (BIBM2021)null. 2021, [4] Zihao Yang, Zhaobin Cao, Xiaohua Wan, Fa Zhang, Guangming Tan. Spatio-temporal features processing network for change detection in remote sensing images. IEEE International Geoscience and Remote Sensing Symposium (IGARSS2021)null. 2021, [5] Senlin Lin, Xuekun Song, Ziheng Xu, Xinyue Zhang, Yinqing Lin, Rui Zhang, Yulong Chen, Fa Zhang, Dehui Qiu, Yuling Zheng, Xiaohua Wan. Moment Invariants with Data Augmentation for Tongue Image Segmentation. IEEE International Conference on Bioinformatics & Biomedicine (BIBM2021)null. 2021, [6] Shikui Zhang, Ce Chi, Kaixuan Ji, Zhiyong Liu, Fa Zhang, Penglei Song, Huimei Yuan, Dehui Qiu, Xiaohua Wan. A new meta-heuristic task scheduling algorithm for optimizing energy efficiency in data centers. 2021 IEEE International Conference on Parallel & Distributed Processing with Applications, Big Data & Cloud Computing, Sustainable Computing & Communications, Social Computing & Networking (ISPA2021)null. 2021, [7] Zihao Wang, Xiaohua Wan, Zhiyong Liu, Qianshuo Fan, Fa Zhang, Guangming Tan. A multi-GPU design for large size cryo-EM 3D reconstruction. 35th IEEE International Parallel and Distributed Processing Symposium (IPDPS2021)null. 2021, [8] Lv, Zhilong, Mi, Fubo, Wu, Zhongke, Zhu, Yicheng, Liu, Xinyu, Tian, Mei, Zhang, Fa, Wang, Xingce, Wan, Xiaohua. A Parallel Cerebrovascular Segmentation Algorithm Based on Focused Multi-Gaussians Model and Heterogeneous Markov Random Field. IEEE TRANSACTIONS ON NANOBIOSCIENCE[J]. 2020, 19(3): 538-546, http://dx.doi.org/10.1109/TNB.2020.2996604.
[9] Shen, Zenan, Gan, Zhimeng, Zhang, Fa, Yi, Xinyao, Zhang, Jinzhi, Wan, Xiaohua. Analysis of codon usage patterns in citrus based on coding sequence data. BMC GENOMICS[J]. 2020, 21(Suppl 5): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739459/.
[10] Wang, Zihao, Zhang, Jingrong, Gao, Weifang, Liu, Zhiyong, Wan, Xiaohua, Zhang, Fa. A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2020, 27(2): 212-222, https://www.webofscience.com/wos/woscc/full-record/WOS:000500391900001.
[11] Gubins, Ilja, Chaillet, Marten L, van der Schot, Gijs, Veltkamp, Remco C, Forster, Friedrich, Hao, Yu, Wan, Xiaohua, Cui, Xuefeng, Zhang, Fa, Moebel, Emmanuel, Wang, Xiao, Kihara, Daisuke, Zeng, Xiangrui, Xu, Min, Nguyen, Nguyen P, White, Tommi, Bunyak, Filiz. SHREC 2020: Classification in cryo-electron tomograms. COMPUTERS & GRAPHICS-UK[J]. 2020, 91: 279-289, http://dx.doi.org/10.1016/j.cag.2020.07.010.
[12] Lv, Zhilong, Yan, Rui, Liu, Xinyu, Wu, Zhongke, Zhu, Yicheng, Sun, Shiwei, Zhang, Fa, Wane, Xingce, Wan, Xiaohua, Yoo, IH, Bi, JB, Hu, X. Cerebrovascular Segmentation Algorithm Based on Focused Multi-Gaussians Model and Weighted 3D Markov Random Field. 2019 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)null. 2019, 846-851, [13] 查礼. A GPU Inference System Scheduling Algorithm with Asynchronous Data Transfer. IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). 2019, [14] Wan Xiaohua. Classifying Mixed Patterns of Proteins in High-throughput Microscopy Images Using Deep Neural Networks. 2019 International Conference on Intelligent Computing. 2019, [15] Wang Zihao, Zhang Jingrong, Liu Xintong, Liu Zhiyong, Wan Xiaohua, Zhang Fa, Cai Z, Skums P, Li M. DM-SIRT: A Distributed Method for Multi-tilt Reconstruction in Electron Tomography. BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2019null. 2019, 11490: 220-231, [16] Han, Renmin, Wan, Xiaohua, Li, Lun, Lawrence, Albert, Yang, Peng, Li, Yu, Wang, Sheng, Sun, Fei, Liu, Zhiyong, Gao, Xin, Zhang, Fa. AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. BIOINFORMATICS[J]. 2019, 35(2): 319-328, https://www.webofscience.com/wos/woscc/full-record/WOS:000459314900017.
[17] Wang Zihao, Zhang Mingzhe, Zhang Jingrong, Yan Rui, Wan Xiaohua, Liu Zhiyong, Zhang Fa, Cui Xuefeng, Zheng H, Callejas Z, Griol D, Wang H, Hu X, Schmidt H, Baumbach J, Dickerson J, Zhang L. Mmalloc: A Dynamic Memory Management on Many-core Coprocessor for the Acceleration of Storage-intensive Bioinformatics Application. PROCEEDINGS 2018 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)null. 2018, 771-774, [18] Hao Yu, Han Renmin, Wan Xiaohua, Zhang Fa, Sun Shiwei, Zheng H, Callejas Z, Griol D, Wang H, Hu X, Schmidt H, Baumbach J, Dickerson J, Zhang L. Fiducial marker detection via deep learning approach for electron tomography. PROCEEDINGS 2018 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)null. 2018, 642-645, [19] Chen, Yu, Wang, Zihao, Li, Lun, Zhang, Jingrong, Wan, Xiaohua, Sun, Fei, Zhang, Fa. AutoGDeterm: Automatic Geometry Determination for Electron Tomography. TSINGHUA SCIENCE AND TECHNOLOGY[J]. 2018, 23(4): 369-376, http://lib.cqvip.com/Qikan/Article/Detail?id=675781147.
[20] Wang, Zihao, Chen, Yu, Zhang, Jingrong, Li, Lun, Wan, Xiaohua, Liu, Zhiyong, Sun, Fei, Zhang, Fa. ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2018, 25(3): 270-281, https://www.webofscience.com/wos/woscc/full-record/WOS:000417292900001.
[21] Yu Chen, Zihao Wang, Jingrong Zhang, Lun Li, Xiaohua Wan, Fei Sun, Fa Zhang. Accelerating electron tomography reconstruction algorithm ICON with GPU. Biophysics Reports[J]. 2017, 3(1-3): 36-42, http://dx.doi.org/10.1007/s41048-017-0041-z.
[22] Han, Renmin, Wan, Xiaohua, Wang, Zihao, Hao, Yu, Zhang, Jingrong, Chen, Yu, Gao, Xin, Liu, Zhiyong, Ren, Fei, Sun, Fei, Zhang, Fa. AuTom: A novel automatic platform for electron tomography reconstruction. JOURNAL OF STRUCTURAL BIOLOGY[J]. 2017, 199(3): 196-208, http://dx.doi.org/10.1016/j.jsb.2017.07.008.
[23] Wan Xiaohua. 3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography.. Advanced Structural and Chemical Imaging. 2017, [24] Wang Zihao, Chen Yu, Zhang Jingrong, Li Lun, Wan Xiaohua, Liu Zhiyong, Sun Fei, Zhang Fa, Cai Z, Daescu O, Li M. Accelerating Electron Tomography Reconstruction Algorithm ICON Using the Intel Xeon Phi Coprocessor on Tianhe-2 Supercomputer. BIOINFORMATICS RESEARCH AND APPLICATIONS (ISBRA 2017)null. 2017, 10330: 258-269, [25] Wan, Xiaohua, Katchalski, Tsvi, Churas, Christopher, Ghosh, Sreya, Phan, Sebastien, Lawrence, Albert, Hao, Yu, Zhou, Ziying, Chen, Ruijuan, Chen, Yu, Zhang, Fa, Ellisman, Mark H. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods. JOURNAL OF STRUCTURAL BIOLOGY[J]. 2017, 198(2): 103-115, http://dx.doi.org/10.1016/j.jsb.2017.04.002.
[26] Chen Yu, Wang Zihao, Li Lun, Wan Xiaohua, Sun Fei, Zhang Fa, Cai Z, Daescu O, Li M. A Fully Automatic Geometric Parameters Determining Method for Electron Tomography. BIOINFORMATICS RESEARCH AND APPLICATIONS (ISBRA 2017)null. 2017, 10330: 385-389, [27] Wan Xiaohua. ET: SPEC an accurate imaging model for electron tomography. Quantitative Bio Imaging. 2017, [28] Zhang, Fa, Chen, Yu, Ren, Fei, Wang, Xuan, Liu, Zhiyong, Wan, Xiaohua. A Two-Phase Improved Correlation Method for Automatic Particle Selection in Cryo-EM. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2017, 14(2): 316-325, https://www.webofscience.com/wos/woscc/full-record/WOS:000399013500010.
[29] Sun Xiujuan, Wan Xiaohua, Zhang Fa, Zhang Jinzhi, Tian T, Jiang Q, Liu Y, Burrage K, Song J, Wang Y, Hu X, Morishita S, Zhu Q, Wang G. aWGRS: Automates Paired-end Whole Genome Re-sequencing Data Analysis Framework. 2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)null. 2016, 910-916, [30] 张静蓉, 万晓华, 张法. 基于曲线投影模型的电子断层三维重构并行算法. 集成技术. 2015, 53-61, http://lib.cqvip.com/Qikan/Article/Detail?id=665101509.
[31] Zhou, Ziying, Li, Yugang, Zhang, Fa, Wan, Xiaohua. FASART: An iterative reconstruction algorithm with inter-iteration adaptive NAD filter. BIO-MEDICAL MATERIALS AND ENGINEERING[J]. 2015, 26: S1409-S1415, https://www.webofscience.com/wos/woscc/full-record/WOS:000361671800157.
[32] Zhang, Fa, Zhang, Jingrong, Lawrence, Albert, Ren, Fei, Wang, Xuan, Liu, Zhiyong, Wan, Xiaohua. BSIRT: A Block-Iterative SIRT Parallel Algorithm Using Curvilinear Projection Model. IEEE TRANSACTIONS ON NANOBIOSCIENCE[J]. 2015, 14(2): 229-236, https://www.webofscience.com/wos/woscc/full-record/WOS:000352740200010.
[33] Han, Renmin, Zhang, Fa, Wan, Xiaohua, Fernandez, JoseJesus, Sun, Fei, Liu, Zhiyong. A marker-free automatic alignment method based on scale-invariant features. JOURNAL OF STRUCTURAL BIOLOGY[J]. 2014, 186(1): 167-180, http://dx.doi.org/10.1016/j.jsb.2014.02.011.
[34] Chen Ruijuan, Wan Xiaohua, Altintas Ilkay, Wang Jianwu, Crawl Daniel, Phan Sébastien, Lawrence Albert, Ellisman Mark. EPiK-a Workflow for Electron Tomography in Kepler. Procedia Computer Science. 2014, 29: 2295-2305, http://dx.doi.org/10.1016/j.procs.2014.05.214.
[35] Wan, Xiaohua, Phan, Sebastien, Lawrence, Albert, Zhang, Fa, Han, Renmin, Liu, Zhiyong, Ellisman, Mark. ITERATIVE METHODS IN LARGE FIELD ELECTRON MICROSCOPE TOMOGRAPHY. SIAM JOURNAL ON SCIENTIFIC COMPUTING[J]. 2013, 35(5): S402-S419, http://dx.doi.org/10.1137/120881464.
[36] Wan, Xiaohua, Zhang, Fa, Chu, Qi, Liu, Zhiyong. High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs. BMC BIOINFORMATICS[J]. 2012, 13(Suppl 10): S4-S4, http://dx.doi.org/10.1186/1471-2105-13-S10-S4.
[37] 万晓华. 电子断层三维算法优化研究. 2012, [38] 张法, 孙飞, 储琪, 张凯, 万晓华, 张茨, 张艳, 张广勇, 沈铂, 卢晓伟, 赵开勇, 褚晓文. ATOM 1.0:基于GPU的电子断层重构软件. 生物物理学报[J]. 2011, 27(3): 231-241, http://lib.cqvip.com/Qikan/Article/Detail?id=37670166.
[39] Wan, Xiaohua, Zhang, Fa, Chu, Qi, Zhang, Kai, Sun, Fei, Yuan, Bo, Liu, Zhiyong. Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. JOURNAL OF STRUCTURAL BIOLOGY[J]. 2011, 175(3): 277-287, http://dx.doi.org/10.1016/j.jsb.2011.06.002.
[40] Chu, Qi, Zhang, Fa, Zhang, Kai, Wan, Xiaohua, Chen, Mingwei, Liu, Zhiyong, Park, T, Chen, L, Wong, L, Tsui, S, Ng, M, Hu, X. An accurate, automatic method for markerless alignment of electron tomographic images. 2010 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINEnull. 2010, 393-396, [41] 万晓华, 张法, 刘志勇. 一种冷冻电子断层三维重构的并行迭代算法. 微电子学与计算机[J]. 2009, 101-103,107, http://lib.cqvip.com/Qikan/Article/Detail?id=31167948.
[42] ZhiyongLiu1, ZihaoWang1,2,3, XiaohuaWan1, LunLi1,4, JingrongZhang1,2, YuChen1,2,3. ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer. Mary Ann Liebert, Inc. Publishers. http://oa.las.ac.cn/oainone/service/browseall/read1?ptype=JA&workid=JA201910258681885ZK.

科研活动

   
科研项目
( 1 ) 面向复杂生物数据处理的高效计算方法, 参与, 国家级, 2013-01--2017-12
( 2 ) 面向高分辨的电子断层三维重构算法研究, 主持, 国家级, 2013-01--2015-12
( 3 ) 面向大尺度生物图像的高精度三维分子结构重构技术研究, 参与, 国家级, 2015-01--2018-12
( 4 ) 面向高通量冷冻电镜图像的电子断层重构算法研究, 主持, 国家级, 2017-01--2020-12
( 5 ) 面向典型疾病的高精度生物大分子三维结构研究, 参与, 国家级, 2017-01--2020-12
( 6 ) 蛋白质机器的高分辨率冷冻电镜前沿技术及应用, 参与, 国家级, 2017-01--2021-12
( 7 ) 地球大数据科学工程, 主持, 部委级, 2018-02--2022-12
( 8 ) 面向深度学习的GPU虚拟化关键方法与技术研究, 主持, 省级, 2018-12--2021-12
( 9 ) 生物大分子原位结构的冷冻电镜重构算法研究, 主持, 国家级, 2021-01--2024-12

指导学生

已指导学生

张恩泽  硕士研究生  085211-计算机技术  

现指导学生

申泽南  硕士研究生  085211-计算机技术  

杨子豪  硕士研究生  081201-计算机系统结构  

林森林  硕士研究生  085400-电子信息