基本信息
万林  男  博导  中国科学院数学与系统科学研究院
电子邮件: lwan@amss.ac.cn
通信地址: 北京市海淀区中关村东路55号
邮政编码: 100190

研究领域

数据科学,机器学习,计算生物学
统计与优化
人工智能

招生信息

   
招生专业
070105-运筹学与控制论
071101-系统理论
070103-概率论与数理统计
招生方向
数据科学,机器学习,计算生物学
统计与优化
人工智能

教育背景

2003-09--2009-07   北京大学   理学博士
1999-09--2003-07   南京大学   理学学士
学历
-- 研究生
学位
-- 博士

工作经历

   
工作简历
2021-04~现在, 中国科学院数学与系统科学研究院, 研究员
2014-03~2021-04,中国科学院数学与系统科学研究院, 副研究员
2011-08~2014-02,中国科学院数学与系统科学研究院, 助理研究员
2009-04~2011-08,中国科学院数学与系统科学研究院, 博士后
社会兼职
2023-10-01-今,CSIAM 数学生命科学专委会, 委员
2023-05-01-今,中国生物信息学学会(筹)生物信息学算法研究专委会, 常务委员
2020-12-01-今,中国自动化学会智能健康与生物信息专业委员会, 委员
2015-01-01-今,中国运筹学会计算系统生物学分会, 理事

教授课程

系统估计
概率论与数理统计
概率论与数理统计习题课-02
概率论与数理统计习题课-01

专利与奖励

   
奖励信息
(1) APBC2019国际会议最佳论文, 特等奖, 其他, 2019
(2) Early Career Award, 研究所(学校), 2016
(3) 关肇直青年研究奖, 研究所(学校), 2014
(4) 中国科学院数学与系统科学研究院优秀教师奖, 研究所(学校), 2014
专利成果
( 1 ) 用于多个分子信号的数据处理方法和装置, 发明专利, 2016, 第 3 作者, 专利号: CN105989248A

出版信息

   
发表论文
[1] Zhang, Lei, Liang, Shu, 万林. A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data. BRIEFINGS IN BIOINFORMATICS[J]. 2024, 第 3 作者  通讯作者  25(4): http://dx.doi.org/10.1093/bib/bbae255.
[2] Qi Jiang, 万林. A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data. BIOINFORMATICS[J]. 2024, 第 2 作者  通讯作者  40(Suppl 2): ii120-ii127, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373338/.
[3] Xiangqi Bai, Zhana Duren, 万林, Li C. Xia. Joint inference of clonal structure using single-cell genome and transcriptome sequencing data. NAR Genomics and Bioinformatics[J]. 2024, 第 3 作者  通讯作者  6(1): lqae017, https://doi.org/10.1093/nargab/lqae017.
[4] Zizhan Gao, Kai Cao, 万林. Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport. Bioinformatics[J]. 2024, 第 3 作者  通讯作者  40(Suppl 2): ii137-ii145, https://doi.org/10.1093/bioinformatics/btae394.
[5] Xiong, Jiankang, 巩馥洲, 马亮, 万林. scVIC: deep generative modeling of heterogeneity for scRNA-seq data. Bioinformatics Advances[J]. 2024, 第 4 作者  通讯作者  4(1): vbae086, https://doi.org/10.1093/bioadv/vbae086.
[6] Chen, Ziwei, Zhang, Bingwei, Gong, Fuzhou, 万林, Ma, Liang. RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data. FRONTIERS IN GENETICS[J]. 2023, 第 4 作者  通讯作者  14: 1110899, http://dx.doi.org/10.3389/fgene.2023.1110899.
[7] Cao, Kai, Gong, Qiyu, Hong, Yiguang, Wan, Lin. A unified computational framework for single-cell data integration with optimal transport. NATURE COMMUNICATIONS[J]. 2022, 第 4 作者  通讯作者  13(1): http://dx.doi.org/10.1038/s41467-022-35094-8.
[8] An, Shaokun, Ren, Jie, Sun, Fengzhu, Wan, Lin. A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2022, 第 4 作者  通讯作者  29(8): 839-856, http://dx.doi.org/10.1089/cmb.2021.0604.
[9] Cao, Kai, Hong, Yiguang, Wan, Lin. Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona. BIOINFORMATICS[J]. 2022, 第 3 作者  通讯作者  38(1): 211-219, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000736120000029.
[10] Qi Jiang, Shuo Zhang, 万林. Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data. PLOS COMPUTATIONAL BIOLOGY[J]. 2022, 第 3 作者  通讯作者  18(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8812873/.
[11] Chen, Ziwei, Gong, Fuzhou, 万林, Ma, Liang. BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data. BRIEFINGS IN BIOINFORMATICS[J]. 2022, 第 3 作者  通讯作者  23(3): http://dx.doi.org/10.1093/bib/bbac092.
[12] Kai Cao, Qiyu Gong, Yiguang Hong, 万林. A unified computational framework for single-cell data integration with optimal transport. Nature Communications[J]. 2022, 第 4 作者  通讯作者  13: 7419, https://doi.org/10.1038/s41467-022-35094-8.
[13] Kai Cao, Yiguang Hong, Lin Wan. Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona. BIOINFORMATICS[J]. 2021, 第 3 作者  通讯作者  38(1): 211-219, 
[14] An, Shaokun, Huang, Jizu, Wan, Lin. D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data. GIGASCIENCE[J]. 2020, 第 3 作者  通讯作者  9(11): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657844/.
[15] Chen, Ziwei, Bai, Xiangqi, Ma, Liang, Wang, Xiawei, Liu, Xiuqin, Liu, Yuting, Chen, Luonan, Wan, Lin. A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2020, 第 8 作者  通讯作者  17(2): 366-375, https://www.webofscience.com/wos/woscc/full-record/WOS:000524236800001.
[16] Chen, Ziwei, Gong, Fuzhou, Wan, Lin, Ma, Liang. RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data. BIOINFORMATICS[J]. 2020, 第 3 作者  通讯作者  36(11): 3299-3306, http://dx.doi.org/10.1093/bioinformatics/btaa172.
[17] Cao, Kai, Bai, Xiangqi, Hong, Yiguang, Wan, Lin. Unsupervised topological alignment for single-cell multi-omics integration. BIOINFORMATICS[J]. 2020, 第 4 作者  通讯作者  36(Suppl 1): 48-56, https://www.webofscience.com/wos/woscc/full-record/WOS:000579894600007.
[18] Xiong, Jiankang, Gong, Fuzhou, Wan, Lin, Ma, Liang. NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data. FRONTIERS IN GENETICS[J]. 2020, 第 3 作者  通讯作者  11: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7587292/.
[19] Chen, Ziwei, An, Shaokun, Bai, Xiangqi, Gong, Fuzhou, Ma, Liang, Wan, Lin. DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data. BIOINFORMATICS[J]. 2019, 第 6 作者  通讯作者  35(15): 2593-2601, http://ir.amss.ac.cn/handle/2S8OKBNM/35572, http://www.irgrid.ac.cn/handle/1471x/6869820, http://ir.amss.ac.cn/handle/2S8OKBNM/35573, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484378200009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[20] Ma, Liang, Rolls, Edmund T, Liu, Xiuqin, Liu, Yuting, Jiao, Zeyu, Wang, Yue, Gong, Weikang, Ma, Zhiming, Gong, Fuzhou, Wan, Lin. Multi-scale analysis of schizophrenia risk genes, brain structure, and clinical symptoms reveals integrative clues for subtyping schizophrenia patients. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2019, 第 10 作者  通讯作者  11(8): 678-687, https://www.webofscience.com/wos/woscc/full-record/WOS:000493042300006.
[21] Bai, Xiangqi, Ma, Liang, Wan, Lin. Statistical test of structured continuous trees based on discordance matrix. BIOINFORMATICS[J]. 2019, 第 3 作者  通讯作者  35(23): 4962-4970, 
[22] Shaokun An, Liang Ma, Lin Wan. TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data. BMC GENOMICS[J]. 2019, 第 3 作者  通讯作者  20(S2): 77-92, https://doaj.org/article/e317474d0c2d4765a67f55dc78ea637b.
[23] Li, Shuo, Dou, Xialiang, Gao, Ruiqi, Ge, Xinzhou, Qian, Minping, Wan, Lin. A remark on copy number variation detection methods. PLOS ONE[J]. 2018, 第 6 作者  通讯作者  13(4): https://doaj.org/article/73c805e7cf894d14b96ac87b95e0ee42.
[24] Gong, Weikang, Wan, Lin, Lu, Wenlian, Ma, Liang, Cheng, Fan, Cheng, Wei, Grunewald, Stefan, Feng, Jianfeng. Statistical testing and power analysis for brain-wide association study. MEDICAL IMAGE ANALYSIS[J]. 2018, 第 2 作者47(-): 15-30, http://dx.doi.org/10.1016/j.media.2018.03.014.
[25] Zhang, Sheng, Wang, Bo, Wan, Lin, 李雷. Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling. BMC BIOINFORMATICS[J]. 2017, 第 3 作者18(1): http://dx.doi.org/10.1186/s12859-017-1743-4.
[26] Rolls, Edmund T, Lu, Wenlian, Wan, Lin, Yan, Hao, Wang, Chuanyue, Yang, Fude, Tan, Yunlong, Li, Lingjiang, Yu, Hao, Liddle, Peter F, Palaniyappan, Lena, Zhang, Dai, Yue, Weihua, Feng, Jianfeng, Chinese Schizophrenia Collabor. Individual differences in schizophrenia. BJPSYCH OPEN[J]. 2017, 第 3 作者3(6): 265-+, https://doaj.org/article/8ccd750777004da0b5459f90a8dc5ff4.
[27] Wang, Bo, Wan, Lin, Wang, Anqi, 李雷. An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters. SCIENTIFIC REPORTS[J]. 2017, 第 2 作者7: https://www.webofscience.com/wos/woscc/full-record/WOS:000394330600001.
[28] Cheng, Wei, Rolls, Edmund T, Zhang, Jie, Sheng, Wenbo, Ma, Liang, Wan, Lin, Luo, Qiang, Feng, Jianfeng. Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis. NEUROIMAGE[J]. 2017, 第 6 作者148: 169-178, http://dx.doi.org/10.1016/j.neuroimage.2016.12.068.
[29] 李雷. Achieving Accurate and Fast Base-calling by a Block Model of the Illumina Sequencing Data. IFAC-PapersOnLine. 2015, 
[30] 万林. Tracking the Evolving Spatial-Temporal Gene Networks. IFAC-PapersOnLine. 2015, 第 1 作者  通讯作者  
[31] 王琳, 李诗卉, 张先闻, 张春崧, 李交, 赵思宇, 邓跃毅, 田建辉, 钱敏平, 万林, 陈以平. 应用全基因组拷贝数变异方法探索参芪膜肾方治疗特发膜性肾病基因水平机制的研究. 中国中西医结合肾病杂志[J]. 2014, 第 10 作者329-332, http://lib.cqvip.com/Qikan/Article/Detail?id=49727178.
[32] Wang, Quan, Peng, Peichao, Qian, Minping, Wan, Lin, Deng, Minghua. Hybridization and amplification rate correction for affymetrix SNP arrays. BMC MEDICAL GENOMICS[J]. 2012, 第 4 作者  通讯作者  5(1): 24-24, https://doaj.org/article/274df2763c7c4a42bfcb941ee3ac2602.
[33] Wan, Lin, Sun, Fengzhu. CEDER: Accurate Detection of Differentially Expressed Genes by Combining Significance of Exons Using RNA-Seq. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2012, 第 1 作者  通讯作者  9(5): 1281-1292, http://dx.doi.org/10.1109/TCBB.2012.83.
[34] Wan, Lin, Yan, Xiting, Chen, Ting, Sun, Fengzhu. Modeling RNA degradation for RNA-Seq with applications. BIOSTATISTICS[J]. 2012, 第 1 作者13(4): 734-747, https://www.webofscience.com/wos/woscc/full-record/WOS:000308885800013.
[35] Liu, Xuemei, Wan, Lin, Li, Jing, Reinert, Gesine, Waterman, Michael S, Sun, Fengzhu. New powerful statistics for alignment-free sequence comparison under a pattern transfer model. JOURNAL OF THEORETICAL BIOLOGY[J]. 2011, 第 2 作者284(1): 106-116, http://dx.doi.org/10.1016/j.jtbi.2011.06.020.
[36] Wang, Quan, Qu, Jianghan, Cheng, Xiaoxing, Kang, Yongjian, Wan, Lin, Qian, Minping, Deng, Minghua. A study of biases of DNA copy number estimation based on PICR model. FRONTIERS OF MATHEMATICS IN CHINA[J]. 2011, 第 5 作者6(6): 1203-1216, https://www.webofscience.com/wos/woscc/full-record/WOS:000297647000011.
[37] Wang, Ying, Mehta, Gaurang, Mayani, Rajiv, Lu, Jingxi, Souaiaia, Tade, Chen, Yangho, Clark, Andrew, Yoon, Hee Jae, Wan, Lin, Evgrafov, Oleg V, Knowles, James A, Deelman, Ewa, Chen, Ting. RseqFlow: workflows for RNA-Seq data analysis. BIOINFORMATICS[J]. 2011, 第 9 作者27(18): 2598-2600, http://dx.doi.org/10.1093/bioinformatics/btr441.
[38] Wan, Lin, Reinert, Gesine, Sun, Fengzhu, Waterman, Michael S. Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. JOURNALOFCOMPUTATIONALBIOLOGY[J]. 2010, 第 1 作者17(11): 1467-+, http://dx.doi.org/10.1089/cmb.2010.0056.
[39] 万林. The biases of copy numbers from Affymetrix SNP arrays and their corrections. Communications in Information and Systems. 2010, 第 1 作者
[40] Wang, Quan, Wan, Lin, Li, Dayong, Zhu, Lihuang, Qian, Minping, Deng, Minghua. Searching for bidirectional promoters in Arabidopsis thaliana. BMC BIOINFORMATICS[J]. 2009, 第 2 作者10(Suppl 1): S29-S29, https://www.webofscience.com/wos/woscc/full-record/WOS:000265601900029.
[41] 万林. Nonlinear cooperation between p53 and ING1 induces bax expression in mouse thymocyte apoptosis: A quantitative approach with cross-platform validation. Apoptosis. 2009, 第 1 作者
[42] Wan, Lin, Sun, Kelian, Ding, Qi, Cui, Yuehua, Li, Ming, Wen, Yalu, Elston, Robert C, Qian, Minping, Fu, Wenjiang J. Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation. NUCLEIC ACIDS RESEARCH[J]. 2009, 第 1 作者37(17): e117-e117, http://dx.doi.org/10.1093/nar/gkp559.
[43] Wan, Lin, Li, Dayong, Zhang, Donglei, Liu, Xue, Fu, Wenjiang J, Zhu, Lihuang, Deng, Minghua, Sun, Fengzhu, Qian, Minping. Conservation and implications of eukaryote transcriptional regulatory regions across multiple species. BMC GENOMICS[J]. 2008, 第 1 作者9(1): 623-623, https://doaj.org/article/266cbfefec474f1f91c7be1f48f714bb.
[44] Wang, CJ, Huang, YN, Wan, L, Yin, HC, Wang, YN, Riande, E. Relaxation dynamics and glass transition in glassy materials. SYNTHETIC METALS[J]. 2003, 135(1-3): 495-496, http://dx.doi.org/10.1016/S0379-6779(02)00708-7.

科研活动

   
科研项目
( 1 ) 精准医学的多尺度因果数学理论与应用, 参与, 国家任务, 2022-11--2027-10
( 2 ) 几何与拓扑型数据分析的理论与方 法及其在高维异质生物数据中的应 用, 负责人, 国家任务, 2021-01--2024-12
( 3 ) 大脑计算同化平台与新一代类脑智能算法理论, 参与, 国家任务, 2020-06--2025-05
( 4 ) 非完整、异构材料数据关联统计分析与挖掘技术, 参与, 国家任务, 2018-07--2022-06
( 5 ) 重大脑精神疾病的遗传影像学分析理论与计算方法, 参与, 国家任务, 2017-01--2019-12
( 6 ) 中国科学院青年创新促进会, 负责人, 中国科学院计划, 2016-01--2019-12
( 7 ) 生物/医学时空型数据的建模、计算与系统综合研究, 负责人, 国家任务, 2016-01--2019-12
( 8 ) 动物复杂形状的进化解析与调控, 参与, 中国科学院计划, 2014-07--2019-06

指导学生

已指导学生

易健平  硕士研究生  070103-概率论与数理统计  

陈紫薇  博士研究生  071101-系统理论  

安少坤  博士研究生  071101-系统理论  

白向琦  博士研究生  071101-系统理论  

高子瞻  硕士研究生  071101-系统理论  

现指导学生

蒋淇  博士研究生  071101-系统理论  

李龙泉  硕士研究生  071101-系统理论  

谭博文  硕士研究生  070105-运筹学与控制论  

郑澍乔  博士研究生  071101-系统理论