1. 数据科学

2. 计量系统生物学和医学

3. 统计建模与统计计算

4. 时间序列分析

5. 信息论​

   

071400-统计学

数据科学
计量系统生物学和医学

1993-08--1998-05   加利福尼亚大学伯克利分校, 统计系   博士
1988-09--1991-05   北京大学, 概率统计系   硕士
1984-09--1988-05   北京大学, 数学系   学士

-- 研究生

-- 博士, 加利福尼亚大学伯克利分校, 统计系
    硕士, 北京大学, 概率统计系
    学士, 北京大学, 数学系

2021.1－至今 中国科学院数学与系统科学研究院, 关肇直首席研究员

2014.8－至今 中国科学院大学特聘教授

2010.2－至今 中国科学院数学与系统科学研究院, 研究员

2005.4-2010.5 南加利福尼亚大学计算生物及数学系, 副教授 (tenure终身职务)

2002.6-2005.4 南加利福尼亚大学数学及计算生物系, 助理教授(tenure track)

2000.9-2000.12 加利福尼亚大学洛杉矶分校，纯粹与应用数学研究所, 博士后

1991.6-1993.7 中国科学院系统科学研究所, 助理研究员

概率论与数理统计
高等数理统计

1998, Evelyn Fix Memorial Medal, UC Berkeley

2013, 中国专利授权，李雷，王安琪，陈士剑，一种测序序列映射方法及系统，申请号：201310282312.1

[1] 曹晟昊, 李梦甜, 李雷. 基因组叠阵、基因组架构、基因组序列组装方法及系统. CN: CN115440302A, 2022-12-06.

[2] 李雷, 王安琪, 李峥, 王占宇. 基因组序列的组装方法、结构变异探测方法和相应的系统. CN: CN107133493A, 2017-09-05.

[3] 李雷, 王博, 万林. 用于多个分子信号的数据处理方法和装置. CN: CN105989248A, 2016-10-05.

[4] 李雷, 王琳. 检测生物分子的变化的方法和检测生物调控分子的变化的方法. CN: CN103729578A, 2014-04-16.

[5] 李雷, 王安琪, 陈士剑. 一种测序序列映射方法及系统. CN: CN103336916A, 2013-10-02.

Publications 

1.         Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun. 2024 Mar 16;15(1):2395. doi: 10.1038/s41467-024-46780-0. PMID: 38493164; PMCID: PMC10944513.

2.         Lei M Li, Empirical Lossless Compression Bound of a Data Sequence, http://arxiv.org/abs/2311.01431

3.         Mengtian Li, Jiachen Li, Ke Wang, Lei M Li Reconstructing COVID-19 incidences from positive RT-PCR tests by deconvolution. BMC Infect Dis 23, 679 (2023). https://doi.org/10.1186/s12879-023-08667-1.

4.         Cao S, Wang L, Feng Y, Peng X-d, Li LM (2023) A data integration approach unveils a transcriptional signature of type 2 diabetes progression in rat and human islets. PLoS ONE 18(10): e0292579. https://doi.org/10.1371/journal.pone.0292579

5.         Cao, S., Li, M. & Li, L.M. RegCloser: a robust regression approach to closing genome gaps. BMC Bioinformatics 24, 249 (2023). https://doi.org/10.1186/s12859-023-05367-0 

6.         Hong H, Zhao Z, Huang X, Guo C, Zhao H, Wang GD, Zhang YP, Zhao JP, Shi J, Wu QF, Jiang YH, Wang Y, Li LM, Du Z, Zhang YQ, Xiong Y. Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains. Mol Cell Proteomics. 2022 Aug;21(8):100261. doi: 10.1016/j.mcpro.2022.100261. Epub 2022 Jun 20. PMID: 35738554

7.         Lei M Li, Mengtian Li, Liang Li, Cis-regulatory Element Frequency Modules and their Phase Transition across Hominidae, chapter in "Handbook of Statistical Bioinformatics", edited by: Henry Horng-Shing Lu, Bernhard Schölkopf, Martin T. Wells, and Hongyu Zhao, Springer-Verlag GmbH, DE, Heidelberger Platz 3, 14197 Berlin, Germany, page, 371-395, 2022

8.         Mengtian Li, Lei M Li, RegScaf: a regression approach to scaffolding, Bioinformatics. Volume 38, Issue 10, 15 May 2022, Pages 2675–2682, doi.org/10.1093/bioinformatics/btac174

9.         Yance Feng, Lei M. Li, MUREN: a Robust and Multi-reference Approach of RNA-seq Transcripts Normalization, BMC Bioinformatics 22, 386 (2021). https://doi.org/10.1186/s12859-021-04288-0.

10.     Liang Li, Sheng Zhang, Lei M Li, Dual Eigen-modules of Cis-element Regulation Profiles and Selection of Cognition-language Eigen-direction along Evolution in Hominidae, Molecular Biology and Evolution, 2020 Jun 1;37(6):1679-1693. doi.org/10.1093/molbev/msaa036.

11.     Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi, Yong Wang, ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor, Quantitative Biology, accepted.

12.     Von Weber, Sheng Zhang, Liang Li, Lei M. Li, The cis-trans Binding Strength Defined by Motif Frequencies Facilitates Statistical Inference of Transcriptional Regulation, 2018, 12th International Conference on Computational Systems Biology， BMC Bioinformatics, 2019 May 1;20(Suppl 7):201. doi: 10.1186/s12859-019-2732-6.

13.     彭小丁, 李雷, 治愈2型糖尿病难题的新视角:及早发现、及早治疗,医学综述，2018年10月，20卷，20期，4060-4067

14.     Anqi Wang, Zhanyu Wang, Zheng Li and Lei M. Li  (2018), BAUM: A DNA Assembler by Adaptive Unique Mapping and Local Overlap-Layout-Consensus， Bioinformatics. 10.1093/bioinformatics/bty020

15.     Zhang, S., Wang, B., Wan, L. & Li, L.M. Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling. BMC Bioinformatics 18, 335 (2017).

16.     Wang, B., Wan, L., Wang, A. & Li, L.M. An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters. Sci Rep 7, 41348 (2017).

17.     Li, L.M., Liu, X., Wang, L., Wang, Y., Liu, X., Tian, X., Gong, F., Shen, L. & Peng, X.D. A Novel Dual Eigen-Analysis of Mouse Multi-Tissues' Expression Profiles Unveils New Perspectives into Type 2 Diabetes. Sci Rep 7, 5044 (2017).

18.     王琳，李雷. 解析复杂疾病分子机制的功能性基因组学统计方法, (中国统计出版社, 2016年5月).

19.     Wang Bo, L.W., Lei M Li. Achieving Accurate and Fast Base-calling by a Block Model of the Illumina Sequencing Data. in 17th IFAC Symposium on System Identification (Beijing, 2015).

20.     Wang, L., Meng, J., Cao, W., Li, Q., Qiu, Y., Sun, B. & Li, L.M. Induction of apoptosis through ER stress and TP53 in MCF-7 cells by the nanoparticle [Gd@C82(OH)22]n: A systems biology study. Methods 67, 394-406 (2014).

21.     Chen, S., Wang, A. & Li, L.M. SEME: a fast mapper of Illumina sequencing reads with statistical evaluation. J Comput Biol 20, 847-60 (2013).

22.     Lei M. Li, Chao Cheng., Huanying Ge. SYSTEMS AND METHODS FOR ANALYZING MICROARRAYS. (United States Patent, 2012).

23.     Lei M. Li (2012) DNA Sequencing and Commentary, in the book, “Selected Works of Terry Speed” edited by Sandrine Dudoit, Springer, Chapter 13, Page 535-561. ISBN  978-1-4614-1346-2

24.     Kremsky, I., Morgan, T.E., Hou, X.G., Li, L. & Finch, C.E. Age-changes in gene expression in primary mixed glia cultures from young vs. old rat cerebral cortex are modified by interactions with neurons. Brain Behavior and Immunity 26, 797-802 (2012).

25.     Li, L.M. Accuracy Assessment of Consensus Sequence from Shotgun Sequencing. in Handbook of Computational Statistics: Statistical Bioinformatics (eds. Lu, H.H.-S., Sch?lkopf, B. & Zhao, H.) (Springer, 2011).

26.     Kim, J.H., Kim, W.C., Li, L.M. & Park, S. HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies. Nucleic Acids Research 39, W557-W561 (2011).

27.     Li, L.M. & Zhang, S. An Out-of-Sample Validation Study of Asset Pricing Models. in Advances in Investment Analysis and Portfolio Management, Vol. 4 (eds. Lee, C.F. & Lee, A.C.) 153 -174 (Center for PBBEFR、Airiti Press Inc., 2010).

28.     Ge, H., Wei, M., Fabrizio, P., Hu, J., Cheng, C., Longo, V.D. & Li, L.M. Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant. Nucleic Acids Res 38, 143-58 (2010).

29.     Wei, M., Fabrizio, P., Madia, F., Hu, J., Ge, H., Li, L.M. & Longo, V.D. Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension. PLoS Genet 5, e1000467 (2009).

30.     Kim, J.H., Kim, W.C., Waterman, M.S., Park, S. & Li, L.M. HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. Bioinformatics 25, 2430-1 (2009).

31.     Cheng, C., Li, L.M., Alves, P. & Gerstein, M. Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics 10, 225 (2009).

32.     Wei, M., Fabrizio, P., Hu, J., Ge, H., Cheng, C., Li, L. & Longo, V.D. Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. PLoS Genet 4, e13 (2008).

33.     Li, L.M. & Cheng, C. Differentiation Detection in Microarray Normalization. in Methods in Microarray Normalization (ed. Stafford, P.) 19-39 (CRC press, Boca Raton, 2008).

34.     Ge, H., Cheng, C. & Li, L.M. A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. BMC Bioinformatics 9, 194 (2008).

35.     Cheng, C. & Li, L.M. Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics 9, 116 (2008).

36.     Cheng, C. & Li, L.M. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One 3, e1989 (2008).

37.     Li, H., Valouev, A., Schwartz, D.C., Waterman, M.S. & Li, L.M. A quantile method for sizing optical maps. J Comput Biol 14, 255-66 (2007).

38.     Kitsantas, P., Hollander, M. & Li, L.M. Assessing the stability of classification trees using Florida birth data. Journal of Statistical Planning and Inference 137, 3917-3929 (2007).

39.     Kim, J.H., Waterman, M.S. & Li, L.M. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res 17, 1101-10 (2007).

40.     Kim, J.H., Waterman, M.S. & Li, L.M. Accuracy assessment of diploid consensus sequences. IEEE/ACM Trans Comput Biol Bioinform 4, 88-97 (2007).

41.     Cheng, C., Yan, X., Sun, F. & Li, L.M. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 8, 452 (2007).

42.     Cheng, C., Fabrizio, P., Ge, H., Wei, M., Longo, V.D. & Li, L.M. Significant and systematic expression differentiation in long-lived yeast strains. PLoS One 2, e1095 (2007).

43.     Cheng, C., Fabrizio, P., Ge, H., Longo, V.D. & Li, L.M. Inference of transcription modification in long-live yeast strains from their expression profiles. BMC Genomics 8, 219 (2007).

44.     Valouev, A., Li, L., Liu, Y.C., Schwartz, D.C., Yang, Y., Zhang, Y. & Waterman, M.S. Alignment of optical maps. J Comput Biol 13, 442-62 (2006).

45.     Nicolas, P., Sun, F. & Li, L.M. A model-based approach to selection of tag SNPs. BMC Bioinformatics 7, 303 (2006).

46.     Li, L.M. Some notes on mutual information between past and future. Journal of Time Series Analysis 27, 309-322 (2006).

47.     Kitsantas, P., Hollander, M. & Li, L. Using classification trees to assess low birth weight outcomes. Artif Intell Med 38, 275-89 (2006).

48.     Cheng, C., Ma, X., Yan, X., Sun, F. & Li, L.M. MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics 22, 2650-7 (2006).

49.     Li, L.M. & Lu, H.H. Explore biological pathways from noisy array data by directed acyclic Boolean networks. J Comput Biol 12, 170-85 (2005).

50.     Li, L.M. Factorization of moving-average spectral densities by state-space representations and stacking. Journal of Multivariate Analysis 96, 425-438 (2005).

51.     Li, L.M. An algorithm for computing exact least-trimmed squares estimate of simple linear regression with constraints. Computational Statistics & Data Analysis 48, 717-734 (2005).

52.     Fabrizio, P., Li, L. & Longo, V.D. Analysis of gene expression profile in yeast aging chronologically. Mech Ageing Dev 126, 11-6 (2005).

53.     Cheng, C. & Li, L.M. Sub-array normalization subject to differentiation. Nucleic Acids Res 33, 5565-73 (2005).

54.     Li, M., Nordborg, M. & Li, L.M. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res 32, 5183-91 (2004).

55.     Li, L.M. & Speed, T.P. Deconvolution of sparse positive spikes. Journal of Computational and Graphical Statistics 13, 853-870 (2004).

56.     Li, L.M., Kim, J.H. & Waterman, M.S. Haplotype reconstruction from SNP alignment. J Comput Biol 11, 505-16 (2004).

57.     Rosenberg, N.A., Li, L.M., Ward, R. & Pritchard, J.K. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73, 1402-22 (2003).

58.     Li, L.M. Blind inversion needs distribution (BIND): General notation and case studies. in Science and statistics: A festschrift for Terry Speed (ed. Goldstein, D.) 275-293 (IMS Press, Fountain Hills, AZ, 2003).

59.     Li, L. DNA sequencing and parametric deconvolution. Statistica Sinica 12, 179-202 (2002).

60.     Li, L. & Speed, T.P. Parametric deconvolution of positive spike trains. Annals of Statistics 28, 1279-1301 (2000).

61.     Lei, L. & Bin, Y. Iterated logarithmic expansions of the pathwise code lengths for exponential families. Information Theory, IEEE Transactions on 46, 2683-2689 (2000).

62.     Li, L. & Speed, T.P. An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing. Electrophoresis 20, 1433-1442 (1999).

63.     Kheterpal, I., Li, L., Speed, T.P. & Mathies, R.A. A three-wavelength labeling approach for DNA sequencing using energy transfer primers and capillary electrophoresis. Electrophoresis 19, 1403-14 (1998).

64.     Li, LM, Xie, Z. (1996) Model selection and order determination for time series by information between the past and the future. Journal of Time Series Analysis, 17:65-84. doi.org/10.1111/j.1467-9892.1996.tb00265.x

65.     Li, L. A method to factorize spectral densities of multiple moving average processes. Journal of Systems Sciences and Mathematics 7, 169-176 (1994).

重大慢性多发疾病的动态网络构建, 中国科学院国家数学与交叉科学中心,数学与生物/医学交叉部

（ 1 ） 医学大数据整合分析的数学方法, 负责人, 中国科学院计划, 2016-01--2016-12
（ 2 ） 高通量测序的可计算建模与应用, 负责人, 国家任务, 2016-01--2018-01
（ 3 ） 生物组学大数据的高性能整合分析, 负责人, 中国科学院计划, 2014-07--2019-06
（ 4 ） 从组学大数据解析2型糖尿病发生发展分子机制的双重特征分析方法, 负责人, 国家任务, 2018-11--2022-12
（ 5 ） 从順式元件频数的双重特征模块角度研究调控进化和性 状的跳变, 负责人, 国家任务, 2022-01--2025-12
（ 6 ） 分子尺度多组学数据的数学表征与耦合集成, 负责人, 国家任务, 2022-12--2027-11

   

山东大学齐鲁医院

中科院云南动物研究所

已指导学生

王琳  博士研究生  070103-概率论与数理统计  

现指导学生

王安琪  博士研究生  070103-概率论与数理统计  

张升  博士研究生  070103-概率论与数理统计  

赵乐天  硕士研究生  071400-统计学  

王博  博士研究生  070103-概率论与数理统计