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1 Li, LM. A method to factorize spectral densities of multiple moving average processes. Journal of Systems Sciences and Mathematics. 1994; 7:169-176.
2 Li, LM, Xie, Z. Model selection and order determination for time series by information between the past and the future. Journal of Time Series Analysis. 1996; 17:65-84.
3. Kheterpa,l I, Li, LM, Speed, TP, Mathies, RA. A three-wavelength labeling approach for DNA sequencing using energy transfer primers and capillary electrophoresis. Electrophoresis. 1998; 19:1403-1414.
4. Li, LM, Speed, TP. Estimation of the color separation matrix in four-dye fluorescence-based DNA sequencing. Electrophoresis. 1999; 20:1433-1442.
5. Li L, Speed TP. Parametric deconvolution of positive spike trains. Annals of Statistics. 2000; 28:1279-1301.
6. Li, LM, Yu, B. Iterated-logarithmic expansion of the pathwise code lengths for
exponential families. IEEE Transactions on Information Theory. 2000; 46:2683-2689.
7. Li, LM. DNA sequencing and parametric deconvolution. Statistica Sinica, Special issue in bioinformatics. 2002; 12:179-202.
8. Li, LM. Blind Inversion needs distribution (BIND): the general notion and case studies. Festschrift for Professor Speed’s 60th Birthday, IMS Lecture Note Series, edited by D. Goldstein, 2003, 40:273-293.
9. Rosenberg, NA, Li, LM, Ward, R and Pritchard, JK. Informativeness of genetic
markers for inference of ancestry, Journal of American Human Genetics, 2003, 73:1402-1422.
10. Li LM, Kim JH, Waterman MS. Haplotype reconstruction from SNP
alignment, Journal of Computational Biology, 2004, 11: 505-516.
11. Li, LM and Speed, TP. Deconvolution of sparse positive spikes, Journal
of Computational and Graphical Statistics, 2004, 13:1-18.
12. Li, LM. An Algorithm for computing exact least trimmed squares estimate of simple linear regression with constraints, Computational Statistics and Data Analysis, 2004, 48:717-734.
13. Li, M, Nordborg, M, Li, LM. Adjust quality scores from alignment and improve sequencing accuracy, Nucleic Acids Research, 2004, 32:5183-5191.
14. Li, LM. Factorization of moving-average spectral densities by state-space representations and stacking, Journal of Multivariate Analysis, 2005, 96: 425-438.
15. Li, LM, Lu, H.-S. Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks, Journal of Computational Biology, 2005, 12: 170-185.
16. Cheng, C. and Li, LM. Sub-array Normalization Subject to Differentiation,
Nucleic Acids Research, 2005, 33(17):5565-5573.
17. Li, LM. Some Notes on Mutual Information between Past and Future, Journal of Time Series Analysis, 2005, 27:309–322.
18. Valouev, A., Li, LM., Liu, Y.-C., Schwartz, D. C., Yang, Y., Zhang, Y. and Waterman, MS. Alignment of Optical Maps, RECOMB05, Lecture Notes in Computer Science, Vol 3500: 489-504, 2005, revision in Journal of Computational Biology, 2006, 13:442–462
19. Fabrizio P., Li, LM. and Longo, VD. (2005) Analysis of Gene Expression Profile in Yeast Aging Chronologically, Mechanisms of Ageing and Development, 2005, 126:11-16.
20. Kitsantas, P, Hollander M, Li LM. (2006) Using classification trees to assess low birth weight outcomes, Journal Artificial Intelligence in Medicine, 38: 275—289
21. Nicolas, P, Sun, F. Li, LM. (2006) A model-based approach to selection of tag SNPs, BMC Bioinformatics, 7:303.
22. Cheng, C., Ma, X., Yan, X., Sun, F. and Li, LM (2006) MARD: A New Method to Detect Differential Gene Expression in Treatment-Control Time Courses, Bioinformatics, 21: 2650-2657.
23. Kitsantas, P, Hollander M, Li LM. (2007) Assessing the Stability of Classifcation Trees, Journal of Statistical Planning and Inference, 137: 3917 – 3929
24. Kim,JH, Waterman, MS, Li, LM. (2007) Accuracy Assessment of Diploid Consensus Sequences, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4:88-97.
25. Li, H, Valouev , A, Schwartz, DC. Waterman, MS and Li, LM (2007) A Quantile Method for Sizing Optical Maps, Journal of Computational Biology, 14: 255–266
26. Kim,JH, Waterman, MS, Li, LM. (2007) Diploid Genome Reconstruction of Ciona intestinalis and Comparative Analysis with Ciona savignyi, Genome Research, 17: 1101-1110
27. Cheng, C., Fabrizio, P., Ge, H. , Longo, VD and Li, LM (2007) Inference of Transcription Modificiation in Long-live Yeast Strains from their Expression Profiles, BMC Genomics, 8:219-228
28. Li, LM, Cheng, C. (2008) Differentiation Detection in Microarray Normalization, in Methods in Microarray Normalization, edited by Stafford, P., CRC press, 19-39
29. Cheng C, Fabrizio P, Ge H, Wei M, Longo VD, and Li LM (2007) Significant and Systematic Expression differentiation in Long-lived Yeast Strains, PLoS ONE 2(10): e1095. doi:10.1371/journal.pone.0001095
30. Zhang S and Li LM (2010) An Out-of-Sample Validation Study of Asset Pricing Models, Advances in Investment Analysis and Portfolio Management, Volume 4.
31. Chao Cheng, Xiting Yan, Fengzhu Sun and Lei M Li, Inferring activity changes of transcription factors by binding association with sorted expression profiles, BMC Bioinformatics, 8:452.
32. Ge H, Cheng C and Li LM (2008), A Probe-Treatment-Reference (PTR) Model for the Analysis of Oligonucleotide Expression Microarrays, BMC Bioinformatics, 9: 194.
33. Cheng, C and Li, LM (2008) Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics, 9:116.
34. Wei M, Fabrizio P, Jia H, Ge H, Cheng C, et al. (2008) Life Span Extension by Calorie Restriction Depends on Rim15 and Transcription Factors Downstream of Ras/PKA, Tor, and Sch9. PLoS Genet. 4(1): e13. doi:10.1371/journal.pgen.0040013
35. Cheng, C and Li, LM (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE. 2008 Apr 23;3(4):e1989.
36. Cheng C, Li LM, Alves P, Gerstein M. (2009) Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics.10:225.
37. Wei M, Fabrizio P, Madia F, Hu J, Ge H, Li LM, Longo VD. (2009) Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension, PLoS Genet. 2009 May; 5(5):e1000467. Epub 2009 May 8.
38. Kim JH, Kim W-C, Waterman MS, Park S, and Li LM (2009) HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome, Bioinformatics, btp399 [pii] 10.1093/bioinformatics/btp399
39. Ge, Huanying; Wei, Min; Fabrizio, Paola; Hu, Jia; Cheng, Chao; Longo, Valter; Li, Lei M (2010) Comparative analyses of time-course gene expression profiles of the long-lived sch9Δmutant，Nucleic Acids Research, doi:10.1093/nar/gkp849.
40. Lei M Li (2011) Accuracy Assessment of Consensus Sequence from Shotgun Sequencing, chapter in the book, “Handbook of Computational Statistics: Statistical Bioinformatics” edited by HS Lu and H Zhao, Springer, Chapter 1, Page 1-?.
41. Jong Hyun Kim, Woo-Cheol Kim, Lei M. Li and Sanghyun Park (2011), HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies Nucl. Acids Res. (2011) first published online May 16, 2011 doi:10.1093/nar/gkr354
42. Lei M. Li (to appear) DNA Sequencing and Commentary, in the book, “Selected Works of Terry Speed” edited by Sandrine Dudoit, Springer, Chapter 13.
43. 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).
44. Chen, S.J., Wang, A.Q. & Li, L.M. SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation. Journal of Computational Biology 20, 847-860 (2013).
45. Wang, L. et al. 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).
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