PUBLICATION
- Fan K, Tang S, Gökbağ B, Cheng L, Li L. Multi-view graph convolutional network for cancer cell-specific synthetic lethality prediction. Front Genet. 2023 Jan 9;13:1103092. doi: 10.3389/fgene.2022.1103092. PMID: 36699450; PMCID: PMC9868610.
- Tang S, Gökbağ B, Fan K, Shao S, Huo Y, Wu X, Cheng L, Li L. Synthetic lethal gene pairs: Experimental approaches and predictive models. Front Genet. 2022 Dec 1;13:961611. doi: 10.3389/fgene.2022.961611. PMID: 36531238; PMCID: PMC9751344.
- Li J, Huo Y, Wu X, Liu E, Zeng Z, Tian Z, Fan K, Stover D, Cheng L, Li L. Essentiality and Transcriptome-Enriched Pathway Scores Predict Drug-Combination Synergy. Biology (Basel). 2020 Sep 7;9(9):278. doi: 10.3390/biology9090278. PMID: 32906805; PMCID: PMC7565142.
- Liu E, Wu X, Wang L, Huo Y, Wu H, Li L, Cheng L. DSCN: Double-target selection guided by CRISPR screening and network. PLoS Comput Biol. 2022 Aug 19;18(8):e1009421. doi: 10.1371/journal.pcbi.1009421. PMID: 35984840; PMCID: PMC9578612.
- Tang S, Wu X, Liu J, Zhang Q, Wang X, Shao S, Gokbag B, Fan K, Liu X, Li F, Cheng L, Li L. Generation of dual-gRNA library for combinatorial CRISPR screening of synthetic lethal gene pairs. STAR Protoc. 2022 Aug 24;3(3):101556. doi: 10.1016/j.xpro.2022.101556. PMID: 36060092; PMCID: PMC9428847.
- Zhao Y, Yu L, Wu X, Li H, Coombes KR, Au KF, Cheng L, Li L. CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression. Bioinformatics. 2022 Nov 30;38(23):5245-5252. doi: 10.1093/bioinformatics/btac668. PMID: 36250792; PMCID: PMC9710553.
- Yazdanparast A, Li L, Zhang C, Cheng L. Bi-EB: Empirical Bayesian Biclustering for Multi-Omics Data Integration Pattern Identification among Species. Genes (Basel). 2022 Oct 30;13(11):1982. doi: 10.3390/genes13111982. PMID: 36360219; PMCID: PMC9690013.
- Cheng L, Karkhanis P, Gokbag B, Liu Y, Li L. DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data. PLoS Comput Biol. 2022 Apr 11;18(4):e1008885. doi: 10.1371/journal.pcbi.1008885. PMID: 35404970; PMCID: PMC9060369.
- Liu E, Li J, Kinnebrew GH, Zhang P, Zhang Y, Cheng L, Li L. A Fast and Furious Bayesian Network and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1325-1335. doi: 10.1109/TCBB.2019.2944826. Epub 2021 Aug 6. PMID: 31581091.
- Teng M, Wang Y, Kim S, Li L, Shen C, Wang G, Liu Y, Huang TH, Nephew KP, Balch C. Empirical bayes model comparisons for differential methylation analysis. Comp Funct Genomics. 2012;2012:376706. doi: 10.1155/2012/376706. Epub 2012 Aug 22. PMID: 22956892; PMCID: PMC3432337.
- Mourad R, Li L, Cuvier O. Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach. PLoS Comput Biol. 2017 May 23;13(5):e1005538. doi: 10.1371/journal.pcbi.1005538. PMID: 28542178; PMCID: PMC5462476.
- Wu HY, Zheng P, Jiang G, Liu Y, Nephew KP, Huang TH, Li L. A modulator based regulatory network for ERα signaling pathway. BMC Genomics. 2012;13 Suppl 6(Suppl 6):S6. doi: 10.1186/1471-2164-13-S6-S6. Epub 2012 Oct 26. PMID: 23134758; PMCID: PMC3481450.
- Shen C, Huang Y, Liu Y, Wang G, Zhao Y, Wang Z, Teng M, Wang Y, Flockhart DA, Skaar TC, Yan P, Nephew KP, Huang TH, Li L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst Biol. 2011 May 9;5:67. doi: 10.1186/1752-0509-5-67. PMID: 21554733; PMCID: PMC3117732.
- Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP. A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. Bioinformatics. 2006 Sep 15;22(18):2210-6. doi: 10.1093/bioinformatics/btl329. Epub 2006 Jun 29. PMID: 16809387.
- Li L, Shi H, Yiannoutsos C, Huang TH, Nephew KP. Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. J Comput Biol. 2005 Apr;12(3):370-90. doi: 10.1089/cmb.2005.12.370. PMID: 15857248.
- Feng W, Liu Y, Wu J, Nephew KP, Huang TH, Li L. A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology. BMC Genomics. 2008 Sep 16;9 Suppl 2(Suppl 2):S23. doi: 10.1186/1471-2164-9-S2-S23. PMID: 18831789; PMCID: PMC2559888.