Our lab is interested in solving statistical and algorithmic problems in computational biology. The beauty of this exciting area lies on the fact that it has a direct impact in the real world and statistics and algorithms really matter in data mining here. In addition, the biological problems challenge the current statistical and algorithmic methods and provide a great opportunity to advance and create novel computational methods. We were one of the international groups funded by NIH to develop technology for the ENCODE projects. Currently, our lab is focusing on the following classification and data integration problems:  gene transcriptional regulation especially distal gene regulation, and Metagenomics.

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Recent Publications

  1. Wang Y, Hu H, Li X. rRNAFilter: a fast approach for ribosomal RNA read removal without a reference database. Journal of Computational Biology, 2016;
  2. Zhao C, Li X, Hu H. PETModule: a motif module based approach for enhancer target gene prediction. Scientific Reports . 2016; 6: 30043.
  3. Wang Y, Hu H, Li X. MBMC: An Effective Markov Chain Approach for Binning Metagenomic Reads from Environmental Shotgun Sequencing Projects. OMICS: A Journal of Integrative Biology. 2016; 20 (8): 470-479.
  4. Li X, Hu H, Li X. Integrative analyses shed new light on human ribosomal protein gene regulation. Scientific Reports. 2016; 6:28619.
  5. Ding J, Li X, Hu H. TarPmiR: a new approach for microRNA target site prediction. Bioinformatics. doi: 10.1093/bioinformatics/btw318. 2016.
  6. Dhillon V, Li X. Transcription factors STAT6 and KLF4 implement macrophage polarization via the dual catalytic powers of MCPIP. Journal of Computer Science & Systems Biology. 2015; 194(12):6011-6023.
  7. Kapoor N, Niu J, Saad Y, Kumar S, Sirakova T, Becerra E, Li,X, Kolattukudy, PE. Single-Cell Genome Sequencing for Viral-Host Interactions. Journal of Computer Science & Systems Biology. 2015; 8:160-165.
  8. Wang Y, Hu H, Li X. MBBC: an efficient approach for metagenomic binning based on clustering. BMC Bioinformatics. 2015; 16(1):1.
  9. Zheng Y, Li X, Hu H. PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. Database. 2015; bav007.
  10. Ding J, Dhillon V, Li X, Hu H. Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS. Methods. 2015; 79: 47-51.
  11. Ding J, Li X, Hu H. MicroRNA modules prefer to bind weak and unconventional target sites. Bioinformatics. 2015; 31(9): 1366-1374.
  12. Zheng Y, Li X, Hu H. Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. Nucleic Acids Research. 2014; doi: 10.1093/nar/gku1261.
  13. Zheng Y, Li X, Hu H. Computational discovery of feature patterns in nucleosomal DNA sequences. Genomics. 2014; 104(2):87-95
  14. Wang Y, Li X, Hu H. H3K4me2 reliably defines transcription factor binding regions. Genomics. 2014; 103(2-3):222-228.
  15. Ding J, Hu H, Li X. SIOMICS: a Novel Approach for Systematic Identification of Motifs in ChIP-seq Data . Nucleic Acids Research. 2014; 42(5): e35.
  16. Ding J, Hu H, Li X. NIM, A novel computational method for predicting nuclear-encoded chloroplast proteins. Journal of Medical and Bioengineering. 2013; 2(2): 115-119.
  17. Ding J, Cai X, Wang Y, Hu H, Li X. ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data. Pac Symp Biocomput. 2013.
  18. Ding J, Li X, Hu H. Systematic Identification of cis-regulatory elements in Chlamydomonas reinhardtii genome using comparative genomics . Plant Physiology. 2012;160(2):613-23.
  19. Wang Y, Ding J, Daniell H, Hu H, Li X. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins . Plant Molecular Biology. 2012;80(2):177-87.
  20. Ruppert SM, Chehtane M, Zhang G, Hu H, Li X, Khaled AR. JunD/AP-1-Mediated Gene Expression Promotes Lymphocyte Growth Dependent on Interleukin-7 Signal Transduction. . Plos One. 2012;7(2):e32262.
  21. Ding J, Hu H, Li X. Thousands of cis-regulatory sequences are shared by Arabidopsis and populus. Plant Physiology. 2012;158(1):145-55. Epub 2011 Nov 4.
  22. Wang Y, Li X, Hu H. Transcriptional regulation of co-expressed microRNA targt genes. Genomics. 2011;98(6):445-52.
  23. Balakrishnan MP, Cilenti L, Ambivero C, Goto Y, Takata M, Turkson J, Li XS, Zervos AS. THAP5 is a DNA binding transcriptional repressor that is regulated in melanoma cells during DNA damage-induced cell death. Biochem Biophys Res Commun. 2011; 404(1):195-200.
  24. Schanen BC, Li X. Transcriptional regulation of mammalian miRNA genes. Genomics. 2011; 97(1):1-6.
  25. Cai X, Hou L, Su N, Hu H, Deng M, Li X. Systematic identification of conserved motif modules in the human genome. BMC Genomics. 2010; 11:567. Database. Software.
  26. Hu H, Li X. Transcription factor binding site identification by phylogenetic footprinting. Book Chapter in Frontiers in Computational and Systems Biology, 113-132, 2010.
  27. Hu H, Li X. Whole genome identification of target genes of transcription factors. The 2010 International Conference On Bioinformatics and Biomedical Technology, Chengdu, China. April 16-18, 2010.
  28. Hu H, Li X. Hierarchical order of gene expression levels . The 2010 International Conference On Bioinformatics and Biomedical Technology, Chengdu, China. April 16-18, 2010.
  29. Cai X, Hu H, Li X. A new measurement of sequence conservation. BMC Genomics. 2009; 10:623
  30. Sadat MA, Dirscherl S, …, Li X, Grez M, Cornetta K, Mooney SD, Dinauer MC. Retroviral vector integration in post-transplant hematopoiesis in mice conditioned with either submyeloablative or ablative irradiation . Gene Ther. 2009; 16:1452-1464.
  31. Ma X, Zhang K, Li X. Evolution of Drosophila Ribosomal Protein Gene Core Promoters. Gene. 2009; 432(2):54-59.
  32. Hu J, Hu H, Li X. MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res. 2008; 36(13):4488-97. Unix version download, cygwin version download, Windows version download.
  33. Peters B, Dirscherl S, Dantzer J, Nowacki J, Cross S, Li X, Cornetta K, Dinauer MC, Mooney SD. Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource .Gene Ther. 2008; 15(18):1294-8.
  34. Georgiadis MM, Luo M, Gaur RK, Delaplane S, Li X, Kelley MR. Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease . Mutat Res. 2008; 643(1-2):54-63.
  35. Hu H, Li X. Networking pathways unveils association between obesity and non-insulin dependent diabetes mellitus . Pac Symp Biocomput. 2008; 13:255-66.

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