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Yue Lu, Ph.D.

Present Title & Affiliation

Primary Appointment

Assistant Professor, Dept. of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX

Research Interests

My primary research interest is the design and application of bioinformatics approaches to deciphering biological mechanisms using next-generation sequencing technologies.  It includes two major parts:

The first is the collaborative research with wet laboratories to address important biological problems.  I have been in collaboration with many labs in and outside MD Anderson in the past several years.  In general, most of the projects can be included in the large topic "characterization of genomic, transcriptomic and epigenomic changes in cancer".  Specifically, we use exome/targeted high-throughput sequencing for genomic variations (single nucleotide variation, small indels, etc.), RNA-Seq for transcriptome alterations (differential expression, novel transcript identification, etc.), methylation-sequencing (DREAM, bisulfite-sequencing, MeDIP-Seq) for DNA methylation, ChIP-Seq for DNA-binding proteins (nuclear lamina, transcription factors, epigenetic modifiers, etc.) and histone modifications, and then integrate these data to elucidating important molecular mechanisms in cancer development and progression.

The second is the development and implementation of novel computational algorithms. In collaboration with other bioinformaticians, we developed novel methods for, e.g. improvement of  the accuracy of RNA-seq, statistical model for the relation of histone marks, sequence error correction and prediction of imprinted genes from deep sequencing. The recent specific topics I'm interested in include: (1) Distribution pattern of epigenetic marks and its effect on biological processes; (2) Bias correction in various NGS technologies; (3) Precise identification of large blocks in ChIP-Seq; and (4) Intra- and inter- platform biological data integration.

From my graduate studies, I'm also very interested in algorithm development of multiple protein sequence alignment.

Office Address


Education & Training

Degree-Granting Education

2008 Texas A&M University, College Station, TX, PHD, Biochemistry
2002 Peking University, Beijing, China, BS, Cell Biology & Genetics

Selected Publications

Peer-Reviewed Original Research Articles

1. Gururaj AE, Gibson L, Panchabhai S, Bai M, Manyam G, Lu Y, Latha K, Rojas ML, Hwang Y, Liang S, Bogler O. Access to the Nucleus and Functional Association with c-Myc Is Required for the Full Oncogenic Potential of ?EGFR/EGFRvIII. J Biol Chem 288(5):3428-38, 2/2013. e-Pub 12/2012. PMCID: PMC3561561.
2. Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res 23(2):312-22, 2/2013. e-Pub 11/2/2012. PMCID: PMC3561872.
3. Yamazaki J, Estecio MR, Lu Y, Long H, Malouf GG, Graber D, Huo Y, Ramagli L, Liang S, Kornblau SM, Jelinek J, Issa JP. The epigenome of AML stem and progenitor cells. Epigenetics 8(1):92-104, 1/2013. e-Pub 12/2012. PMCID: PMC3549884.
4. Jelinek J, Liang S, Lu Y, He R, Ramagli LS, Shpall EJ, Estecio MR, Issa JP. Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. Epigenetics 7(12):1368-78, 12/2012. e-Pub 10/2012. PMCID: PMC3528692.
5. Estecio MR, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa JP. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res 10(10):1332-42, 10/2012. e-Pub 9/2012. PMCID: PMC3475755.
6. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet 44(1):23-31, 1/2012. e-Pub 12/2011. PMCID: PMC3637952.
7. Cai G, Li H, Lu Y, Huang X, Lee J, Müller P, Ji Y, Liang S. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics 13 Suppl 13:S5, 2012. e-Pub 8/24/2012. PMCID: PMC3426807.
8. Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S. BM-BC: a Bayesian method of base calling for Solexa sequence data. BMC Bioinformatics 13 Suppl 13:S6, 2012. e-Pub 8/24/2012. PMCID: PMC3426806.
9. Li H, Su X, Gallegos J, Lu Y, Ji Y, Molldrem JJ, Liang S. dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. BMC Bioinformatics 13:271, 2012. e-Pub 10/2012. PMCID: PMC3497615.
10. Tonthat NK, Arold ST, Pickering BF, Van Dyke MW, Liang S, Lu Y, Beuria TK, Margolin W, Schumacher MA. Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. EMBO J 30(1):154-64, 1/2011. e-Pub 11/2010. PMCID: PMC3020112.
11. Jelinek J, Gharibyan V, Estecio MR, Kondo K, He R, Chung W, Lu Y, Zhang N, Liang S, Kantarjian HM, Cortes JE, Issa JP. Aberrant DNA methylation is associated with disease progression, resistance to imatinib and shortened survival in chronic myelogenous leukemia. PLoS One 6(7):e22110, 2011. e-Pub 7/2011. PMCID: PMC3132778.
12. Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT. TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell 40(6):1016-23, 12/2010. PMCID: PMC3090733.
13. Lu Y, Sze SH. Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res 37(2):463-72, 2/2009. e-Pub 12/2008. PMCID: PMC2632924.
14. Lu Y, Sze SH. Multiple sequence alignment based on profile alignment of intermediate sequences. J Comput Biol 15(7):767-77, 9/2008. PMID: 18662101.
15. Lu Y and Sze SH. Multiple sequence alignment based on profile alignment of intermediate sequences. Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB'2007), Lecture Notes in Bioinformatics 4453:283-295, 2007.
16. Sze SH, Lu Y, Yang Q. A polynomial time solvable formulation of multiple sequence alignment. J Comput Biol 13(2):309-19, 3/2006. PMID: 16597242.
17. Sze SH, Lu Y and Yang Q. A polynomial time solvable formulation of multiple sequence alignment. Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB'2005), Lecture Notes in Bioinformatics 3500:204-216, 2005.
Other Articles
1. Liang S, Lu Y, Jelinek J, Estecio M, Li H, Issa JP. Analysis of epigenetic modifications by next generation sequencing. Conf Proc IEEE Eng Med Biol Soc. 2009:6730, 2009.

Last updated: 7/2/2014