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Yunlong Liu, Ph.D.

Associate Professor of Medical and Molecular Genetics
Adjunct Associate Professor of Medicine (Biostatistics) and of Informatics
Center for Computational Biology and Bioinformatics
Center for Medical Genomics

Lab Website: http://compbio.iupui.edu/group/6/pages/about_us

CCBB Website: http://compbio.iupui.edu/people/details/10

  • 1992-1996: B.Eng. in Control theories, Harbin Engineering University, Harbin, China
  • 1996-1999: M.Eng. in Control theories, Tsinghua University, Beijing, China
  • 2001-2004: Ph.D. in Biomedical Engineering, Purdue University, West Lafayette
  • 2004-2006: Postdoctoral fellow in Biochemistry, Indiana University School of Medicine

Research Introduction

The Liu Laboratory (Laboratory for Computational Genomics) uses systems biology approaches to understand regulatory mechanisms of gene expression, including transcriptional regulation, post-transcriptional regulation, and epigenetic regulation. This area involves several interdisciplinary components, including functional genomics, genetics, computational and statistical modeling, computer science/engineering, and data management.
Detailed research information can be found: http://compbio.iupui.edu/liu/Research

Publications

Zhang X., Dangaiah D., Muson RS Jr., Spinola SM, and Liu Y., Correcting imbalanced reads coverage in a bacterial transcriptome sequencing with extreme deep coverage, in press

Zhang X., Dangaiah D., Muson RS Jr., Spinola SM, and Liu Y., Correcting imbalanced reads coverage in a bacterial transcriptome sequencing with extreme deep coverage, in press

Radovich, M., Clare, SE., Atale, R., Pardo, I., Hancock, BA., Solzak, JP., Kassem, N., Mathieson, T., Storniolo, AM., Rufenbarger, C., Lillemoe, HA., Blosser, RJ., Choi, MR., Sauder, CA., Doxey, D., Henry, JE., Hilligoss, EE., Sakarya, O., Hyland, FC., Hickenbotham, M., Zhu, J., Glasscock, J., Badve, S., Ivan, M., Liu, Y., Sledge, GW., Schneider, BP. Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing. Breast Cancer Res. Treat. 2014 Jan;143(1):57-68

Gangaiah, D., Labandeira-Rey, M., Zhang, X., Fortney, KR., Ellinger, S., Zwickl, B., Baker, B., Liu, Y., Janowicz, DM., Katz, BP., Brautigam, CA., Munson, RS., Hansen, EJ., Spinola, SM. Haemophilus ducreyi Hfq contributes to virulence gene regulation as cells enter stationary phase. MBio 2014;5(1):e01081-13

Todd, AG., Lin, H., Ebert, AD., Liu, Y., Androphy, EJ. COPI transport complexes bind to specific RNAs in neuronal cells. Hum. Mol. Genet. 2013 Feb 15;22(4):729-36

Wang, G., Qi, K., Zhao, Y., Li, Y., Juan, L., Teng, M., Li, L., Liu, Y., Wang, Y. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Med Genomics 2013;6 Suppl 1:S5

Juan, L., Wang, G., Radovich, M., Schneider, BP., Clare, SE., Wang, Y., Liu, Y. Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genomics 2013;6 Suppl 1:S7

Breese, MR., Liu, Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics 2013 Feb 15;29(4):494-6

Zhao, H., Yang, Y., Lin, H., Zhang, X., Mort, M., Cooper, DN., Liu, Y., Zhou, Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol. 2013 Mar 13;14(3):R23

Kelly, KJ., Liu, Y., Zhang, J., Goswami, C., Lin, H., Dominguez, JH. Comprehensive genomic profiling in diabetic nephropathy reveals the predominance of proinflammatory pathways. Physiol. Genomics 2013 Aug 15;45(16):710-9

Gangaiah, D., Zhang, X., Fortney, KR., Baker, B., Liu, Y., Munson, RS., Spinola, SM. Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. J. Bacteriol. 2013 Aug;195(15):3486-502

Jiang, G., Chakraborty, A., Wang, Z., Boustani, M., Liu, Y., Skaar, T., Li, L. New aQTL SNPs for the CYP2D6 identified by a novel mediation analysis of genome-wide SNP arrays, gene expression arrays, and CYP2D6 activity. Biomed Res Int 2013;2013:493019

Hsu, PY., Hsu, HK., Lan, X., Juan, L., Yan, PS., Labanowska, J., Heerema, N., Hsiao, TH., Chiu, YC., Chen, Y., Liu, Y., Li, L., Li, R., Thompson, IM., Nephew, KP., Sharp, ZD., Kirma, NB., Jin, VX., Huang, TH. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell 2013 Aug 12;24(2):197-212

Ramamoorthy, A., Liu, Y., Philips, S., Desta, Z., Lin, H., Goswami, C., Gaedigk, A., Li, L., Flockhart, DA., Skaar, TC. Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab. Dispos. 2013 Oct;41(10):1763-8

Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

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