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Structural and Computational Biology and Molecular Biophysics

Houston, Texas

A BCM research lab.
Structural and Computational Biology & Molecular Biophysics
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Zhandong Liu, Ph.D.

Zhandong Liu, Ph.D.Assistant Professor


Ph.D. - Cancer Biology and Genomics - University of Pennsylvania, Philadelphia PA
Postdoctoral Fellowship - Cancer Biology and Genomics - University of Pennsylvania, Philadelphia PA

Membership in Professional Organizations

Member - International Society of Computational Biology

Research Interests

Dr. Zhandong Liu develops bioinformatics approaches for analyzing high-throughput biological data produced by gene expression arrays, RNA-seq and genomic sequencing. His work integrates multiple data types in the interest of advancing our understanding of neurological diseases.Consider the case of genome-wide expression data, which can provide important snapshots of differences between normal and pathological cellular processes. Yet the hope of being able to assess the activation status of a particular signaling pathway or transcriptional network using only gene expression data remains an elusive goal. Dr. Liu developed a graphical random walk (GRW)-based algorithm that can accurately predict pathway activity from microarray gene expression data. GRW uses gene-gene interaction data to construct a pathway signature in a manner analogous to particle-particle interactions described by Coulomb’s law. By comparing GRW to other standard approaches, he has demonstrated that GRW can sensitively and specifically predict pathway activity across tissues, species, and platforms.The Liu lab’s long-term goal is to develop computational models and algorithms in areas of genomics and computational biology. These tools will allow us to better understand the etiology of neurological diseases from computational and systems biology perspectives.

Recent Publications

  • Hawkins SM, Loomans HA, Wan YW, Ghosh-Choudhury T, Coffey D, Xiao W, Liu Z, Sangi-Haghpeykar H and Anderson ML. Expression and Functional Pathway Analysis of Nuclear Receptor NR2F2 in Ovarian Cancer. J Clin Endorinol Metab, [Epub ahead of print] (2013. PubMed
  • Zhong Y, Wan YW, Pang K, Chow LM and Liu Z. Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics, 14:89 (2013). PubMed
  • Han K, Gennarino VA, Lee Y, Pang K, Hashimoto-Torri K, Choufani S, Raju CS, Oldham MC, Weksberg R, Rakic P, Liu Z and Zoghbi HY. Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p. Genes Dev, 27(5):485-90 (2013). PubMed
  • Ivanova A, Ivanov S, Prudkin L, Nonaka D, Liu Z, Tsao A, Wistuba I, Roth J and Pass I. Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects. Molecular Cancer, 8:91 (2009). PubMed
  • Wertheim G, Yang T, Pan T, Ramne A, Liu Z, Gardner H, The snf1-Related Kinase, Hunk, is Essential for Mammary Tumor Metastasis. Proc Natl Acad Sci, 106(37):15855-60 (2009). PubMed
  • Liu Z, Venkatesh S and Maley C. Sequence Space Coverage, Entropy of Genomes and the Potential to Detect Non-Human DNA in Human Samples. BMC Genomics, 9(1):509.3 (2008). PubMed
  • Liu Z, Wang M, Alavrez J, Bonney M, Chen CC, D'Cruz C, Pan TC, Tadesse MG and Chodosh LA. SVD regression identifies cross talk between Ras and TGF signaling in vivo. Genome Biology, 9(12):R180 (2008).

For more publications, see listing on PubMed.

Contact Information:

Department: Pediatrics-Neurology
Address: The Jan and Duncan Neurological Research Institute
1250 Moursund St. Suite NR-1350, RM 1365.08
Houston, TX 77030
Phone: 832-824-8878
Fax: 832-825-1251

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