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Zhandong Liu Lab

Publications

Master
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2014

Content

[25] S. Yamamoto, M. Jaiswal, W.-L. Charng, T. Gambin, E. Karaca, G. Mirzaa, W. Wiszniewski, H. Sandoval, N. A. Haelterman, B. Xiong, K. Zhang, V. Bayat, G. David, T. Li, K. Chen, U. Gala, T. Harel, D. Pehlivan, S. Penney, L. E. L. M. Vissers, J. de Ligt, S. N. Jhangiani, Y. Xie, S. H. Tsang, Y. Parman, M. Sivaci, E. Battaloglu, D. Muzny, Y.-W. Wan, Z. Liu, A. T. Lin-Moore, R. D. Clark, C. J. Curry, N. Link, K. L. Schulze, E. Boerwinkle, W. B. Dobyns, R. Allikmets, R. A. Gibbs, R. Chen, J. R. Lupski, M. F. Wangler, and H. J. Bellen, “A Drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases.,” Cell, vol. 159, no. 1, pp. 200–214, Sep. 2014

[24] J. Ye, J. Fan, S. Venneti, Y.-W. Wan, B. R. Pawel, J. Zhang, L. W. S. Finley, C. Lu, T. Lindsten, J. Cross, G. Qing, Z. Liu, M. C. Simon, J. D. Rabinowitz, and C. B. Thompson, “Serine catabolism regulates mitochondrial redox control during hypoxia.,” Cancer Discov, Sep. 2014.

[23] E. Yang, Y. Baker, P. Ravikumar, G. I. Allen, Z. Liu, “Mixed Graphical Models via Exponential Families”, In Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, pp. 1042-1050. 2014. [pdf]

[22] Kaifang Pang; Ying-Wooi Wan; William T. Choi; Lawrence A. Donehower; Jingchun Sun; Dhruv Pant; Zhandong Liu, “Combinatorial Therapy Discovery using Mixed Integer Linear Programming”, Bioinformatics 2014; doi: 10.1093/bioinformatics/btu046 [pdf]

[21] Ying-Wooi Wan, Claire M. Mach, Genevera Allen, Matthew L. Anderson, and Zhandong Liu ” On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles” PLOS one 2014. [pdf]

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2013

Content

[20] Ying-Wooi Wan, John Nagorski, Genevera Allen, Zhaohui Li, Zhandong Liu “Identifying Cancer Biomarkers through a network regularized cox model,” IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2013. [pdf]

[19] Sangeetha Mahadevan, Shu Wen, Ying-Wooi Wan, Hsiu-Huei Peng, Subhendu Otta, Zhandong Liu, Michelina Iacovino, Elisabeth M. Mahen, Michael Kyba, Bekim Sadikovic, Ignatia B. Van den Veyver, “NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation”, Human Molecular Genetics, 2013. [pdf]

[18] E. Yang, P. Ravikumar, G. I. Allen, and Z. Liu, “On Poisson Graphical Models”, In Neural Information Processing Systems (NIPS), 2013. [pdf]

[17] E. Yang, P. Ravikumar, G. I. Allen, and Z. Liu, “Conditional Random Fields via Univariate Exponential Families”, In Neural Information Processing Systems (NIPS), 2013 [pdf]

[16] W. Zhang, W.Y. Wan, G. I. Allen, K. Pang, M. L. Anderson, and Z. Liu “Molecular pathway identification using biological network-regularized logistic models”, BMC Genomics, vol. 14, supp. 8, p. S7, 2013 [pdf]

[15] G. I. Allen and Z. Liu, “A Local Poisson Graphical Model for Inferring Genetic Networks from Next Generation Sequencing Data”, IEEE Transactions on NanoBioscience, 12:3, 1-10, 2013. [pdf]

[14] S. M. Hawkins, H. A. Loomans, Y.-W. Wan, T. Ghosh-Choudhury, D. Coffey, W. Xiao, Z. Liu, H. Sangi-Haghpeykar, and M. L. Anderson, “Expression and Functional Pathway Analysis of Nuclear Receptor NR2F2 in Ovarian Cancer.,” J. Clin. Endocrinol. Metab., May 2013.

[13] Y. Zhong, Y.-W. Wan, K. Pang, L. M. Chow, and Z. Liu, “Digital sorting of complex tissues for cell type-specific gene expression profiles.,” BMC Bioinformatics, vol. 14, no. 1, p. 89, Mar. 2013. [pdf]

[12] K. Han, V. A. Gennarino, Y. Lee, K. Pang, K. Hashimoto-Torii, S. Choufani, C. S. Raju, M. C. Oldham, R. Weksberg, P. Rakic, Z. Liu, and H. Y. Zoghbi, “Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p.,” Genes Dev., vol. 27, no. 5, pp. 485–490, Mar. 2013. [pdf]

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2012

Content

[11] Y. Zhong and Z. Liu, “Gene expression deconvolution in linear space.,” Nat. Methods, vol. 9, no. 1, pp. 8–9, Jan. 2012. [pdf]

[10] G. Allen and Z. Liu, “A Log-Linear Graphical Model for Inferring Genetic Networks from High-Throughput Sequencing Data,” The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), 2012. [pdf]

[9] E. Yang, P. K. Ravikumar, G. I. Allen, and Z. Liu, “Graphical Models via Generalized Linear Models,” NIPS, vol. 25, pp. 1367–1375, 2012. [pdf]

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Before 2011

Content

[8] G. B. W. Wertheim, T. W. Yang, T.-C. Pan, A. Ramne, Z. Liu, H. P. Gardner, K. D. Dugan, P. Kristel, B. Kreike, M. J. van de Vijver, R. D. Cardiff, C. Reynolds, and L. A. Chodosh, “The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis,” Proceedings of the National Academy of Sciences, vol. 106, no. 37, pp. 15855–15860, Jan. 2009. [pdf]

[7] A. V. Ivanova, S. V. Ivanov, L. Prudkin, D. Nonaka, Z. Liu, A. Tsao, I. Wistuba, J. Roth, and H. I. Pass, “Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects,” Mol. Cancer, vol. 8, p. 91, 2009. [pdf]

[6] Z. Liu, M. Wang, J. Alvarez, M. Bonney, C.-C. Chen, C. D’Cruz, T.-C. Pan, M. Tadesse, and L. Chodosh, “Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo,” Genome Biol., vol. 9, no. 12, p. R180, 2008. [pdf]

[5] Z. Liu, S. Venkatesh, and C. Maley, “Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples,” BMC Genomics, vol. 9, no. 1, p. 509, 2008. [pdf]

[4] H. I. Pass, D. Lott, F. Lonardo, M. Harbut, Z. Liu, N. Tang, M. Carbone, C. Webb, and A. Wali, “Asbestos exposure, pleural mesothelioma, and serum osteopontin levels.,” N. Engl. J. Med., vol. 353, no. 15, pp. 1564–1573, Oct. 2005. [pdf]

[3] S. A. Krawetz, S. Draghici, R. Goodrich, Z. Liu, and G. C. Ostermeier, “In silico and wet-bench identification of nuclear matrix attachment regions.,” Methods Mol. Med., vol. 108, pp. 439–458, 2005.

[2] H. I. Pass, Z. Liu, A. Wali, R. Bueno, S. Land, D. Lott, F. Siddiq, F. Lonardo, M. Carbone, and S. Draghici, “Gene expression profiles predict survival and progression of pleural mesothelioma.,” Clin. Cancer Res., vol. 10, no. 3, pp. 849–859, Feb. 2004. Featured Cover Article [pdf]

[1] G. C. Ostermeier, Z. Liu, R. P. Martins, R. R. Bharadwaj, J. Ellis, S. Draghici, and S. A. Krawetz, “Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR.,” Nucleic Acids Res., vol. 31, no. 12, pp. 3257–3266, Jun. 2003. [pdf]