Loading...

Publications

Home / Publications

2017


[39] Hyun-Hwan Jeong, Seon Young Kim, Maxime WC Rousseaux, Huda Y Zoghbi, Zhandong Liu. “CRISPRcloud: A secure cloud-based pipeline for CRISPR pooled screen deconvolution.” Bioinformatics. doi: 10.1093/bioinformatics/btx335

[38] Julia Wang, Rami Al-Ouran, Yanhui Hu, Seon-Young Kim, Ying-Wooi Wan, Michael F. Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Aram Comjean, Stephanie E. Mohr, UDN, Norbert Perrimon, Zhandong Liu, Hugo J. Bellen. “MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.” The American Journal of Human Genetics 100, 1–11, 2017 June 1. doi: 10.1016/j.ajhg.2017.04.010

[37] Haijing Jin, Ying-Wooi Wan, Zhandong Liu. “Comprehensive evaluation of RNA-seq quantification methods for linearity.” BMC Bioinformatics.

[36] Lu HC, Tan Q, Rousseaux MW, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. “Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans.” Nature Genetics, 2017 Mar 13. doi: 10.1038/ng.3808

2016


[35] Qiumin Tan, Hari Krishna Yalamanchili, Jeehye Park, Antonia De Maio, Hsiang-Chih Lu, Ying-Wooi Wan, Joshua J. White, Vitaliy V Bondar, Layal S. Sayegh, Xiuyun Liu, Yan Gao, Roy V. Sillitoe, Harry T. Orr, Zhandong Liu, and Huda Y. Zoghbi. “Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models.” Human molecular genetics, 2016.

[34] Veeraragavan S, Wan YW, Connolly DR, Hamilton SM, Ward CS, Soriano S1, Pitcher MR, McGraw CM, Huang SG, Green JR, Yuva LA, Liang AJ, Neul JL, Yasui DH, LaSalle JM, Liu Z, Paylor R, Samaco RC. “Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome.” Human molecular genetics, 2016.

[33] Yuan-Hung Lo, Eunah Chung, Zhaohui Li, Ying-Wooi Wan, Maxime M. Mahe, Min-Shan Chen, Taeko K. Noah, Kristin N. Bell, Hari Krishna Yalamanchili, Tiemo J. Klisch, Zhandong Liu, Joo-Seop Park, Noah F. Shroyer, “Transcriptional regulation by ATOH1 and its target SPDEF in the intestine”, Cellular and Molecular Gastroenterology and Hepatology, 2016.

[32] G. I. Allen, N. Amoroso, C. Anghel, V. Balagurusamy, C. J. Bare, D. Beaton, R. Bellotti, D. A. Bennett, K. Boehme, P. C. Boutros, L. Caberlotto, C. Caloian, F. Campbell, E. C. Neto, Y.-C. Chang, B. Chen, C.-Y. Chen, T.-Y. Chien, T. Clark, S. Das, C. Davatzikos, J. Deng, D. Dillenberger, R. J. Dobson, Q. Dong, J. Doshi, D. Duma, R. Errico, G. Erus, E. Everett, D. W. Fardo, S. H. Friend, H. Fröhlich, J. Gan, P. St George-Hyslop, S. S. Ghosh, E. Glaab, R. C. Green, Y. Guan, M.-Y. Hong, C. Huang, J. Hwang, J. Ibrahim, P. Inglese, Q. Jiang, Y. Katsumata, J. S. Kauwe, A. Klein, D. Kong, R. Krause, E. Lalonde, M. Lauria, E. Lee, X. Lin, Z. Liu, J. Livingstone, B. A. Logsdon, S. Lovestone, A. Lyappan, M. Ma, A. Malhotra, L. M. Mangravite, T. J. Maxwell, E. Merrill, J. Nagorski, A. Namasivayam, M. Narayan, M. Naz, S. J. Newhouse, T. C. Norman, R. N. Nurtdinov, Y.-J. Oyang, Y. Pawitan, S. Peng, M. A. Peters, S. R. Piccolo, P. Praveen, C. Priami, V. Y. Sabelnykova, P. Senger, X. Shen, A. Simmons, A. Sotiras, G. Stolovitzky, S. Tangaro, A. Tateo, Y.-A. Tung, N. J. Tustison, E. Varol, G. Vradenburg, M. W. Weiner, G. Xiao, L. Xie, Y. Xie, J. Xu, H. Yang, X. Zhan, Y. Zhou, F. Zhu, H. Zhu, S. Zhu, Alzheimer’s Disease Neuroimaging Initiative, “Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease.,” Alzheimers Dement, Apr. 2016.

2015


[31]       Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Zhandong Liu. XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data. BMC Systems Biology.

[30]       Sztainberg Y, Chen HM, Swann JW, Hao S, Tang B, Wu Z, Tang J, Wan YW, Liu Z, Rigo F, Zoghbi HY. Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides. Nature. 2015 Nov 25. doi: 10.1038/nature16159

[29]       Ying-Wooi Wan, Genevera I. Allen and Zhandong Liu, “TCGA2STAT: Simple TCGA Data Access for Integrated Statistical Analysis in R”, Bioinformatics (2015) doi: 10.1093/bioinformatics/btv677.

[28]     Su-Yeon Choi, Kaifang Pang, Joo Yeon Kim, Jae Ryun Ryu, Hyojin Kang, Zhandong Liu, Won-Ki Kim, Woong Sun, Hyun Kim and Kihoon Han, “Post-transcriptional regulation of SHANK3 expression by microRNAs related to multiple neuropsychiatric disorders” Molecular Brain 20158:74.

[27]     Adekunle M. Adesina,  Bethany L. Veo, Girard Courteau, Vidya Mehta, Xuli Wu, Kaifang Pang, Zhandong Liu, Xiao-Nan Li, Lori Peters, “FOXG1 expression shows correlation with neuronal differentiation in cerebellar development, aggressive phenotype in medulloblastomas, and survival in a xenograft model of medulloblastoma”, Human Pathology,  2015.

[26]       Eunho Yang, Pradeep Ravikumar, Genevera Allen and Zhandong Liu. “Graphical Models via Univariate Exponential Family Distributions”, Journal of Machine Learning Research 16 (2015) 3813-3847.

 2014


[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] Highlighted by

2013


[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]

2012


[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]

Before 2011


[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]