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2018


[57] Maxime W.C. Rousseaux, Gabriel E. Vázquez-Vélez, Ismael Al-Ramahi, Hyun-Hwan Jeong, Aleksandar Bajic, Jean-Pierre Revelli, Hui Ye, Emily T. Phan, Jennifer M. Deger, Alma M. Perez, Ji-Yoen Kim, Laura A. Lavery, Qikia Xu, Mamie Z. Li, Hyojin Kang, Jean J. Kim, Joshua M. Shulman, Thomas F. Westbrook, Stephen J. Elledge, Zhandong Liu, Juan Botas, Huda Y. Zoghbi. “A druggable genome screen identifies modifiers of α-synuclein levels via a tiered cross-species validation approach.” Journal of Neuroscience. doi:10.1523/JNEUROSCI.0254-18.2018

[56] Heidi Martini-Stoica, Allysa L. Cole, Daniel B. Swartzlander, Fading Chen, Ying-Wooi Wan, Lakshya Bajaj, David A. Bader,Virginia M.Y. Lee, John Q. Trojanowski, Zhandong Liu, Marco Sardiello, Hui Zheng. “TFEB enhances astroglial uptake of extracellular tau species and reduces tau spreading.” Journal of Experiment Medicine. doi:10.1084/jem.20172158

[55] Ayush T. Raman, Amy E. Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E. Lowry, Huda Y. Zoghbi, Zhandong Liu. “Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.” Nature Communications. doi:10.1038/s41467-018-05627-1

[54] Ismael Al-Ramahi, Boxun Lu, Simone Di Paola, Kaifang Pang, Maria de Haro, Ivana Peluso, Tatiana Gallego-Flores, Nazish T. Malik, Kelly Erikson, Benjamin A. Bleiberg, Matthew Avalos, George Fan, Laura Elizabeth Rivers, Andrew M. Laitman, Javier R. Diaz-García, Marc Hild, James Palacino, Zhandong Liu, Diego L. Medina, Juan Botas. “High-Throughput Functional Analysis Distinguishes Pathogenic, Nonpathogenic, and Compensatory Transcriptional Changes in Neurodegeneration.” Cell Systems. doi:10.1016/j.cels.2018.05.010

[53] Caiwei Guo, Hyun-Hwan Jeong, Yi-Chen Hsieh, Hans-Ulrich Klein, David A. Bennett, Philip L. De Jager, Zhandong Liu, and Joshua M. Shulman. “Tau Activates Transposable Elements in Alzheimer’s Disease.” Cell Reports. doi:10.1016/j.celrep.2018.05.004

[52] Aya Ito-Ishida, Hari Krishna Yamalanchili, Yingyao Shao, Steven A. Baker, Laura D. Heckman, Laura A. Lavery, Ji-yoen Kim, Laura M. Lombardi, Yaling Sun, Zhandong Liu & Huda Y. Zoghbi. “Genome-wide distribution of linker histone H1.0 is independent of MeCP2.” Nature Neuroscience. doi:10.1038/s41593-018-0155-8

[51] Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu,Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu,Zhandong Liu, Yaoyang Zhang, Rui Liu, Zheng-Jiang Zhu, Nan Liu. “Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila.” eLIFE. doi:10.7554/eLife.35368

[50] Amy E. Pohodich, Hari Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi. “Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity.” eLIFE. doi:10.7554/eLife.34031

[49] Maxime W.C. Rousseaux, Tyler Tschumperlin, Hsiang-Chih Lu11, Elizabeth P. Lackey, Vitaliy V. Bondar, Ying-Wooi Wan, Qiumin Tan, Carolyn J. Adamski, Jillian Friedrich, Kirk Twaroski, Weili Chen, Jakub Tolar, Christine Henzler, Ajay Sharma, Aleksandar Bajić, Tao Lin, Lisa Duvick, Zhandong Liu, Roy V. Sillitoe, Huda Y. Zoghbi, Harry T. Orr. “ATXN1-CIC Complex Is the Primary Driver of Cerebellar Pathology in Spinocerebellar Ataxia Type 1 through a Gain-of-Function Mechanism.” Neuron. doi:10.1016/j.neuron.2018.02.013

[48] Qiumin Tan, Lorenzo Brunetti, Maxime W. C. Rousseaux, Hsiang-Chih Lu, Ying-Wooi Wan, Jean-Pierre Revelli, Zhandong Liu, Margaret A. Goodell, Huda Y. Zoghbi. “Loss of Capicua alters early T cell development and predisposes mice to T cell lymphoblastic leukemia/lymphoma.” PNAS. doi:10.1073/pnas.1716452115

[47] Jiani Yin, Wu Chen, Eugene S. Chao, Sirena Soriano, Li Wang, Wei Wang, Steven E. Cummock, Huifang Tao, Kaifang Pang, Zhandong Liu, Fred A. Pereira, Rodney C. Samaco, Huda Y. Zoghbi, Mingshan Xue, Christian P. Schaaf. “Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome.” The American Journal of Human Genetics. doi:10.1016/j.ajhg.2018.01.005

[46] Cynthia K. McClard, Mikhail Y. Kochukov, Isabella Herman, Zhandong Liu, Aiden Eblimit, Yalda Moayedi, Joshua Ortiz-Guzman, Daniel Colchado, Brandon Pekarek, Sugi Panneerselvam, Graeme Mardon and Benjamin R. Arenkiel. “POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain.” The Journal of Neuroscience. doi:10.1523/JNEUROSCI.1641-17.2017

[45] Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data.” Biocomputing 2018. doi: 10.1142/9789813235533_0016

2017


[44] Qiankun Dong, Chao Liu, Tao Li, Zhandong Liu. “PIM: Parallelization of Ising Model for Genomics Data.” Big Data Computing and Communications (BIGCOM), doi:10.1109/BIGCOM.2017.41

[43] Haidong Yi, Ayush T Raman, Han Zhang, Genevera I Allen, Zhandong Liu. “Detecting hidden batch factors through data adaptive adjustment for biological effects.” Bioinformatics. doi: 10.1093/bioinformatics/btx635

[42] Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu. “Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing.” Current Protocols in Bioinformatics. doi:10.1002/cpbi.33

[41] Xue Jiang, Han Zhang, Xiongwen Quan, Zhandong Liu, Yanbin Yin. “Disease-related gene module detection based on a multi-label propagation clustering algorithm.” PLoS ONE. doi: 0.1371/journal.pone.0178006

[40] Meaghan A. Delaney, Ying-Wooi Wan, Gyoung-Eun Kim, Chad J. Creighton, Margaret G Taylor, Ramya Masand, Andrew Park, Cecilia Valdes, William Gibbons, Zhandong Liu, Matthew L. Anderson. “A Role for Progesterone-Regulated sFRP4 Expression in Uterine Leiomyomas.” J Clin Endocrinol Metab 2017 jc.2016-4014. doi: 10.1210/jc.2016-4014

[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. doi: 10.1186/s12859-017-1526-y

[36] Hsiang-Chih Lu, Qiumin Tan, Maxime W C Rousseaux, Wei Wang, Ji-Yoen Kim, Ronald Richman, Ying-Wooi Wan, Szu-Ying Yeh, Jay M Patel, Xiuyun Liu, Tao Lin, Yoontae Lee, John D Fryer, Jing Han, Maria Chahrour, Richard H Finnell, Yunping Lei, Maria E Zurita-Jimenez, Priyanka Ahimaz, Kwame Anyane-Yeboa, Lionel Van Maldergem, Daphne Lehalle, Nolwenn Jean-Marcais, Anne-Laure Mosca-Boidron, Julien Thevenon, Margot A Cousin, Della E Bro, Brendan C Lanpher, Eric W Klee, Nora Alexander, Matthew N Bainbridge, Harry T Orr, Roy V Sillitoe, M Cecilia Ljungberg, Zhandong Liu, Christian P Schaaf, Huda Y Zoghbi. “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, 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]