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2021


[98] Weijie Zhang, Igor L Bado, Jingyuan Hu, Ying-Wooi Wan, Ling Wu, Hai Wang, Yang Gao, Hyun-Hwan Jeong, Zhan Xu, Xiaoxin Hao, Bree M Lege, Rami Al-Ouran, Lucian Li, Jiasong Li, Liqun Yu, Swarnima Singh, Hin Ching Lo, Muchun Niu, Jun Liu, Weiyu Jiang, Yi Li, Stephen TC Wong, Chonghui Cheng, Zhandong Liu, Xiang H-F Zhang. “The bone microenvironment invigorates metastatic seeds for further dissemination.” Cell. doi: 10.1016/j.cell.2021.03.011

[97] Yingyao Shao, Yehezkel Sztainberg, Qi Wang, Sameer S Bajikar, Alexander J Trostle, Ying-Wooi Wan, Paymaan Jafar-Nejad, Frank Rigo, Zhandong Liu, Jianrong Tang, Huda Y Zoghbi. “Antisense oligonucleotide therapy in a humanized mouse model of MECP2 duplication syndrome.” Science Translational Medicine. doi: 10.1126/scitranslmed.aaz7785

[96] Francesca Clementina Radio, Kaifang Pang, Andrea Ciolfi, Michael A. Levy, Andrés Hernández-García, Lucia Pedace, Francesca Pantaleoni, Zhandong Liu, Elke de Boer, Adam Jackson, Alessandro Bruselles, Haley McConkey, Emilia Stellacci, Stefania Lo Cicero, Marialetizia Motta, Rosalba Carrozzo, Maria Lisa Dentici, Kirsty McWalter, Megha Desai, Kristin G. Monaghan, Aida Telegrafi, Christophe Philippe, Antonio Vitobello, Margaret Au, Katheryn Grand, Pedro A. Sanchez-Lara, Joanne Baez, Kristin Lindstrom, Peggy Kulch, Jessica Sebastian, Suneeta Madan-Khetarpal, Chelsea Roadhouse, Jennifer J. MacKenzie, Berrin Monteleone, Carol J. Saunders, July K. Jean Cuevas, Laura Cross, Dihong Zhou, Taila Hartley, Sarah L. Sawyer, Fabíola Paoli Monteiro, Tania Vertemati Secches, Fernando Kok, Laura E. Schultz-Rogers, Erica L. Macke, Eva Morava, Eric W. Klee, Jennifer Kemppainen, Maria Iascone, Angelo Selicorni, Romano Tenconi, David J. Amor, Lynn Pais, Lyndon Gallacher, Peter D. Turnpenny, Karen Stals, Sian Ellard, Sara Cabet, Gaetan Lesca, Joset Pascal, Katharina Steindl, Sarit Ravid, Karin Weiss, Alison M.R. Castle, Melissa T. Carter, Louisa Kalsner, Bert B.A. de Vries, Bregje W. van Bon, Marijke R. Wevers, Rolph Pfundt, Alexander P.A. Stegmann, Bronwyn Kerr, Helen M. Kingston, Kate E. Chandler, Willow Sheehan, Abdallah F. Elias, Deepali N. Shinde, Meghan C. Towne, Nathaniel H. Robin, Dana Goodloe, Adeline Vanderver, Omar Sherbini, Krista Bluske, R. Tanner Hagelstrom, Caterina Zanus, Flavio Faletra, Luciana Musante, Evangeline C. Kurtz-Nelson, Rachel K. Earl, Britt-Marie Anderlid, Gilles Morin, Marjon van Slegtenhorst, Karin E.M. Diderich, Alice S. Brooks, Joost Gribnau, Ruben G. Boers, Teresa Robert Finestra, Lauren B. Carter, Anita Rauch, Paolo Gasparini, Kym M. Boycott, Tahsin Stefan Barakat, John M. Graham Jr., Laurence Faivre, Siddharth Banka, Tianyun Wang, Evan E. Eichler, Manuela Priolo, Bruno Dallapiccola, Lisenka E.L.M. Vissers
Bekim Sadikovic, Daryl A. Scott, Jimmy Lloyd Holder Jr., Marco Tartaglia. “SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.” American Journal of Human Genetics. doi: 10.1016/j.ajhg.2021.01.015

[95] Tarik Seref Onur, Andrew Laitman, He Zhao, Ryan Keyho, Hyemin Kim, Jennifer Wang, Megan Mair, Huilan Wang, Lifang Li, Alma Perez, Maria de Haro, Ying-Wooi Wan, Genevera Allen, Boxun Lu, Ismael Al-Ramahi, Zhandong Liu, Juan Botas. “Downregulation of glial genes involved in synaptic function mitigates Huntington’s disease pathogenesis.” eLife. doi: 10.7554/eLife.64564

[94] Larissa Nitschke, Stephanie L Coffin, Eder Xhako, Dany B El-Najjar, James P Orengo, Elizabeth Alcala, Yanwan Dai, Ying-Wooi Wan, Zhandong Liu, Harry T Orr, Huda Y Zoghbi. “Modulation of ATXN1 S776 phosphorylation reveals the importance of allele-specific targeting in SCA1.” JCI Insight. doi: 10.1172/jci.insight.144955

[93] Won‐Seok Lee, Laura Lavery, Maxime WC Rousseaux, Eric B Rutledge, Youjin Jang, Ying‐Wooi Wan, Sih‐Rong Wu, Wonho Kim, Ismael Al‐Ramahi, Smruti Rath, Carolyn J Adamski, Vitaliy V Bondar, Ambika Tewari, Shirin Soleimani, Samantha Mota, Hari K Yalamanchili, Harry T Orr, Zhandong Liu, Juan Botas, Huda Y Zoghbi. “Dual targeting of brain region‐specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1.” EMBO Journal. doi: 10.15252/embj.2020106106

[92] Haijing Jin, Zhandong Liu. “A benchmark for RNA-seq deconvolution analysis under dynamic testing environments.” Genome Biology. doi : 10.1186/s13059-021-02290-6

[91] Weijie Zhang, Igor L Bado, Jingyuan Hu, Ying-Wooi Wan, Ling Wu, Hai Wang, Yang Gao, Hyun-Hwan Jeong, Zhan Xu, Xiaoxin Hao, Bree M Lege, Rami Al-Ouran, Lucian Li, Jiasong Li, Liqun Yu, Swarnima Singh, Hin Ching Lo, Muchun Niu, Jun Liu, Weiyu Jiang, Yi Li, Stephen TC Wong, Chonghui Cheng, Zhandong Liu, Xiang H-F Zhang. ” The bone microenvironment invigorates metastatic seeds for further dissemination.” Developmental Cell. doi: 10.1016/j.cell.2021.03.011

2020


[90] Li Wang, Kaifang Pang, Kihoon Han, Carolyn J Adamski, Wei Wang, Lingjie He, Jason K Lai, Vitaliy V Bondar, Joseph G Duman, Ronald Richman, Kimberley F Tolias, Patrick Barth, Timothy Palzkill, Zhandong Liu, J Lloyd Holder, Huda Y Zoghbi. “An autism-linked missense mutation in SHANK3 reveals the modularity of Shank3 function.” Molecular psychiatry. doi: 10.1038/s41380-018-0324-x

[89] Solveig K Sieberts, Thanneer M Perumal, Minerva M Carrasquillo, Mariet Allen, Joseph S Reddy, Gabriel E Hoffman, Kristen K Dang, John Calley, Philip J Ebert, James Eddy, Xue Wang, Anna K Greenwood, Sara Mostafavi, CommonMind Consortium (CMC); The AMP-AD Consortium; Larsson Omberg, Mette A Peters, Benjamin A Logsdon, Philip L De Jager, Nilüfer Ertekin-Taner, Lara M Mangravite. “Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions. Scientific Data. doi: 10.1038/s41597-020-00642-8

[88] Li Wang, Carolyn J Adamski, Vitaliy V Bondar, Evelyn Craigen, John R Collette, Kaifang Pang, Kihoon Han, Antrix Jain, Sung Y Jung, Zhandong Liu, Richard N Sifers, J Lloyd Holder, Huda Y Zoghbi. “A kinome-wide RNAi screen identifies ERK2 as a druggable regulator of Shank3 stability”. Molecular Psychiatry. doi: 10.1038/s41380-018-0325-9

[87] Larissa Nitschke, Ambika Tewari, Stephanie L Coffin, Eder Xhako, Kaifang Pang, Vincenzo A Gennarino, Jennifer L Johnson, Francisco A Blanco, Zhandong Liu, Huda Y Zoghbi. “miR760 regulates ATXN1 levels via interaction with its 5′ untranslated region.” Genes & development. doi: 10.1101/gad.339317.120

[86] Russell Li, Zhandong Liu. “Stress detection using deep neural networks.” BMC Medical Informatics and Decision Making. doi: 10.1186/s12911-020-01299-4

[85] Chun-An Chen, Wei Wang, Steen E Pedersen, Ayush Raman, Michelle L Seymour, Fernanda R Ruiz, Anping Xia, Meike E van der Heijden, Li Wang, Jiani Yin, Joanna Lopez, Megan E Rech, Richard A Lewis, Samuel M Wu, Zhandong Liu, Fred A Pereira, Robia G Pautler, Huda Y Zoghbi, Christian P Schaaf. “Nr2f1 heterozygous knockout mice recapitulate neurological phenotypes of Bosch-Boonstra-Schaaf optic atrophy syndrome and show impaired hippocampal synaptic plasticity.” Human Molecular Genetics. doi: 10.1093/hmg/ddz233

[84] Ying-Wooi Wan, Rami Al-Ouran, Carl G. Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek M. Philip, Gareth R. Howell, Heidi Martini-Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping-Chieh Pao, Li-Huei Tsai, Jean-Vianney Haure-Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen D. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuss, Ayla Ergun, Phillip J. Ebert, David C. Airey, Sara Mostafavi, Lei Yu, Hans-Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Allan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric Schadt, Philip L. {De Jager}, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Joshua M. Shulman, Lara M. Mangravite, Benjamin A. Logsdon. “Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.” Cell Reports. doi: 10.1016/j.celrep.2020.107908

[83] Kaifang Pang, Li Wang, Wei Wang, Jian Zhou, Chao Cheng, Kihoon Han, Huda Y. Zoghbi, Zhandong Liu. “Co-expression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders.” Genome Research. doi: 10.1101/gr.254987.119

[82] Jingyuan Hu, Rami Al-Ouran, Xiang Zhang, Zhandong Liu, Hyun-Hwan Jeong “TraceQC: An R package for quality control of CRISPR lineage tracing data.” BioRxiv. doi: 10.1101/2020.06.05.137141

[81] Hari Krishna Yalamanchili, Callison E Alcott, Ping Ji, Eric J Wagner, Huda Y Zoghbi, Zhandong Liu. “PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3′ Seq data using vector projections and non-negative matrix factorization.” Nucleic Acid Research. doi: 10.1093/nar/gkaa398

[80] Xiao Wang, Haidong Yi, Jia Wang, Zhandong Liu, Yanbin Yin, Han Zhang. “GDASC: A GPU parallel based web server for detecting hidden batch factors.” Bioinformatics. doi: 10.1093/bioinformatics/btaa427!

[79] Hyundoo Jeong and Zhandong Liu. “PRIME: a probabilistic imputation method to reduce dropout effects in single cell RNA sequencing.” Bioinformaitcs. doi: 10.1093/bioinformatics/btaa278

[78] Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander Saltzman, Nathan Elrod, Ai Lin, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J Wagner, Zhandong Liu, Huda Y Zoghbi. “Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation.” eLIFE. doi: 10.7554/eLife.50895

[77] Laura A Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, Joanna Lopez, Jacinta Lucero, Mark A Durham, Rosa Castanon, Joseph R Nery, Zhandong Liu, Margaret Goodell, Joseph R Ecker, M Margarita Behrens, Huda Y Zoghbi. “Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome.” eLIFE. doi: 10.7554/eLife.52981

[76] Carl Grant Mangleburg, Timothy Wu, Hari K. Yalamanchili, Caiwei Guo, Yi-Chen Hsieh, Duc M. Duong, Eric B. Dammer, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Joshua M. Shulman. “Integrated analysis of the aging brain transcriptome and proteome in tauopathy.” BioRxiv. doi: 10.1101/2020.02.19.954578

[75] Tiana M. Scott Hui Guo Evan E. Eichler Jill A. Rosenfeld Kaifang Pang Zhandong Liu Seema Lalani Weimin Bi Yaping Yang Carlos A. Bacino Haley Streff Andrea M. Lewis Mary K. Koenig Isabelle Thiffault Allison Bellomo David B. Everman Julie R. Jones Roger E. Stevenson Raphael Bernier Christian Gilissen Rolph Pfundt Susan M. Hiatt Gregory M. Cooper Jimmy L. Holder Daryl A. Scott. “BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder.” Human Mutation. doi:10.1002/humu.23992

[74] Jidong Liu, Guolian Ding, Kexin Zou, Ziru Jiang, Junyu Zhang, Yunhua Lu, Antonella Pignata, Eric Venner, Pengfei Liu, Zhandong Liu, Michael F. Wangler, Zheng Sun. “Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia.” Molecular Genetics & Genomic Medicine. doi: 10.1002/mgg3.1130

[73] Ethan R.Roy, Baiping Wang, Ying-Wooi Wan, Gabriel S. Chiu, Allysa L. Cole, Zhuoran Yin, Nicholas E. Propson, Yin Xu, Joanna L. Jankowsky, Zhandong Liu, Virginia M.-Y. Lee, John Q. Trojanowski, Stephen D. Ginsberg, Oleg Butovsky, Hui Zheng, and Wei Cao. “Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease.” The Journal of Clinical Investigation. doi:10.1172/JCI133737

2019


[72] Hyun-Hwan Jeong and Zhandong Liu. “Are HHV-6A and HHV-7 really more abundant in Alzheimer’s disease?.” Neuron 104, no. 6 (2019): 1034-1035. doi:10.1016/j.neuron.2019.11.009

[71] Yi-Chen Hsieh, Caiwei Guo, Hari K. Yalamanchili, Measho Abreha, Rami Al-Ouran, Yarong Li, Eric B. Dammer, James J. Lah, Allan I. Levey, David A. Bennett, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Joshua M. Shulman, “Tau-Mediated Disruption of the Spliceosome Triggers Cryptic RNA Splicing and Neurodegeneration in Alzheimer’s Disease.”” Cell Reports 29:2 (2019) doi:10.1016/j.celrep.2019.08.104

[70] Chun-An Chen, Wei Wang, Steen E. Pedersen, Ayush Raman, Michelle L. Seymour, Fernanda R. Ruiz, Anping Xia et al. “Nr2f1 heterozygous knockout mice recapitulate neurological phenotypes of Bosch-Boonstra-Schaaf optic atrophy syndrome and show impaired hippocampal synaptic plasticity.” Human molecular genetics (2019). doi:10.1093/hmg/ddz233

[69] Rami Al-Ouran, Ying-Wooi Wan, Carl Grant Mangleburg, Tom V. Lee, Katherine Allison, Joshua M. Shulman, and Zhandong Liu. “A portal to visualize transcriptome profiles in mouse models of neurological disorders.” Genes 10, no. 10 (2019): 759. doi:10.3390/genes10100759

[68] Julia Wang, Zhandong Liu, Hugo J. Bellen, and Shinya Yamamoto. “Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information.” Journal of visualized experiments: JoVE 150 (2019). doi:10.3791/59542

[67] Julia Wang, Dongxue Mao, Fatima Fazal, Seon‐Young Kim, Shinya Yamamoto, Hugo Bellen, and Zhandong Liu. “Using MARRVEL v1. 2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity.” Current protocols in bioinformatics 67, no. 1 (2019): e85. doi:10.1002/cpbi.85

[66] Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu. “Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives.” Genome Research. doi: 10.1101/gr.245571.118

[65] Li Wang, Carolyn J. Adamski, Vitaliy V. Bondar, Evelyn Craigen, John R. Collette, Kaifang Pang, Kihoon Han, Antrix Jain, Sung Y. Jung, Zhandong Liu, Richard N. Sifers, J. Lloyd Holder Jr., Huda Y. Zoghbi. “A kinome-wide RNAi screen identifies ERK2 as a druggable regulator of Shank3 stability.” Molecular Psychiatry. doi:10.1038/s41380-018-0325-9

[64] Wenjun Zhou, Yanlin He, Atteeq U Rehman, Yan Kong, Sungguan Hong, Guolian Ding, Hari Krishna Yalamanchili, Ying-Wooi Wan, Basil Paul, Chuhan Wang, Yingyun Gong, Wenxian Zhou, Hao Liu, John Dean, Emmanuel Scalais, Mary O’Driscoll, Jenny E. V Morton, DDD study, Xinguo Hou, Qi Wu, Qingchun Tong, Zhandong Liu, Pengfei Liu, Yong Xu, Zheng Sun. “Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus–CA3 projection.” Nature Neuroscience. doi:10.1038/s41593-018-0311-1

[63] Benjamin A. Logsdon, Thanneer M. Perumal, Vivek Swarup, Minghui Wang, Cory Funk, Chris Gaiteri, Mariet Allen, Xue Wang, Eric Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen D. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuss, Ayla Ergun, Phillip J Ebert, David C. Airey, Gregory W. Carter, Sara Mostafavi, Lei Yu, Hans-Ulrich Klein, the AMP-AD Consortium, David A. Collier, Todd Golde, Allan Levey, David A. Bennett, Karol Estrada, Michael Decker, Zhandong Liu, Joshua M. Shulman, Bin Zhang, Eric Schadt, Phillip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Lara M. Mangravite. “Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach.” BioRxiv. doi:10.1101/510420

[62] Ying-Wooi Wan, Rami Al-Ouran, Carl Grant Mangleburg, Tom V. Lee, Katherine Allison, Sarah Neuner, Catherine Kaczorowski, Vivek Phillip, Gareth Howell, Heidi Martini-Stoica, Hui Zheng, Jungwoo Wren Kim, Valina Dawson, Ted Dawson, Ping-Chieh Pao, Li-Huei Tsai, Jean-Vianney Haure-Mirande, Minghui Wang, Michelle E. Ehrlich, Hongkang Mei, Xiaoyan Zhong, Paramita Chakrabarty, Yona Levites, Todd E. Golde, Allan I. Levey, Accelerating Medicines Partnership-Alzheimer’s Disease Consortium, Benjamin Logsdon, Lara Mangravite, Zhandong Liu, Joshua M. Shulman “Functional dissection of Alzheimer’s disease brain gene expression signatures in humans and mouse models.” BioRxiv. doi:10.1101/506873

[61] Li Wang, Kaifang Pang, Kihoon Han, Carolyn J. Adamski, Wei Wang, Lingjie He, Jason K. Lai, Vitaliy V Bondar, Joseph G. Duman, Ronald Richman, Kimberley F. Tolias, Patrick Barth, Timothy Palzkill, Zhandong Liu, J. Lloyd Holder Jr., Huda Y. Zoghbi. “An autism-linked missense mutation in SHANK3 reveals the modularity of Shank3 function.” Molecular Psychiatry. doi:10.1038/s41380-018-0324-x

2018


[60] William T. Choi, Mehmet Tosun, Hyun-Hwan Jeong, Cemal Karakas, Fatih Semerci, Zhandong LiuEmail author and Mirjana Maletić-Savatić. “Metabolomics of mammalian brain reveals regional differences.” BMC Systems Biology. doi:10.1186/s12918-018-0644-0

[59] Alexandra Litvinchuk, Ying-Wooi Wan, Dan B. Swartzlander, Fading Chen, Allysa Cole, Nicholas E. Propson, Qian Wang, Bin Zhang, Zhandong Liu, Hui Zheng. “Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer’s Disease.” Neuron. doi:10.1016/j.neuron.2018.10.031

[58] Antonia De Maio, Hari Krishna Yalamanchili, Carolyn J. Adamski, Vincenzo A. Gennarino, Zhandong Liu, Jun Qin, Sung Y. Jung, Ronald Richman, Harry Orr, Huda Y. Zoghbi. “RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins.” Cell Reports. doi:10.1016/j.celrep.2018.09.041

[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]