Research Achievements
A comprehensive collection of our academic publications, intellectual property, and collective honors.
Published Papers
Improving Physics-Informed Neural Network Extrapolation via Transfer Learning and Adaptive Activation Functions
Athanasios Papastathopoulos-Katsaros, Alexandra Stavrianidi, Zhandong Liu
Artificial Neural Networks and Machine Learning – ICANN 2025 · 2026
Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis
Sameer S. Bajikar, Jian Zhou, Ryan O’Hara, Harini P. Tirumala, Mark A. Durham, Alexander J. Trostle, Michelle Dias, Yingyao Shao, Hu Chen, Wei Wang, Hari Krishna Yalamanchili, Ying-Wooi Wan, Laura A. Banaszynski, Zhandong Liu, Huda Y. Zoghbi
Neuron · 2025
Lemur: A Single-Cell Foundation Model with Fine-Tuning-Free Hierarchical Cell-Type Generation for \textitDrosophila melanogaster
Jorge Botas, Johnathan Jia, Sasidhar Pasupuleti, Hu Chen, Xia Hu, Zhaozhuo Xu, Zhandong Liu
Unknown Venue · 2025
MYC-Targeting PROTACs Lead to Bimodal Degradation and N-Terminal Truncation
Shelton R. Boyd, Srinivas Chamakuri, Alexander J. Trostle, Hu Chen, Zhandong Liu, Antrix Jian, Jian Wang, Anna Malovannaya, Damian W. Young
ACS Chemical Biology · 2025
Computationally resolved neuroprogenitor cell biomarkers associate with human disorders
Gerarda Cappuccio, William T. Choi, Fatih Semerci, Jill A. Rosenfeld, Toni Claire Tacorda, Guantong Qi, Anthony W. Zoghbi, Yi Zhong, Hu Chen, Pengfei Liu, Zhandong Liu, Mirjana Maletić-Savatić
Stem Cell Reports · 2025
Revealing the nervous system requirements of Alzheimer disease risk genes in Drosophila
Jennifer M. Deger, Shabab B. Hannan, Mingxue Gu, Colleen E. Strohlein, Lindsey D. Goodman, Sasidhar Pasupuleti, Zahid Shaik, Liwen Ma, Yarong Li, Jiayang Li, Morgan C. Stephens, Michal Tyrlík, Zhandong Liu, Ismael Al-Ramahi, Juan Botas, Chad A. Shaw, Oguz Kanca, Hugo J. Bellen, Joshua M. Shulman
The American Journal of Human Genetics · 2025
MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery
Zachary Everton, Jorge Botas, Seon Young Kim, Zhandong Liu, Hyun-Hwan Jeong
Unknown Venue · 2025
ConSol: Sequential Probability Ratio Testing to Find Consistent LLM Reasoning Paths Efficiently
Jaeyeon Lee, Guantong Qi, Matthew Brady Neeley, Zhandong Liu, Hyun-Hwan Jeong
arXiv · 2025
LA-MARRVEL: A Knowledge-Grounded and Language-Aware LLM Reranker for AI-MARRVEL in Rare Disease Diagnosis
Jaeyeon Lee, Hyun-Hwan Jeong, Zhandong Liu
arXiv · 2025
Early transcriptional signatures of MeCP2 positive and negative cells in Rett syndrome
Yan Li, Ashley G. Anderson, Guangtong Qi, Sih-Rong Wu, Jean-Pierre Revelli, Zhandong Liu, Huda Y. Zoghbi
Unknown Venue · 2025
Multi‐omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model
Xin Li, Chaozhong Liu, Wenbo Li, Guantong Qi, Yanwan Dai, Chaohao Gu, Yuxiang Sun, Wenjun Zhou, Veronica C. Ciliberto, Jing Liang, Udhaya Kumar S, Dongyin Guan, Zhaoyong Hu, Hui Zheng, Zhandong Liu, Hu Chen, Ying‐Wooi Wan, Zheng Sun
Alzheimer's \& Dementia · 2025
Genomic Medicine for Alzheimer’s Disease (P3-3.012)
Joshua M. Shulman, Ismael Al-Ramahi, Juan Botas, Fatima Chavez, Kelly Erikson Carter, Sarah H. Elsea, Michelle Etoundi, Jamie C. Fong, Andrea Franco, Mohammed Hamdan, Jianhong Hu, George R. Jackson, Tom V. Lee, Olivier Lichtarge, Chi-Ying R. Lin, Zhandong Liu, Valerie Lozano, Mirjana Maletic-Savatic, Janet Malek, Nicole Matute, Amy L. McGuire, Luis D. Medina, Donna Muzny, Maria B. Pascual, Valory Pavlik, Christine B. Rizk, Jill Robinson, Hiba Saade, Chad Shaw, Hadley Smith, Jonathan Sober, Juan B. Toledo, Nora Vanegas-Arroyave, Eric Venner, Kimberly Walker, Melissa Yu, Bo Yuan, Huda Zoghbi, Joseph Masdeu
Neurology · 2025
MetaboLINK is a novel algorithm for unveiling cell-specific metabolic pathways in longitudinal datasets
Jared Lichtarge, Gerarda Cappuccio, Soumya Pati, Alfred Kwabena Dei-Ampeh, Senghong Sing, LiHua Ma, Zhandong Liu, Mirjana Maletic-Savatic
Frontiers in Neuroscience · 2025
Survey and Improvement Strategies for Gene Prioritization with Large Language Models
Matthew Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu
arXiv · 2025
Modeling antisense oligonucleotide therapy in \textitMECP2 duplication syndrome human iPSC-derived neurons reveals gene expression programs responsive to MeCP2 levels
Sameer S Bajikar, Yehezkel Sztainberg, Alexander J Trostle, Harini P Tirumala, Ying-Wooi Wan, Caroline L Harrop, Jesse D Bengtsson, Claudia M B Carvalho, Davut Pehlivan, Bernhard Suter, Jeffrey L Neul, Zhandong Liu, Paymaan Jafar-Nejad, Frank Rigo, Huda Y Zoghbi
Human Molecular Genetics · 2024
Comparative Analysis of AAV Serotypes for Transduction of Olfactory Sensory Neurons
Benjamin D.W. Belfort, Johnathan D. Jia, Alexandra Garza, Anthony M. Insalaco, Jp McGinnis, Brandon T. Pekarek, Joshua Ortiz-Guzman, Burak Tepe, Hu Chen, aSCENT-PD Investigators, Zhandong Liu, Benjamin R. Arenkiel
Unknown Venue · 2024
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon
Angelica Maria Delgado-Vega, Helene Cederroth, Fulya Taylan, Katja Ekholm, Marlene Ek, Håkan Thonberg, Anders Jemt, Daniel Nilsson, Jesper Eisfeldt, Kristine Bilgrav Saether, Ida Höijer, Ozlem Akgun-Dogan, Yui Asano, Tahsin Stefan Barakat, Dominyka Batkovskyte, Gareth Baynam, Olaf Bodamer, Wanna Chetruengchai, Pádraic Corcoran, Madeline Couse, Daniel Danis, German Demidov, Eisuke Dohi, Mattias Erhardsson, Luis Fernandez-Luna, Toyofumi Fujiwara, Neha Garg, Roberto Giugliani, Claudia Gonzaga-Jauregui, Giedre Grigelioniene, Tudor Groza, Cecilia Gunnarsson, Anna Hammarsjö, Charles Kumi Hammond, Özden Hatirnaz Ng, Sirisha Hesketh, Dineshani Hettiarachchi, Maria Johansson Soller, Umn Ahmed Kirmani, Martin Kjellberg, Malin Kvarnung, Oleg Kvlividze, Kristina Lagerstedt-Robinson, Paul Lasko, Timo Lassmann, Lynette Y. S. Lau, Steven Laurie, Weng Khong Lim, Zhandong Liu, Mariya Lysenkova Wiklander, Prince Makay, Alassane Baneye Maiga, Carolina Maya-González, M. Stephen Meyn, Ramprasad Neethiraj, Vincenzo Nigro, Felix Nordgren, Jessica Nordlund, Sara Orrsjö, Jesper Ottosson, Ugur Ozbek, Özkan Özdemir, Clyde Partin, David A. Pearce, Raquel Peck, Annie Pedersen, Maria Pettersson, Monnat Pongpanich, Manuel Posada De La Paz, Arun Ramani, Juan Andres Romero, Vanessa I. Romero, Richard Rosenquist, Aung Min Saw, Matthew Spencer, Eva-Lena Stattin, Chalurmpon Srichomthong, Isabel Tapia-Paez, Domenica Taruscio, Julie P. Taylor, Tinatin Tkemaladze, Ian Tully, Zeynep Tümer, Wendy A. G. Van Zelst-Stams, Alain Verloes, Emma Västerviga, Sailan Wang, Rachel Yang, Shinya Yamamoto, Vicente A. Yépez, Qing Zhang, Vorasuk Shotelersuk, Samuel Agyei Wiafe, Yasemin Alanay, Lorenzo D. Botto, Salman Kirmani, Aimé Lumaka, Elizabeth Emma Palmer, Ratna Dua Puri, Valtteri Wirta, Anna Lindstrand, Orion J. Buske, Mikk Cederroth, Ann Nordgren
Nature Genetics · 2024
A network regularized linear model to infer spatial expression pattern for single cell
Chaohao Gu, Hu Chen, Zhandong Liu
Unknown Venue · 2024
PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data
Venkata Soumith Jonnakuti, Eric J Wagner, Mirjana Maletić-Savatić, Zhandong Liu, Hari Krishna Yalamanchili
Cell Reports Methods · 2024
\textlessspan style="font-variant:small-caps;"\textgreaterMATR3\textless/span\textgreater pathogenic variants differentially impair its cryptic splicing repression function
Mashiat Khan, Xiao Xiao Lily Chen, Michelle Dias, Jhune Rizsan Santos, Sukhleen Kour, Justin You, Rebekah Van Bruggen, Mohieldin M. M. Youssef, Ying‐Wooi Wan, Zhandong Liu, Jill A. Rosenfeld, Qiumin Tan, Udai Bhan Pandey, Hari Krishna Yalamanchili, Jeehye Park
FEBS Letters · 2024
Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer’s mouse model
Xin Li, Chaozhong Liu, Wenbo Li, Yanwan Dai, Chaohao Gu, Wenjun Zhou, Veronica C. Ciliberto, Jing Liang, Udhaya Kumar. S, Dongyin Guan, Zhaoyong Hu, Hui Zheng, Hu Chen, Zhandong Liu, Ying-Wooi Wan, Zheng Sun
Unknown Venue · 2024
The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing
Shenglan Li, Sen Zhao, Jefferson C. Sinson, Aleksandar Bajic, Jill A. Rosenfeld, Matthew B. Neeley, Mezthly Pena, Kim C. Worley, Lindsay C. Burrage, Monika Weisz-Hubshman, Shamika Ketkar, William J. Craigen, Gary D. Clark, Seema Lalani, Carlos A. Bacino, Keren Machol, Hsiao-Tuan Chao, Lorraine Potocki, Lisa Emrick, Jennifer Sheppard, My T.T. Nguyen, Anahita Khoramnia, Paula Patricia Hernandez, Sandesh Cs. Nagamani, Zhandong Liu, Christine M. Eng, Brendan Lee, Pengfei Liu
The American Journal of Human Genetics · 2024
Quantification and visualization of \textitcis -regulatory dynamics in single-cell multi-omics data with TREASMO
Chaozhong Liu, Linhua Wang, Zhandong Liu
NAR Genomics and Bioinformatics · 2024
AI-MARRVEL — A Knowledge-Driven AI System for Diagnosing Mendelian Disorders
Dongxue Mao, Chaozhong Liu, Linhua Wang, Rami AI-Ouran, Cole Deisseroth, Sasidhar Pasupuleti, Seon Young Kim, Lucian Li, Jill A. Rosenfeld, Linyan Meng, Lindsay C. Burrage, Michael F. Wangler, Shinya Yamamoto, * , Michael Santana, Victor Perez, Priyank Shukla, Christine M. Eng, Brendan Lee, Bo Yuan, Fan Xia, Hugo J. Bellen, Pengfei Liu, Zhandong Liu
NEJM AI · 2024
Survey and improvement strategies for gene prioritization with large language models
Matthew B Neeley, Guantong Qi, Guanchu Wang, Ruixiang Tang, Dongxue Mao, Chaozhong Liu, Sasidhar Pasupuleti, Bo Yuan, Fan Xia, Pengfei Liu, Zhandong Liu, Xia Hu
Bioinformatics Advances · 2024
Improving access to exome sequencing in a medically underserved population through the Texome Project
Blake Vuocolo, Ryan J. German, Seema R. Lalani, Chaya N. Murali, Carlos A. Bacino, Stephanie Baskin, Rebecca Littlejohn, John D. Odom, Scott McLean, Carrie Schmid
Genetics in Medicine · 2024
P495: Improving access to exome sequencing in medically underserved populations through the Texome Project: A summary of the first 74 cases
Blake Vuocolo, Ryan German, Carlos Bacino, Chaya Murali, Seema Lalani, Stephanie Baskin, Elizabeth Roeder, Carrie Schmid, Scott McLean, Rebecca Littlejohn
Genetics in Medicine Open · 2024
Assessing and Enhancing Large Language Models in Rare Disease Question-answering
Guanchu Wang, Junhao Ran, Ruixiang Tang, Chia-Yuan Chang, Yu-Neng Chuang, Zirui Liu, Vladimir Braverman, Zhandong Liu, Xia Hu
arXiv · 2024
CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model
Jiasheng Wang, Ying-Wooi Wan, Rami Al-Ouran, Meichen Huang, Zhandong Liu
Briefings in Bioinformatics · 2024
Systems genetic dissection of Alzheimer’s disease brain gene expression networks
Pinghan Zhao, Omar El Fadel, Anh Le, Carl Grant Mangleburg, Justin Dhindsa, Timothy Wu, Jinghan Zhao, Meichen Huang, Bismark Amoh, Aditi Sai Marella, Yarong Li, Nicholas T. Seyfried, Allan I. Levey, Zhandong Liu, Ismael Al-Ramahi, Juan Botas, Joshua M Shulman
Unknown Venue · 2024
Loss of the Maternal Effect Gene Nlrp2 Alters the Transcriptome of Ovulated Mouse Oocytes and Impacts Expression of Histone Demethylase KDM1B
Zahra Anvar, Imen Chakchouk, Momal Sharif, Sangeetha Mahadevan, Eleni Theodora Nasiotis, Li Su, Zhandong Liu, Ying-Wooi Wan, Ignatia B. Van Den Veyver
Reproductive Sciences · 2023
MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function
Sameer S Bajikar, Ashley G Anderson, Jian Zhou, Mark A Durham, Alexander J Trostle, Ying-Wooi Wan, Zhandong Liu, Huda Y Zoghbi
Elife · 2023
Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1
Stephanie L Coffin, Mark A Durham, Larissa Nitschke, Eder Xhako, Amanda M Brown, Jean-Pierre Revelli, Esmeralda Villavicencio Gonzalez, Tao Lin, Hillary P Handler, Yanwan Dai
Neuron · 2023
Literature-based predictions of Mendelian disease therapies
Cole A Deisseroth, Won-Seok Lee, Jiyoen Kim, Hyun-Hwan Jeong, Ryan S Dhindsa, Julia Wang, Huda Y Zoghbi, Zhandong Liu
The American Journal of Human Genetics · 2023
SPA-STOCSY: An Automated Tool for Identification of Annotated and Non-Annotated Metabolites in High-Throughput NMR Spectra
Xu Han, Wanli Wang, Li-Hua Ma, Ismael Al-Ramahi, Juan Botas, Kevin MacKenzie, Genevera I Allen, Damian W Young, Zhandong Liu, Mirjana Maletic-Savatic
bioRxiv · 2023
PolyAMiner-Bulk: a machine learning based bioinformatics algorithm to infer and decode alternative polyadenylation dynamics from bulk RNA-seq data
Venkata Soumith Jonnakuti, Eric J Wagner, Mirjana Maletić-Savatić, Zhandong Liu, Hari Krishna Yalamanchili
bioRxiv · 2023
Evolutionarily conserved regulators of tau identify targets for new therapies
Jiyoen Kim, Maria de Haro, Ismael Al-Ramahi, Lorena Laura Garaicoechea, Hyun-Hwan Jeong, Jun Young Sonn, Bakhos Tadros, Zhandong Liu, Juan Botas, Huda Yahya Zoghbi
Neuron · 2023
scGREAT: Graph-based regulatory element analysis tool for single-cell multi-omics data
Chaozhong Liu, Linhua Wang, Zhandong Liu
bioRxiv · 2023
Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss
Chaozhong Liu, Linhua Wang, Zhandong Liu
BMC Bioinformatics · 2023
A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics
Alexander J Trostle, Lucian Li, Seon-Young Kim, Jiasheng Wang, Rami Al-Ouran, Hari Krishna Yalamanchili, Zhandong Liu, Ying-Wooi Wan
International Journal of Molecular Sciences · 2023
NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples
Wanli Wang, Li-Hua Ma, Mirjana Maletic-Savatic, Zhandong Liu
bioRxiv · 2023
Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
Linhua Wang, Chaozhong Liu, Yang Gao, Xiang H-F Zhang, Zhandong Liu
Bioinformatics · 2023
Tau polarizes an aging transcriptional signature to excitatory neurons and glia
Timothy Wu, Jennifer M Deger, Hui Ye, Caiwei Guo, Justin Dhindsa, Brandon T Pekarek, Rami Al-Ouran, Zhandong Liu, Ismael Al-Ramahi, Juan Botas
Elife · 2023
A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels
Jian Zhou, Claudia Cattoglio, Yingyao Shao, Harini P Tirumala, Carlo Vetralla, Sameer S Bajikar, Yan Li, Hu Chen, Qi Wang, Zhenyu Wu
Genes \& Development · 2023
Latent factor in Brain RNA-seq studies reflects cell type and clinical heterogeneity
Rami Al-Ouran, Chaozhong Liu, Linhua Wang, Ying-Wooi Wan, Xiqi Li, Aleksandar Milosavljevic, Joshua M Shulman, Zhandong Liu
bioRxiv · 2022
Losing the maternal effect gene Nlrp2 alters the ovulated mouse oocytes transcriptome and impacts histone demethylase KDM1B expression
Zahra Anvar, Imen Chakchouk, Momal Sharif, Sangeetha Mahadevan, Eleni Theodora Nasiotis, Li Su, Zhandong Liu, Ying-Wooi Wan, Ignatia B Veyver
Unknown Venue · 2022
Literature-based predictions of treatments for genetic disease pathology
Cole A Deisseroth, Won-Seok Lee, Ji-Yoen Kim, Hyun-Hwan Jeong, Julia Wang, Huda Y Zoghbi, Zhandong Liu
bioRxiv · 2022
ModelMatcher: A scientist‐centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research
J. Michael Harnish, Lucian Li, Sanja Rogic, Guillaume Poirier‐Morency, Seon‐Young Kim, Undiagnosed Diseases Network, Kym M. Boycott, Michael F. Wangler, Hugo J. Bellen, Philip Hieter, Paul Pavlidis, Zhandong Liu, Shinya Yamamoto
Human Mutation · 2022
Genome Sequencing in the Parkinson Disease Clinic
Emily J. Hill, Laurie A. Robak, Rami Al-Ouran, Jennifer Deger, Jamie C. Fong, Paul Jerrod Vandeventer, Emily Schulman, Sindhu Rao, Hiba Saade, Joseph M. Savitt, Rainer Von Coelln, Neeja Desai, Harshavardhan Doddapaneni, Sejal Salvi, Shannon Dugan-Perez, Donna M. Muzny, Amy L. McGuire, Zhandong Liu, Richard A. Gibbs, Chad Shaw, Joseph Jankovic, Lisa M. Shulman, Joshua M. Shulman
Neurology Genetics · 2022
Cross-species genetic screens identify transglutaminase 5 as a regulator of polyglutamine-expanded ataxin-1
Won-Seok Lee, Ismael Al-Ramahi, Hyun-Hwan Jeong, Youjin Jang, Tao Lin, Carolyn J Adamski, Laura A Lavery, Smruti Rath, Ronald Richman, Vitaliy V Bondar
The Journal of clinical investigation · 2022
Most high throughput expression data sets are underpowered
Alexander J Trostle, Jiasheng Wang, Lucian Li, Ying-Wooi Wan, Zhandong Liu
BioRxiv · 2022
Accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
Linhua Wang, Ling Wu, Chaozhong Liu, Wanli Wang, Xiang H-F Zhang, Zhandong Liu
bioRxiv · 2022
Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data
Linhua Wang, Mirjana Maletic-Savatic, Zhandong Liu
Nature Communications · 2022
Disruption of MeCP2–TCF20 complex underlies distinct neurodevelopmental disorders
Jian Zhou, Hamdan Hamdan, Hari Krishna Yalamanchili, Kaifang Pang, Amy E. Pohodich, Joanna Lopez, Yingyao Shao, Juan A. Oses-Prieto, Lifang Li, Wonho Kim, Mark A. Durham, Sameer S. Bajikar, Donna J. Palmer, Philip Ng, Michelle L. Thompson, E. Martina Bebin, Amelie J. Müller, Alma Kuechler, Antje Kampmeier, Tobias B. Haack, Alma L. Burlingame, Zhandong Liu, Matthew N. Rasband, Huda Y. Zoghbi
Proceedings of the National Academy of Sciences · 2022
Genome-Wide Association Study Meta-Analysis for Parkinson Disease Motor Subtypes
Isabel Alfradique-Dunham, Rami Al-Ouran, Rainer Von Coelln, Cornelis Blauwendraat, Emily Hill, Lan Luo, Amanda Stillwell, Emily Young, Anita Kaw, Manuela Tan, Calwing Liao, Dena Hernandez, Lasse Pihlstrom, Donald Grosset, Lisa M. Shulman, Zhandong Liu, Guy A. Rouleau, Mike Nalls, Andrew B. Singleton, Huw Morris, Joseph Jankovic, Joshua M. Shulman
Neurology Genetics · 2021
The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells
Igor L Bado, Weijie Zhang, Jingyuan Hu, Zhan Xu, Hai Wang, Poonam Sarkar, Lucian Li, Ying-Wooi Wan, Jun Liu, William Wu
Developmental cell · 2021
A network regularized linear model to infer spatial expression pattern for single cells
Chaohao Gu, Zhandong Liu
bioRxiv · 2021
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees
Wuming Gong, Alejandro A Granados, Jingyuan Hu, Matthew G Jones, Ofir Raz, Irepan Salvador-Martínez, Hanrui Zhang, Ke-Huan K Chow, Il-Youp Kwak, Renata Retkute
Cell systems · 2021
Dysfunction of D2 dopamine receptor expressing neurons underlies manic-like behaviors in mice modeling SHANK3 duplication disorder
Jimmy Holder, Kaifang Pang, Michel Weiwer, Kihoon Han, Wei Wang, Theresa Estiphan, Blake Vuocolo, Karen Jaunarajs, Edward Holson, Mike Lewis
Unknown Venue · 2021
A comprehensive evaluation of CRISPR lineage recorders using TraceQC
Jingyuan Hu, Hyun-Hwan Jeong, Rami Al-Ouran, Igor Bado, Weijie Zhang, Xiang Zhang, Zhandong Liu
bioRxiv · 2021
Application and design considerations for 3′-end sequencing using click-chemistry
Madeline K Jensen, Nathan D Elrod, Hari Krishna Yalamanchili, Ping Ji, Ai Lin, Zhandong Liu, Eric J Wagner
Methods in Enzymology · 2021
A benchmark for RNA-seq deconvolution analysis under dynamic testing environments
Haijing Jin, Zhandong Liu
Genome Biology · 2021
Dual targeting of brain region‐specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1
Won‐Seok Lee, Laura Lavery, Maxime W C 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
The EMBO Journal · 2021
A hybrid deep neural network for robust single-cell genome-wide DNA methylation detection
Russell A. Li, Zhandong Liu
Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics · 2021
Downregulation of glial genes involved in synaptic function mitigates Huntington's disease pathogenesis
Tarik Seref Onur, Andrew Laitman, He Zhao, Ryan Keyho, Hyemin Kim, Jennifer Wang, Megan Mair, Huilan Wang, Lifang Li, Alma Perez
elife · 2021
SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females
Francesca Clementina Radio, Kaifang Pang, Andrea Ciolfi, Michael A Levy, Andrés Hernández-García, Lucia Pedace, Francesca Pantaleoni, Zhandong Liu, Elke de Boer, Adam Jackson
The American Journal of Human Genetics · 2021
Modulation of ATXN1 S776 phosphorylation reveals the importance of allele-specific targeting in SCA1
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
JCI insight · 2021
Antisense oligonucleotide therapy in a humanized mouse model of \textitMECP2 duplication syndrome
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
Science Translational Medicine · 2021
MECP2pedia: a comprehensive transcriptome portal for MECP2 disease research
Alexander J Trostle, Lucian Li, Seon-Young Kim, Jiasheng Wang, Rami Al-Ouran, Hari Krishna Yalamanchili, Zhandong Liu, Ying-Wooi Wan
bioRxiv · 2021
Identification of spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics by region-specific denoising
Linhua Wang, Zhandong Liu
Unknown Venue · 2021
Missing-value imputation and in-silico region detection for spatially resolved transcriptomics
Linhua Wang, Zhandong Liu
BioRxiv · 2021
A computational pipeline to infer alternative poly-adenylation from 3′ sequencing data
Hari Krishna Yalamanchili, Nathan D Elrod, Madeline K Jensen, Ping Ji, Ai Lin, Eric J Wagner, Zhandong Liu
Methods in enzymology · 2021
The bone microenvironment invigorates metastatic seeds for further dissemination
Weijie Zhang, Igor L Bado, Jingyuan Hu, Ying-Wooi Wan, Ling Wu, Hai Wang, Yang Gao, Hyun-Hwan Jeong, Zhan Xu, Xiaoxin Hao
Cell · 2021
Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation
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
Elife · 2020
PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing
Hyundoo Jeong, Zhandong Liu
Bioinformatics · 2020
Nr2f1 heterozygous knockout mice recapitulate neurological phenotypes of Bosch-Boonstra-Schaaf optic atrophy syndrome and show impaired hippocampal synaptic plasticity
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
Human Molecular Genetics · 2020
TraceQC: An R package for quality control of CRISPR lineage tracing data
Jingyuan Hu, Rami Al-Ouran, Xiang Zhang, Zhandong Liu, Hyun-Hwan Jeong
BioRxiv · 2020
A comparative study of deconvolution methods for RNA-seq data under a dynamic testing landscape
Haijing Jin, Zhandong Liu
bioRxiv · 2020
Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome
Laura A Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, Joanna Lopez, Jacinta Lucero, Mark A Durham
elife · 2020
Stress detection using deep neural networks
Russell Li, Zhandong Liu
BMC Medical Informatics and Decision Making · 2020
Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia
Jidong Liu, Guolian Ding, Kexin Zou, Ziru Jiang, Junyu Zhang, Yunhua Lu, Antonella Pignata, Eric Venner, Pengfei Liu, Zhandong Liu
Molecular Genetics \& Genomic Medicine · 2020
Integrated analysis of the aging brain transcriptome and proteome in tauopathy
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
Molecular Neurodegeneration · 2020
miR760 regulates ATXN1 levels via interaction with its 5′ untranslated region
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
Genes \& development · 2020
Modulating glial genes involved in synaptic function mitigates pathogenesis and behavioral deficits in a Drosophila model of Huntington’s Disease
Tarik S Onur, Andrew Laitman, He Zhao, Ryan Keyho, Hyemin Kim, Jennifer Wang, Megan Mair, Alma Perez, Maria de Haro, Huilan Wang
bioRxiv · 2020
Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease
Ethan R Roy, Baiping Wang, Ying-wooi Wan, Gabriel Chiu, Allysa Cole, Zhuoran Yin, Nicholas E Propson, Yin Xu, Joanna L Jankowsky, Zhandong Liu
The Journal of clinical investigation · 2020
Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders
Kaifang Pang, Li Wang, Wei Wang, Jian Zhou, Chao Cheng, Kihoon Han, Huda Y Zoghbi, Zhandong Liu
Genome Research · 2020
BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder
Tiana M Scott, Hui Guo, Evan E Eichler, Jill A Rosenfeld, Kaifang Pang, Zhandong Liu, Seema Lalani, Weimin Bi, Yaping Yang, Carlos A Bacino
Human mutation · 2020
Abstract B54: Single-cell analytics in claudin-low TNBC reveals immunostimulatory effects of low-dose metronomic cyclophosphamide treatment
Swarnima Singh, Ying-Wooi Wan, Nigel Lee, Se-Jin Kim, Zhandong Liu, Charles M Perou, Xiang Zhang, Jeffrey Rosen
Cancer Immunology Research · 2020
Meta-analysis of the Alzheimer’s disease human brain transcriptome and functional dissection in mouse models
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
Cell reports · 2020
A kinome-wide RNAi screen identifies ERK2 as a druggable regulator of Shank3 stability
Li Wang, Carolyn J Adamski, Vitaliy V Bondar, Evelyn Craigen, John R Collette, Kaifang Pang, Kihoon Han, Antrix Jain, Sung Y. Jung, Zhandong Liu
Molecular psychiatry · 2020
An autism-linked missense mutation in SHANK3 reveals the modularity of Shank3 function
Li Wang, Kaifang Pang, Kihoon Han, Carolyn J Adamski, Wei Wang, Lingjie He, Jason K Lai, Vitaliy V Bondar, Joseph G Duman, Ronald Richman
Molecular psychiatry · 2020
PolyA-miner: Accurate assessment of differential alternative poly-adenylation from 3′ Seq data using vector projections and non-negative matrix factorization
Hari Krishna Yalamanchili, Callison E Alcott, Ping Ji, Eric J Wagner, Huda Y Zoghbi, Zhandong Liu
Nucleic acids research · 2020
A portal to visualize transcriptome profiles in mouse models of neurological disorders
Rami Al-Ouran, Ying-Wooi Wan, Carl Grant Mangleburg, Tom V Lee, Katherine Allison, Joshua M Shulman, Zhandong Liu
Genes · 2019
Partial loss of CFIm25 causes aberrant alternative polyadenylation and learning deficits
Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B Saltzman, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba
bioRxiv · 2019
Genome-Wide Association Study Meta-Analysis For Parkinson Disease Motor Subtypes (S53. 005)
Isabel Alfradique-Dunham, Cornelis Blauwendraat, Rami Al-Ouran, Rainer von Coelln, Manuela Tan, Emily Hill, Lan Luo, Emily Young, Amanda Stillwell, Zhandong Liu
AAN Enterprises · 2019
P4‐130: TAU‐MEDIATED DISRUPTION OF THE SPLICEOSOME TRIGGERS CRYPTIC RNA SPLICING AND NEURODEGENERATION IN ALZHEIMER'S DISEASE
Caiwei Guo, Yi-Chen Hsieh, Hari K Yalamanchili, Measho Abreha, Rami Al-Ouran, Yarong Li, Eric B Dammer, James J Lah, Allan I Levey, David A Bennett
Alzheimer's \& Dementia · 2019
Tau-mediated disruption of the spliceosome triggers cryptic RNA splicing and neurodegeneration in Alzheimer’s disease
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
Cell reports · 2019
Are HHV-6A and HHV-7 really more abundant in Alzheimer’s disease?
Hyun-Hwan Jeong, Zhandong Liu
Neuron · 2019
Spinocerebellar ataxia
Thomas Klockgether, Caterina Mariotti, Henry L Paulson
Nature reviews Disease primers · 2019
Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
Hyun-Hwan Jeong, Seon Young Kim, Maxime WC Rousseaux, Huda Y Zoghbi, Zhandong Liu
Genome research · 2019
Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome
Laura A Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Joanna Lopez, Jacinta Lucero, Mark A Durham, Rosa Castanon
bioRxiv · 2019
Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach
Benjamin A Logsdon, Thanneer M Perumal, Vivek Swarup, Minghui Wang, Cory Funk, Chris Gaiteri, Mariet Allen, Xue Wang, Eric Dammer, Gyan Srivastava
BioRxiv · 2019
O4‐10‐03: FUNCTIONAL DISSECTION OF ALZHEIMER'S DISEASE BRAIN GENE EXPRESSION SIGNATURES IN HUMANS AND MOUSE MODELS
Carl Grant Mangleburg, Ying-Wooi Wan, Rami Al-Ouran, Tom V Lee, Katherine S Allison, Benjamin A Logsdon, Lara M Mangravite, Zhandong Liu, Joshua M Shulman
Alzheimer's \& Dementia · 2019
Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors
Akash J Patel, Ying-Wooi Wan, Rami Al-Ouran, Jean-Pierre Revelli, Maria F Cardenas, Mazen Oneissi, Liu Xi, Ali Jalali, John F Magnotti, Donna M Muzny
Proceedings of the National Academy of Sciences · 2019
Augmented Reality Based Therapy System for Social Skill Deficits
Kewei Sha, Zhandong Liu, Jack Dempsey
IEEE · 2019
Functional dissection of Alzheimer’s disease brain gene expression signatures in humans and mouse models
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
bioRxiv · 2019
Navigating MARRVEL, a web-based tool that integrates human genomics and model organism genetics information
Julia Wang, Zhandong Liu, Hugo J Bellen, Shinya Yamamoto
JoVE (Journal of Visualized Experiments) · 2019
Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus–CA3 projection
Wenjun Zhou, Yanlin He, Atteeq U Rehman, Yan Kong, Sungguan Hong, Guolian Ding, Hari Krishna Yalamanchili, Ying-Wooi Wan, Basil Paul, Chuhan Wang
Nature neuroscience · 2019
Using MARRVEL v1. 2 for bioinformatics analysis of human genes and variant pathogenicity
Julia Wang, Dongxue Mao, Fatima Fazal, Seon‐Young Kim, Shinya Yamamoto, Hugo Bellen, Zhandong Liu
Current protocols in bioinformatics · 2019
High-throughput functional analysis distinguishes pathogenic, nonpathogenic, and compensatory transcriptional changes in neurodegeneration
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
Cell systems · 2018
Metabolomics of mammalian brain reveals regional differences
William T Choi, Mehmet Tosun, Hyun-Hwan Jeong, Cemal Karakas, Fatih Semerci, Zhandong Liu, Mirjana Maletić-Savatić
BMC systems biology · 2018
Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science. 361: eaar2555
S Chong, C Dugast-Darzacq, Z Liu, P Dong, GM Dailey, C Cattoglio, A Heckert, S Banala, L Lavis, X Darzacq
Unknown Venue · 2018
P3‐179: TAU‐INDUCED DISRUPTION OF THE SPLICEOSOME IN ALZHEIMER'S DISEASE
Caiwei Guo, Yi-Chen Hsieh, Hari K Yalamanchili, Measho Abreha, Duc Duong, Yarong Li, Nicholas T Seyfried, Zhandong Liu, Joshua M Shulman
Alzheimer's \& Dementia · 2018
Tau activates transposable elements in Alzheimer’s disease
Caiwei Guo, Hyun-Hwan Jeong, Yi-Chen Hsieh, Hans-Ulrich Klein, David A Bennett, Philip L De Jager, Zhandong Liu, Joshua M Shulman
Cell reports · 2018
Genome-wide distribution of linker histone H1. 0 is independent of MeCP2
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
Nature neuroscience · 2018
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M Shulman, Zhandong Liu
World Scientific · 2018
CRISPRCloud2: A cloud-based platform for deconvolving CRISPR screen data
Hyun-Hwan Jeong, Seon Young Kim, Maxime WC Rousseaux, Huda Y Zoghbi, Zhandong Liu
BioRxiv · 2018
Complement C3aR inactivation attenuates tau pathology and reverses an immune network deregulated in tauopathy models and Alzheimer’s disease
Alexandra Litvinchuk, Ying-Wooi Wan, Dan B Swartzlander, Fading Chen, Allysa Cole, Nicholas E Propson, Qian Wang, Bin Zhang, Zhandong Liu, Hui Zheng
Neuron · 2018
Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila
Zaijun Ma, Hui Wang, Yuping Cai, Han Wang, Kongyan Niu, Xiaofen Wu, Huanhuan Ma, Yun Yang, Wenhua Tong, Feng Liu
Elife · 2018
POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain.
Mikhail Y Kochukov, Brandon Pekarek, Graeme Mardon, Cynthia K McClard, Benjamin R Arenkiel, Daniel Colchado, Sugi Panneerselvam, Isabella Herman, Joshua Ortiz-Guzman, Zhandong Liu
Journal of Neuroscience · 2018
RBM17 interacts with U2SURP and CHERP to regulate expression and splicing of RNA-processing proteins
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
Cell reports · 2018
TFEB enhances astroglial uptake of extracellular tau species and reduces tau spreading
Heidi Martini-Stoica, Allysa L Cole, Daniel B Swartzlander, Fading Chen, Ying-Wooi Wan, Lakshya Bajaj, David A Bader, Virginia MY Lee, John Q Trojanowski, Zhandong Liu
Journal of Experimental Medicine · 2018
Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Amy E Pohodich, Hari Yalamanchili, Ayush T Raman, Ying-Wooi Wan, Michael Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y Zoghbi
Elife · 2018
Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations
Ayush T Raman, Amy E Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E Lowry, Huda Y Zoghbi, Zhandong Liu
Nature communications · 2018
A druggable genome screen identifies modifiers of α-synuclein levels via a tiered cross-species validation approach
Maxime WC Rousseaux, Gabriel E Vázquez-Vélez, Ismael Al-Ramahi, Hyun-Hwan Jeong, Aleksandar Bajić, Jean-Pierre Revelli, Hui Ye, Emily T Phan, Jennifer M Deger, Alma M Perez
Journal of Neuroscience · 2018
Loss of Capicua alters early T cell development and predisposes mice to T cell lymphoblastic leukemia/lymphoma
Qiumin Tan, Lorenzo Brunetti, Maxime WC Rousseaux, Hsiang-Chih Lu, Ying-Wooi Wan, Jean-Pierre Revelli, Zhandong Liu, Margaret A Goodell, Huda Y Zoghbi
Proceedings of the National Academy of Sciences · 2018
Detecting hidden batch factors through data-adaptive adjustment for biological effects
Haidong Yi, Ayush T Raman, Han Zhang, Genevera I Allen, Zhandong Liu
Bioinformatics · 2018
Decoding TDP-43 Dependent Cryptic Splicing in Amyotrophic Lateral Sclerosis and Identifying Novel Disease-causing Genes
Hari Krishna Yalamanchili, Hyun-Hwan Jeong, Zhandong Liu
Unknown Venue · 2018
Otud7a knockout mice recapitulate many neurological features of 15q13. 3 microdeletion syndrome
Jiani Yin, Wu Chen, Eugene S Chao, Sirena Soriano, Li Wang, Wei Wang, Steven E Cummock, Huifang Tao, Kaifang Pang, Zhandong Liu
The American Journal of Human Genetics · 2018
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution
Hyun-Hwan Jeong, Seon Young Kim, Maxime WC Rousseaux, Huda Y Zoghbi, Zhandong Liu
Bioinformatics · 2017
SAVE: A secure cloud-based pipeline for CRISPR pooled screen deconvolution
Hyun-Hwan Jeong, Seon Young Kim, Maxime WC Rosseaux, Huda Y Zoghbi, Zhandong Liu
bioRxiv · 2017
A role for progesterone-regulated sfrp4 expression in uterine leiomyomas
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
The Journal of Clinical Endocrinology \& Metabolism · 2017
Comprehensive evaluation of RNA-seq quantification methods for linearity
Haijing Jin, Ying-Wooi Wan, Zhandong Liu
BMC bioinformatics · 2017
Ford Boots Pre For Tom Women Black Suede owned BqaSdxw78 \& screw. chiguire53. com
Haijing Jin, Ying-Wooi Wan, Zhandong Liu
Ford Boots Pre For Tom Women Black Suede owned BqaSdxw78 \& screw. chiguire53. com · 2017
The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools
Zhandong Liu, W Jim Zheng, Genevera I Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
BMC bioinformatics · 2017
Disruption of the ATXN1–CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans
Hsiang-Chih Lu, Qiumin Tan, Maxime WC Rousseaux, Wei Wang, Ji-Yoen Kim, Ronald Richman, Ying-Wooi Wan, Szu-Ying Yeh, Jay M Patel, Xiuyun Liu
Nature genetics · 2017
Transcriptional regulation by ATOH1 and its target SPDEF in the intestine
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
Cellular and molecular gastroenterology and hepatology · 2017
Bias toward long gene misregulation in synaptic disorders can be an artefact of amplification-based methods
Ayush T Raman, Amy E Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, Bill Lowry, Huda Y Zoghbi, Zhandong Liu
bioRxiv · 2017
CSIG-36. DECREASED CAPICUA (CIC) ENHANCES ONCOGENIC ETV4 SIGNALING IN A MOUSE MODEL OF ASTROCYTOMA AND GLIOMA STEM CELLS
Annmarie Ramkissoon, Amanda Smith, Alexander Merk, Ralph Salloum, Ying-Wooi Wan, Mutsuko Minata, Ichiro Nakano, Christine Fuller, Zhandong Liu, Lionel ML Chow
Neuro-Oncology · 2017
MARRVEL: integration of human and model organism genetic resources to facilitate functional annotation of the human genome
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
The American Journal of Human Genetics · 2017
Data analysis pipeline for RNA‐seq experiments: from differential expression to cryptic splicing
Hari Krishna Yalamanchili, Ying‐Wooi Wan, Zhandong Liu
Current protocols in bioinformatics · 2017
The international conference on intelligent biology and medicine (ICIBM) 2016: summary and innovation in genomics
Zhongming Zhao, Zhandong Liu, Ken Chen, Yan Guo, Genevera I Allen, Jiajie Zhang, W Jim Zheng, Jianhua Ruan
BMC genomics · 2017
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease
Genevera I Allen, Nicola Amoroso, Catalina Anghel, Venkat Balagurusamy, Christopher J Bare, Derek Beaton, Roberto Bellotti, David A Bennett, Kevin L Boehme, Paul C Boutros
Alzheimer's \& Dementia · 2016
Transcriptomic analysis of mouse cochlear supporting cell maturation reveals large-scale changes in Notch responsiveness prior to the onset of hearing
Juan C Maass, Rende Gu, Tiantian Cai, Ying-Wooi Wan, Silvia C Cantellano, Joanna ST Asprer, Hongyuan Zhang, Hsin-I Jen, Renée K Edlund, Zhandong Liu
PloS one · 2016
Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models
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
Human molecular genetics · 2016
Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome
Surabi Veeraragavan, Ying-Wooi Wan, Daniel R Connolly, Shannon M Hamilton, Christopher S Ward, Sirena Soriano, Meagan R Pitcher, Christopher M McGraw, Sharon G Huang, Jennie R Green
Human molecular genetics · 2016
XMRF: an R package to fit Markov Networks to high-throughput genetics data
Ying-Wooi Wan, Genevera I Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson, Zhandong Liu
BMC systems biology · 2016
TCGA2STAT: simple TCGA data access for integrated statistical analysis in R
Ying-Wooi Wan, Genevera I Allen, Zhandong Liu
Bioinformatics · 2016
FOXG1 expression shows correlation with neuronal differentiation in cerebellar development, aggressive phenotype in medulloblastomas, and survival in a xenograft model of medulloblastoma
Adekunle M Adesina, Bethany L Veo, Girard Courteau, Vidya Mehta, Xuli Wu, Kaifang Pang, Zhandong Liu, Xiao-Nan Li, Lori Peters
Human pathology · 2015
Post-transcriptional regulation of SHANK3 expression by microRNAs related to multiple neuropsychiatric disorders
Su-Yeon Choi, Kaifang Pang, Joo Yeon Kim, Jae Ryun Ryu, Hyojin Kang, Zhandong Liu, Won-Ki Kim, Woong Sun, Hyun Kim, Kihoon Han
Molecular brain · 2015
Progesterone Promotes Smooth Muscle Tumorigenesis By Down-Regulating SFRP4 Overexpression
Meaghan A Delaney, Ying-Wooi Wan, Margret G Taylor, Gyoung Eun Kim, Cecilia Valdes, Zhandong Liu, Matthew L Anderson
SAGE PUBLICATIONS INC 2455 TELLER RD, THOUSAND OAKS, CA 91320 USA · 2015
Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides
Yehezkel Sztainberg, Hong-mei Chen, John W Swann, Shuang Hao, Bin Tang, Zhenyu Wu, Jianrong Tang, Ying-Wooi Wan, Zhandong Liu, Frank Rigo
Nature · 2015
Differential gene expression profile of tissue factor pathway inhibitor-2 (TFPI-2) in malignant pleural mesothelioma
Anil Wali, Ying Wang, Adi Tarca, Fulvio Lonardo, Zhandong Liu, Arun K Rishi, Harvey I Pass
Cancer Research · 2015
Graphical models via univariate exponential family distributions
Eunho Yang, Pradeep Ravikumar, Genevera I Allen, Zhandong Liu
The Journal of Machine Learning Research · 2015
Loss of MiR-148 Enhances Ovarian Cancer Growth and Metastasis by Promoting MTMR9 Expression
Triparna Ghosh-Choudhury, Ying-Wooi Wan, Zhandong Liu, Matthew Anderson
SAGE PUBLICATIONS INC 2455 TELLER RD, THOUSAND OAKS, CA 91320 USA · 2014
NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation
Sangeetha Mahadevan, Shu Wen, Ying-Wooi Wan, Hsiu-Huei Peng, Subhendu Otta, Zhandong Liu, Michelina Iacovino, Elisabeth M Mahen, Michael Kyba, Bekim Sadikovic
Human molecular genetics · 2014
Combinatorial therapy discovery using mixed integer linear programming
Kaifang Pang, Ying-Wooi Wan, William T Choi, Lawrence A Donehower, Jingchun Sun, Dhruv Pant, Zhandong Liu
Bioinformatics · 2014
On the reproducibility of TCGA ovarian cancer microRNA profiles
Ying-Wooi Wan, Claire M Mach, Genevera I Allen, Matthew L Anderson, Zhandong Liu
PloS one · 2014
A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases
Shinya Yamamoto, Manish Jaiswal, Wu-Lin Charng, Tomasz Gambin, Ender Karaca, Ghayda Mirzaa, Wojciech Wiszniewski, Hector Sandoval, Nele A Haelterman, Bo Xiong
Cell · 2014
A general framework for mixed graphical models
Eunho Yang, Pradeep Ravikumar, Genevera I Allen, Yulia Baker, Ying-Wooi Wan, Zhandong Liu
arXiv preprint arXiv:1411.0288 · 2014
Serine catabolism regulates mitochondrial redox control during hypoxia
Jiangbin Ye, Jing Fan, Sriram Venneti, Ying-Wooi Wan, Bruce R Pawel, Ji Zhang, Lydia WS Finley, Chao Lu, Tullia Lindsten, Justin R Cross
Cancer discovery · 2014
Mixed graphical models via exponential families
Eunho Yang, Yulia Baker, Pradeep Ravikumar, Genevera Allen, Zhandong Liu
PMLR · 2014
A local poisson graphical model for inferring networks from sequencing data
Genevera I Allen, Zhandong Liu
IEEE transactions on nanobioscience · 2013
Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p
Kihoon Han, Vincenzo Alessandro Gennarino, Yoontae Lee, Kaifang Pang, Kazue Hashimoto-Torii, Sanaa Choufani, Chandrasekhar S Raju, Michael C Oldham, Rosanna Weksberg, Pasko Rakic
Genes \& development · 2013
Expression and functional pathway analysis of nuclear receptor NR2F2 in ovarian cancer
Shannon M Hawkins, Holli A Loomans, Ying-Wooi Wan, Triparna Ghosh-Choudhury, Donna Coffey, Weimin Xiao, Zhandong Liu, Haleh Sangi-Haghpeykar, Matthew L Anderson
The Journal of Clinical Endocrinology \& Metabolism · 2013
Abstract 1955: LIN28 paralogs impact ovarian cancer predisposition and tumorigenicity via distinct molecular pathways.
Claire Mach, Ying-Wooi Wan, Zhandong Liu, Matthew L. Anderson
Cancer Research · 2013
Identifying cancer biomarkers through a network regularized Cox model
Ying-Wooi Wan, John Nagorski, Genevera I Allen, Zhaohui Li, Zhandong Liu
IEEE · 2013
Conditional random fields via univariate exponential families
Eunho Yang, Pradeep K Ravikumar, Genevera I Allen, Zhandong Liu
Advances in Neural Information Processing Systems · 2013
On Poisson graphical models
Eunho Yang, Pradeep K Ravikumar, Genevera I Allen, Zhandong Liu
Advances in neural information processing systems · 2013
Molecular pathway identification using biological network-regularized logistic models
Wen Zhang, Ying-wooi Wan, Genevera I Allen, Kaifang Pang, Matthew L Anderson, Zhandong Liu
BMC genomics · 2013
Digital sorting of complex tissues for cell type-specific gene expression profiles
Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel ML Chow, Zhandong Liu
BMC bioinformatics · 2013
A log-linear graphical model for inferring genetic networks from high-throughput sequencing data
Genevera I Allen, Zhandong Liu
IEEE · 2012
Graphical models via generalized linear models
Eunho Yang, Genevera Allen, Zhandong Liu, Pradeep Ravikumar
Advances in neural information processing systems · 2012
Gene expression deconvolution in linear space
Yi Zhong, Zhandong Liu
Nature methods · 2012
Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex
Akash J Patel, Ying-Wooi Wan, Rami Al-Ouran, Jean-Pierre Revelli, Maria F Cardenas, Mazen Oneissi, Liu Xi, Ali Jalali, John F Magnotti, Donna M Muzny
Oncology · 2010
Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects
Alla V Ivanova, Sergey V Ivanov, Ljudmila Prudkin, Daisuke Nonaka, Zhandong Liu, Anne Tsao, Ignacio Wistuba, Jack Roth, Harvey I Pass
Molecular cancer · 2009
The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis
Gerald BW Wertheim, Thomas W Yang, Tien-chi Pan, Anna Ramne, Zhandong Liu, Heather P Gardner, Katherine D Dugan, Petra Kristel, Bas Kreike, Marc J van de Vijver
Proceedings of the National Academy of Sciences · 2009
Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples
Zhandong Liu, Santosh S Venkatesh, Carlo C Maley
BMC genomics · 2008
Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo
Zhandong Liu, Min Wang, James V Alvarez, Megan E Bonney, Chien-chung Chen, Celina D'Cruz, Tien-chi Pan, Mahlet G Tadesse, Lewis A Chodosh
Genome biology · 2008
Differential gene expression profile of Stratifin (14:3:3 sigma) in malignant pleural mesothelioma
Anil Wali, Fulvio Lonardo, Deepa Kanakapalli, Zhandong Liu, Ying Wang, Guri Tzivion, Arun Rishi, Michele Carbone, John Ruckdeschel, Harvey Pass
Cancer Research · 2008
Role of Ubiquitin-proteasome proteolytic pathway in malignant pleural mesothelioma.
Anil Wali, Ying Wang, Deepa Kanakapalli, Zhandong Liu, Sunita Sharma, Fulvio Lonardo, Arun Rishi, Adhip Majumdar, Q Ping Dou, Michele Carbone
Cancer Research · 2007
Intelectin overexpression causes chromosomal aberrations in immortalized human mesothelial cells
Anil Wali, Fauzia Siddiq, Deepa Kanakapalli, Zhandong Liu, Fulvio Lonardo, Arun K Rishi, Adhip PN Majumdar, Michele Carbone, Henry HQ Heng, Harvey I Pass
AMER ASSOC CANCER RESEARCH 615 CHESTNUT ST, 17TH FLOOR, PHILADELPHIA, PA … · 2006
In silico and wet-bench identification of nuclear matrix attachment regions
Stephen A Krawetz, Sorin Draghici, Robert Goodrich, Zhandong Liu, G Charles Ostermeier
Hypertension: Methods and Protocols · 2005
Asbestos exposure, pleural mesothelioma, and serum osteopontin levels
Harvey I Pass, Dan Lott, Fulvio Lonardo, Michael Harbut, Zhandong Liu, Naimei Tang, Michele Carbone, Craig Webb, Anil Wali
New England Journal of Medicine · 2005
Gene expression profiles predict survival and progression of pleural mesothelioma
Harvey I Pass, Zhandong Liu, Anil Wali, Raphael Bueno, Susan Land, Daniel Lott, Fauzia Siddiq, Fulvio Lonardo, Michele Carbone, Sorin Draghici
Clinical Cancer Research · 2004
Nuclear matrix association of the human β‐globin locus utilizing a novel approach to quantitative real‐time PCR
G Charles Ostermeier, Zhandong Liu, Rui Pires Martins, Rikki R Bharadwaj, James Ellis, Sorin Draghici, Stephen A Krawetz
Nucleic Acids Research · 2003
Book Chapters
No book chapters listed yet.
Software
Intelligent Medical Image Analysis System
Developers: Zhang San, Li Si, Wang Wu
Intelligent Image Processing System V1.0
Developers: Wei Zhang, Michael Brown
Grants/Funds
VALIDATE ASD: Independent Multimodal Replication and Validation of Autism Data-Science Models
Granted PIs: Zhandong Liu, Ananth V. Annapragada, Holly Kathryn Harris, Hyun-Hwan Jeong, Bhagavatula Moorthy
1OT2OD040565
Cancer Prevention and Research Institute of Texas Grant
Granted PIs: Zhandong Liu
RP240131
NSF PFI-TT: Creation of an Augmented-Reality Platform for Treatment of Phobias/Anxiety in Children with ASD
Granted PIs: Zhandong Liu, Jack Dempsey
IIP-1827668
CPRIT Individual Investigator Research Award
Granted PIs: Zhandong Liu
RP170387
Advanced Computational Approaches for NMR Data-Mining
Granted PIs: Mirjana Maletic-Savatic, Zhandong Liu
R01GM120033
Functional Dissection of Alzheimer's Disease Networks in Drosophila
Granted PIs: Juan Botas, Zhandong Liu, Nicholas Thomas Seyfried, Joshua M Shulman
R01AG057339
NSF I-Corps: Augmented Reality Based Technologies in Treating Specific Phobia
Granted PIs: Zhandong Liu
IIP-1744114
NSF: Statistical Methods for Integrated Analysis of High-Throughput Biomedical Data
Granted PIs: Zhandong Liu
DMS-1263932
Group Honors
2020 Dream Challenge
Allen Institute Cell Lineage Reconstruction DREAM Challenge
1st place, Subchallenge 1