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Zhuorui Xie

Icahn School of Medicine at Mount Sinai

14H-index
31Paper Count
4.5KCitation Count
Published Papers 12
Publication Date
The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
err2026-01-06
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errJohn Erol Evangelista; Daniel J.B. Clarke; Anna I. Byrd; Shivaramakrishna Srinivasan; Sumana Srinivasan; Mano R. Maurya; Sherry L. Jenkins; Ido Diamant; Ethan Sanchez; Zhuorui Xie; Stephanie Olaiya; Heesu Kim; Giacomo B. Marino; Nasheath Ahmed; Srinivasan Ramachandran; Shankar Subramaniam; Avi Ma’ayan
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Playbook workflow builder: Interactive construction of bioinformatics workflows
err2025-04-03
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errClarke, Daniel J. B.; Evangelista, John Erol; Xie, Zhuorui; Marino, Giacomo B.; Byrd, Anna I.; Maurya, Mano R.; Srinivasan, Sumana; Yu, Keyang; Petrosyan, Varduhi; Roth, Matthew E.; Milinkov, Miroslav; King, Charles Hadley; Vora, Jeet Kiran; Keeney, Jonathon; Nemarich, Christopher; Khan, William; Lachmann, Alexander; Ahmed, Nasheath; Agris, Alexandra; Pan, Juncheng; Ramachandran, Srinivasan; Fahy, Eoin; Esquivel, Emmanuel; Mihajlovic, Aleksandar; Jevtic, Bosko; Milinovic, Vuk; Kim, Sean; McNeely, Patrick; Wang, Tianyi; Wenger, Eric; Brown, Miguel A.; Sickler, Alexander; Zhu, Yuankun; Jenkins, Sherry L.; Blood, Philip D.; Taylor, Deanne M.; Resnick, Adam C.; Mazumder, Raja; Milosavljevic, Aleksandar; Subramaniam, Shankar; Ma'ayan, Avi
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Rummagene: massive mining of gene sets from supporting materials of biomedical research publications
err2024-04-20
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errClarke, Daniel J. B.; Marino, Giacomo B.; Deng, Eden Z.; Xie, Zhuorui; Evangelista, John Erol; Ma'ayan, Avi
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Toxicology knowledge graph for structural birth defects
err2023-07-17
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errEvangelista, John Erol; Clarke, Daniel J. B.; Xie, Zhuorui; Marino, Giacomo B.; Utti, Vivian; Jenkins, Sherry L.; Ahooyi, Taha Mohseni; Bologa, Cristian G.; Yang, Jeremy J.; Binder, Jessica L.; Kumar, Praveen; Lambert, Christophe G.; Grethe, Jeffrey S.; Wenger, Eric; Taylor, Deanne; Oprea, Tudor, I; de Bono, Bernard; Ma'ayan, Avi
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Enrichr-KG: bridging enrichment analysis across multiple libraries
err2023-05-11
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errEvangelista, John Erol; Xie, Zhuorui; Marino, Giacomo B.; Nguyen, Nhi; Clarke, Daniel J. B.; Ma'ayan, Avi
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GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery
err2023-05-11
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errMarino, Giacomo B.; Ngai, Michael; Clarke, Daniel J. B.; Fleishman, Reid H.; Deng, Eden Z.; Xie, Zhuorui; Ahmed, Nasheath; Ma'ayan, Avi
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Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells
err2023-04-20
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errDeng, Eden Z.; Fleishman, Reid H.; Xie, Zhuorui; Marino, Giacomo B.; Clarke, Daniel J. B.; Ma'ayan, Avi
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lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs
err2023-03-04
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errMarino, Giacomo B.; Wojciechowicz, Megan L.; Clarke, Daniel J. B.; Kuleshov, Maxim, V; Xie, Zhuorui; Jeon, Minji; Lachmann, Alexander; Ma'ayan, Avi
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A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
err2022-10-07
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errGross, Sean M.; Dane, Mark A.; Smith, Rebecca L.; Devlin, Kaylyn L.; McLean, Ian C.; Derrick, Daniel S.; Mills, Caitlin E.; Subramanian, Kartik; London, Alexandra B.; Torre, Denis; Evangelista, John Erol; Clarke, Daniel J. B.; Xie, Zhuorui; Erdem, Cemal; Lyons, Nicholas; Natoli, Ted; Pessa, Sarah; Lu, Xiaodong; Mullahoo, James; Li, Jonathan; Adam, Miriam; Wassie, Brook; Liu, Moqing; Kilburn, David F.; Liby, Tiera A.; Bucher, Elmar; Sanchez-Aguila, Crystal; Daily, Kenneth; Omberg, Larsson; Wang, Yunguan; Jacobson, Connor; Yapp, Clarence; Chung, Mirra; Vidovic, Dusica; Lu, Yiling; Schurer, Stephan; Lee, Albert; Pillai, Ajay; Subramanian, Aravind; Papanastasiou, Malvina; Fraenkel, Ernest; Feiler, Heidi S.; Mills, Gordon B.; Jaffe, Jake D.; Ma'ayan, Avi; Birtwistle, Marc R.; Sorger, Peter K.; Korkola, James E.; Gray, Joe W.; Heiser, Laura M.
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SigCom LINCS: data and metadata search engine for a million gene expression signatures
err2022-05-07
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errEvangelista, John Erol; Clarke, Daniel J. B.; Xie, Zhuorui; Lachmann, Alexander; Jeon, Minji; Chen, Kerwin; Jagodnik, Kathleen M.; Jenkins, Sherry L.; Kuleshov, Maxim, V; Wojciechowicz, Megan L.; Schurer, Stephan C.; Medvedovic, Mario; Ma'ayan, Avi
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KEA3: improved kinase enrichment analysis via data integration
err2021-05-21
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errKuleshov, Maxim, V; Xie, Zhuorui; London, Alexandra B. K.; Yang, Janice; Evangelista, John Erol; Lachmann, Alexander; Shu, Ingrid; Torre, Denis; Ma'ayan, Avi
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Appyters: Turning Jupyter Notebooks into data-driven web apps
err2021-03-01
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errClarke, Daniel J. B.; Jeon, Minji; Stein, Daniel J.; Moiseyev, Nicole; Kropiwnicki, Eryk; Dai, Charles; Xie, Zhuorui; Wojciechowicz, Megan L.; Litz, Skylar; Hom, Jason; Evangelista, John Erol; Goldman, Lucas; Zhang, Serena; Yoon, Christine; Ahamed, Tahmid; Bhuiyan, Samantha; Cheng, Minxuan; Karam, Julie; Jagodnik, Kathleen M.; Shu, Ingrid; Lachmann, Alexander; Ayling, Sam; Jenkins, Sherry L.; Ma'ayan, Avi
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