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Journal Articles
- 2023
[j9]Giacomo B. Marino
, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan:
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation 2023 (2023)- [j8]John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan:
Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. 51(W1): 168-179 (2023) - [j7]Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan:
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. 51(W1): 213-224 (2023) - 2022
- [j6]Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan:
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinform. 38(8): 2356-2357 (2022) - [j5]Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan:
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. 23(1): 76 (2022) - [j4]Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma'ayan:
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. 23(1): 374 (2022) - [j3]John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz, Stephan C. Schürer, Mario Medvedovic, Avi Ma'ayan:
SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 50(W1): 697-709 (2022) - 2021
- [j2]Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan:
KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Res. 49(Webserver-Issue): 304-316 (2021) - [j1]Daniel J. B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan:
Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns 2(3): 100213 (2021)
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