KEA3: improved kinase enrichment analysis via data integration. - Maxim V. Kuleshov; Zhuorui Xie; Alexandra B. K. London; Janice Yang; John Erol Evangelista; Alexander Lachmann; Ingrid Shu; Denis Torre; Avi Ma'ayan (Nucleic Acids Res., 2021)

Appyters: Turning Jupyter Notebooks into data-driven web apps. - 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; et al. (Patterns, 2021)

blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. - Alexander Lachmann; Zhuorui Xie; Avi Ma'ayan (Bioinform., 2022)

Transforming L1000 profiles to RNA-seq-like profiles with deep learning. - Minji Jeon; Zhuorui Xie; John Erol Evangelista; Megan L. Wojciechowicz; Daniel J. B. Clarke; Avi Ma'ayan (BMC Bioinform., 2022)

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. - Eryk Kropiwnicki; Alexander Lachmann; Daniel J. B. Clarke; Zhuorui Xie; Kathleen M. Jagodnik; Avi Ma'ayan (BMC Bioinform., 2022)

SigCom LINCS: data and metadata search engine for a million gene expression signatures. - 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; et al. (Nucleic Acids Res., 2022)

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. - Giacomo B. Marino; Megan L. Wojciechowicz; Daniel J. B. Clarke; Maxim V. Kuleshov; Zhuorui Xie; Minji Jeon; Alexander Lachmann; Avi Ma'ayan (Database J. Biol. Databases Curation, 2023)

Enrichr-KG: bridging enrichment analysis across multiple libraries. - John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Nhi Nguyen; Daniel J. B. Clarke; Avi Ma'ayan (Nucleic Acids Res., 2023)

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. - Giacomo B. Marino; Michael Ngai; Daniel J. B. Clarke; Reid H. Fleishman; Eden Z. Deng; Zhuorui Xie; Nasheath Ahmed; Avi Ma'ayan (Nucleic Acids Res., 2023)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - Daniel J. B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano Ram Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; et al. (PLoS Comput. Biol., 2025)