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)

RummaGEO: Automatic mining of human and mouse gene sets from GEO. - Giacomo B. Marino; Daniel J. B. Clarke; Alexander Lachmann; Eden Z. Deng; Avi Ma'ayan (Patterns, 2024)

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)