ChEA3: transcription factor enrichment analysis by orthogonal omics integration. - Alexandra B. Keenan; Denis Torre; Alexander Lachmann; Ariel K. Leong; Megan L. Wojciechowicz; Vivian Utti; Kathleen M. Jagodnik; Eryk Kropiwnicki; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2019)

modEnrichr: a suite of gene set enrichment analysis tools for model organisms. - Maxim V. Kuleshov; Jennifer E. L. Diaz; Zachary N. Flamholz; Alexandra B. Keenan; Alexander Lachmann; Megan L. Wojciechowicz; Ross L. Cagan; Avi Ma'ayan (Nucleic Acids Res., 2019)

Geneshot: search engine for ranking genes from arbitrary text queries. - Alexander Lachmann; Brian M. Schilder; Megan L. Wojciechowicz; Denis Torre; Maxim V. Kuleshov; Alexandra B. Keenan; Avi Ma'ayan (Nucleic Acids Res., 2019)

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)

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)

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)