SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. - Avi Ma'ayan; Sherry L. Jenkins; Ryan L. Webb; Seth I. Berger; Sudarshan P. Purushothaman; Noura S. Abul-Husn; Jeremy M. Posner; Tony Flores; Ravi Iyengar (BMC Syst. Biol., 2009)

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. - Caroline Baroukh; Sherry L. Jenkins; Ruth Dannenfelser; Avi Ma'ayan (Source Code Biol. Medicine, 2011)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. - Maxim V. Kuleshov; Matthew R. Jones; Andrew D. Rouillard; Nicolas F. Fernandez; Qiaonan Duan; Zichen Wang 002; Simon Koplev; Sherry L. Jenkins; Kathleen M. Jagodnik; Alexander Lachmann; Michael G. McDermott; Caroline D. Monteiro; et al. (Nucleic Acids Res., 2016)

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. - Kathleen M. Jagodnik; Simon Koplev; Sherry L. Jenkins; Lucila Ohno-Machado; Benedict Paten; Stephan C. Schürer; Michel Dumontier; Ruben Verborgh; Alex A. T. Bui; Peipei Ping; Neil J. McKenna; Ravi K. Madduri; et al. (J. Biomed. Informatics, 2017)

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. - Amar Koleti; Raymond Terryn; Vasileios Stathias; Caty Chung; Daniel J. Cooper; John Paul Turner; Dusica Vidovic; Michele Forlin; Tanya T. Kelley; Alessandro D'Urso; Bryce K. Allen; Denis Torre; et al. (Nucleic Acids Res., 2018)

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)

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)

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)