A fully integrated open-source toolkit for mining healthcare big-data: architecture and applications. - A. Ravishankar Rao; Daniel J. B. Clarke (ICHI, 2016)

An open-source framework for the interactive exploration of Big Data: Applications in understanding health care. - A. Ravishankar Rao; Daniel J. B. Clarke (IJCNN, 2017)

Hiding in plain sight: insights about health-care trends gained through open health data. - A. Ravishankar Rao; Daniel J. B. Clarke (CoRR, 2017)

A comparison of models to predict medical procedure costs from open public healthcare data. - A. Ravishankar Rao; Daniel Clarke 002 (IJCNN, 2018)

A system for exploring big data: an iterative k-means searchlight for outlier detection on open health data. - A. Ravishankar Rao; Subrata Garai; Daniel J. B. Clarke; Soumyabrata Dey (IJCNN, 2018)

Building an Open Health Data Analytics Platform: a Case Study Examining Relationships and Trends in Seniority and Performance in Healthcare Providers. - A. Ravishankar Rao; Daniel Clarke 002; Maryelena Vargas (J. Heal. Informatics Res., 2018)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. - Daniel J. B. Clarke; Maxim V. Kuleshov; Brian M. Schilder; Denis Torre; Mary E. Duffy; Alexandra B. Keenan; Alexander Lachmann; Axel S. Feldmann; Gregory W. Gundersen; Moshe C. Silverstein; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2018)

Capacity Building for a Cybersecurity Workforce Through Hands-on Labs for Internet-of-Things Security. - A. Ravishankar Rao; Daniel J. B. Clarke (NCS, 2019)

EnrichrBot: Twitter bot tracking tweets about human genes. - Alon Bartal; Alexander Lachmann; Daniel J. B. Clarke; Allison H. Seiden; Kathleen M. Jagodnik; Avi Ma'ayan (Bioinform., 2020)

Perspectives on emerging directions in using IoT devices in blockchain applications. - A. Ravishankar Rao; Daniel Clarke 002 (Internet Things, 2020)

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. - Vasileios Stathias; John Paul Turner; Amar Koleti; Dusica Vidovic; Daniel J. Cooper; Mehdi Fazel-Najafabadi; Marcin Pilarczyk; Raymond Terryn; Caty Chung; Afoma Umeano; Daniel J. B. Clarke; Alexander Lachmann; et al. (Nucleic Acids Res., 2020)

The COVID-19 Drug and Gene Set Library. - Maxim V. Kuleshov; Daniel J. Stein; Daniel J. B. Clarke; Eryk Kropiwnicki; Kathleen M. Jagodnik; Alon Bartal; John Erol Evangelista; Jason Hom; Minxuan Cheng; Allison Bailey; Abigail Zhou; Laura B. Ferguson; et al. (Patterns, 2020)

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. - Eryk Kropiwnicki; John Erol Evangelista; Daniel J. Stein; Daniel J. B. Clarke; Alexander Lachmann; Maxim V. Kuleshov; Minji Jeon; Kathleen M. Jagodnik; Avi Ma'ayan (Database J. Biol. Databases Curation, 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)

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)

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)