Daniel J. B. Clarke

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 18

Top Topics

Gene Expression

Detect Outliers

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan
Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. 51 (W1) (2023)
Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. 51 (W1) (2023)
Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation 2023 (2023)
A. Ravishankar Rao, Daniel J. B. Clarke, Subrata Garai, Soumyabrata Dey
A system for exploring big data: an iterative k-means searchlight for outlier detection on open health data. CoRR (2023)
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, Avi Ma'ayan
SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 50 (W1) (2022)
Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma'ayan
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. 23 (1) (2022)
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. 23 (1) (2022)
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, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan
Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns 2 (3) (2021)
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
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database J. Biol. Databases Curation 2021 (2021)
Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
EnrichrBot: Twitter bot tracking tweets about human genes. Bioinform. 36 (12) (2020)
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, Alexander Lachmann, Avi Ma'ayan
The COVID-19 Drug and Gene Set Library. Patterns 1 (6) (2020)
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, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 48 (Database-Issue) (2020)
A. Ravishankar Rao, Daniel J. B. Clarke
Capacity Building for a Cybersecurity Workforce Through Hands-on Labs for Internet-of-Things Security. NCS (2019)
A. Ravishankar Rao, Subrata Garai, Daniel J. B. Clarke, Soumyabrata Dey
A system for exploring big data: an iterative k-means searchlight for outlier detection on open health data. IJCNN (2018)
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, Avi Ma'ayan
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
A. Ravishankar Rao, Daniel J. B. Clarke
Hiding in plain sight: insights about health-care trends gained through open health data. CoRR (2017)
A. Ravishankar Rao, Daniel J. B. Clarke
An open-source framework for the interactive exploration of Big Data: Applications in understanding health care. IJCNN (2017)
A. Ravishankar Rao, Daniel J. B. Clarke
A fully integrated open-source toolkit for mining healthcare big-data: architecture and applications. ICHI (2016)