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ORCIDKathleen M. Jagodnik
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Journal Articles
- 2022
[j15]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): 76 (2022)- [j14]Alon Bartal, Kathleen M. Jagodnik:
Progress in and Opportunities for Applying Information Theory to Computational Biology and Bioinformatics. Entropy 24(7): 925 (2022) - [j13]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): 697-709 (2022) - 2021
- [j12]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) - [j11]Alon Bartal, Kathleen M. Jagodnik:
Role-Aware Information Spread in Online Social Networks. Entropy 23(11): 1542 (2021) - [j10]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): 100213 (2021) - 2020
- [j9]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): 3932-3934 (2020) - [j8]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): 100090 (2020) - 2019
- [j7]Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan:
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinform. 35(7): 1247-1248 (2019) - [j6]Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan:
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47(Webserver-Issue): W212-W224 (2019) - 2018
- [j5]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, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas A. Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer:
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. 46(Database-Issue): D558-D566 (2018) - 2017
- [j4]Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan:
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 71: 49-57 (2017) - 2016
- [j3]Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicolas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma'ayan:
GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinform. 17: 461:1-461:12 (2016) - [j2]Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan:
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44(Webserver-Issue): W90-W97 (2016) - [j1]Kathleen M. Jagodnik, Philip S. Thomas, Antonie J. van den Bogert, Michael S. Branicky, Robert F. Kirsch:
Human-Like Rewards to Train a Reinforcement Learning Controller for Planar Arm Movement. IEEE Trans. Hum. Mach. Syst. 46(5): 723-733 (2016)
Conference and Workshop Papers
- 2017
- [c3]Amrapali Zaveri, Shima Dastgheib, Chunlei Wu, Trish Whetzel, Ruben Verborgh, Paul Avillach, Gabor Korodi, Raymond Terryn, Kathleen M. Jagodnik, Pedro Assis, Michel Dumontier:
smartAPI: Towards a More Intelligent Network of Web APIs. ESWC (2) 2017: 154-169 - [c2]Shima Dastgheib, Trish Whetzel, Amrapali Zaveri, Cyrus Afrasiabi, Pedro Assis, Paul Avillach, Kathleen M. Jagodnik, Gabor Korodi, Marcin Pilarczyk, Jeff de Pons, Stephan C. Schürer, Raymond Terryn, Ruben Verborgh, Chunlei Wu, Michel Dumontier:
The SmartAPI Ecosystem for Making Web APIs FAIR. ISWC (Posters, Demos & Industry Tracks) 2017 - 2009
- [c1]Philip S. Thomas, Antonie J. van den Bogert, Kathleen M. Jagodnik, Michael S. Branicky:
Application of the Actor-Critic Architecture to Functional Electrical Stimulation Control of a Human Arm. IAAI 2009
Informal and Other Publications
- 2024
- [i1]Alon Bartal, Kathleen M. Jagodnik, Nava Pliskin, Abraham Seidmann:
Utilizing AI and Social Media Analytics to Discover Adverse Side Effects of GLP-1 Receptor Agonists. CoRR abs/2404.01358 (2024)
Coauthor Index
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