Kathleen M. Jagodnik

21 papers C 1Journal 18Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
LIT-GRAPH: Evaluating Deep vs. Shallow Graph Embeddings for High-Quality Text Recommendation in Domain-Specific Knowledge Graphs.
CoRR
Nirmal Gelal, Chloe Snow, Kathleen M. Jagodnik, Ambyr Rios, Hande Küçük-McGinty
2025 J jnl
DruGNNosis-MoA: Elucidating Drug Mechanisms as Etiological or Palliative With Graph Neural Networks Employing a Large Language Model.
IEEE J. Biomed. Health Informatics
Liad Brettler, Eden Berman, Kathleen M. Jagodnik, Alon Bartal
2024 J jnl
Utilizing AI and Social Media Analytics to Discover Adverse Side Effects of GLP-1 Receptor Agonists.
CoRR
Alon Bartal, Kathleen M. Jagodnik, Nava Pliskin, Abraham Seidmann
2022 J jnl
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.
BMC Bioinform.
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
2022 J jnl
Progress in and Opportunities for Applying Information Theory to Computational Biology and Bioinformatics.
Entropy
Alon Bartal, Kathleen M. Jagodnik
2022 J jnl
SigCom LINCS: data and metadata search engine for a million gene expression signatures.
Nucleic Acids Res.
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
2021 J jnl
Appyters: Turning Jupyter Notebooks into data-driven web apps.
Patterns
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
2021 J jnl
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.
Database J. Biol. Databases Curation
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
2021 J jnl
Role-Aware Information Spread in Online Social Networks.
Entropy
Alon Bartal, Kathleen M. Jagodnik
2020 J jnl
EnrichrBot: Twitter bot tracking tweets about human genes.
Bioinform.
Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
2020 J jnl
The COVID-19 Drug and Gene Set Library.
Patterns
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
2019 J jnl
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Nucleic Acids Res.
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
2019 J jnl
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.
Bioinform.
Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan
2018 J jnl
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.
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
2017 J jnl
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.
J. Biomed. Informatics
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, Ajay Pillai, Avi Ma'ayan
2017 — conf
The SmartAPI Ecosystem for Making Web APIs FAIR.
ISWC (Posters, Demos & Industry Tracks)
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
2017 — conf
smartAPI: Towards a More Intelligent Network of Web APIs.
ESWC (2)
Amrapali Zaveri, Shima Dastgheib, Chunlei Wu, Trish Whetzel, Ruben Verborgh, Paul Avillach, Gabor Korodi, Raymond Terryn, Kathleen M. Jagodnik, Pedro Assis, Michel Dumontier
2016 J jnl
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res.
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
2016 J jnl
GEN3VA: aggregation and analysis of gene expression signatures from related studies.
BMC Bioinform.
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
2016 J jnl
Human-Like Rewards to Train a Reinforcement Learning Controller for Planar Arm Movement.
IEEE Trans. Hum. Mach. Syst.
Kathleen M. Jagodnik, Philip S. Thomas, Antonie J. van den Bogert, Michael S. Branicky, Robert F. Kirsch
2009 C conf
Application of the Actor-Critic Architecture to Functional Electrical Stimulation Control of a Human Arm.
IAAI
Philip S. Thomas, Antonie J. van den Bogert, Kathleen M. Jagodnik, Michael S. Branicky