Stephen A. Ramsey

22 papers Misc 2Journal 14Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Causal analysis for multivariate integrated clinical and environmental exposures data.
BMC Medical Informatics Decis. Mak.
Meghamala Sinha, Perry Haaland, Ashok K. Krishnamurthy, Bo Lan, Stephen A. Ramsey, Patrick L. Schmitt, Priya Sharma, Hao Xu, Karamarie Fecho
2025 J jnl
Correction: Causal analysis for multivariate integrated clinical and environmental exposures data.
BMC Medical Informatics Decis. Mak.
Meghamala Sinha, Perry Haaland, Ashok K. Krishnamurthy, Bo Lan, Stephen A. Ramsey, Patrick L. Schmitt, Priya Sharma, Hao Xu, Karamarie Fecho
2025 J jnl
PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs.
Bioinform.
Amy Glen, Eric W. Deutsch, Stephen A. Ramsey
2025 — conf
Using AI to Improve Diagnosis and Treatment of Rare Diseases: A Chat Agent for Equitable and Accessible Healthcare.
AIME (2)
Frank M. Hodges, Sundareswar Pullela, Guy Cohen, Akshay Mulgund, Jared C. Roach, Stephen A. Ramsey
2024 — conf
Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoring.
BCB
Sangam Buddhacharya, Noël Lefevre, Elain S. Fu, Stephen A. Ramsey
2024 J jnl
Predicting Time-to-Healing from a Digital Wound Image: A Hybrid Neural Network and Decision Tree Approach Improves Performance.
Comput.
Aravind Kolli, Qi Wei, Stephen A. Ramsey
2023 J jnl
ARAX: a graph-based modular reasoning tool for translational biomedicine.
Bioinform.
Amy Glen, Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G. Kvarfordt, Ross C. Peene, Shaopeng Liu, Andrew S. Hoffman, Jared C. Roach, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki
2022 J jnl
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.
CoRR
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
2022 J jnl
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.
BMC Bioinform.
E. C. Wood, Amy Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey
2022 J jnl
The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren.
Frontiers Artif. Intell.
Aleksandra Foksinska, Camerron M. Crowder, Andrew B. Crouse, Jeff Henrikson, William E. Byrd, Gregory Rosenblatt, Michael J. Patton, Kaiwen He, Thi K. Tran-Nguyen, Marissa Zheng, Stephen A. Ramsey, Nada Amin, John D. Osborne, Matthew Might
2021 J jnl
Predicting chemotherapy response using a variational autoencoder approach.
BMC Bioinform.
Qi Wei, Stephen A. Ramsey
2021 — conf
Structural Generalizability: The Case of Similarity Search.
SIGMOD Conference
Yodsawalai Chodpathumwan, Arash Termehchy, Stephen A. Ramsey, Aayam Shrestha, Amy Glen, Zheng Liu
2021 — conf
Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning.
AAAI Spring Symposium: Combining Machine Learning with Knowledge Engineering
Meghamala Sinha, Stephen A. Ramsey
2020 Misc conf
CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs.
PSB
Yao Yao, Stephen A. Ramsey
2019 J jnl
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.
BMC Bioinform.
Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey
2019 Misc conf
Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.
PSB
Zheng Liu, Yao Yao, Qi Wei, Benjamin Weeder, Stephen A. Ramsey
2017 — conf
CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome.
BCB
Yao Yao, Zheng Liu, Satpreet Singh, Qi Wei, Stephen A. Ramsey
2016 — conf
Exploration of regression models for cancer noncoding mutation recurrence.
BCB
Tanjin Xu, Stephen A. Ramsey
2015 J jnl
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Bioinform.
Jichen Yang, Stephen A. Ramsey
2010 J jnl
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Bioinform.
Stephen A. Ramsey, Theo A. Knijnenburg, Kathleen A. Kennedy, Daniel E. Zak, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Aaron E. Lampano, Vladimir Litvak, Garnet Navarro, Tetyana Stolyar, Alan Aderem, Ilya Shmulevich
2010 J jnl
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.
BMC Bioinform.
David B. Burdick, Christopher C. Cavnor, Jeremy Handcock, Sarah A. Killcoyne, Jake Lin, Bruz Marzolf, Stephen A. Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John Boyle
2008 J jnl
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.
PLoS Comput. Biol.
Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich