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2020 – today
- 2025
[j12]Meghamala Sinha, Perry Haaland, Ashok K. Krishnamurthy, Bo Lan, Stephen A. Ramsey, Patrick L. Schmitt, Priya Sharma, Hao Xu, Karamarie Fecho:
Causal analysis for multivariate integrated clinical and environmental exposures data. BMC Medical Informatics Decis. Mak. 25(1): 27 (2025)- [j11]Meghamala Sinha, Perry Haaland, Ashok K. Krishnamurthy, Bo Lan, Stephen A. Ramsey, Patrick L. Schmitt, Priya Sharma, Hao Xu, Karamarie Fecho:
Correction: Causal analysis for multivariate integrated clinical and environmental exposures data. BMC Medical Informatics Decis. Mak. 25(1): 78 (2025) - 2024
- [j10]Aravind Kolli, Qi Wei
, Stephen A. Ramsey:
Predicting Time-to-Healing from a Digital Wound Image: A Hybrid Neural Network and Decision Tree Approach Improves Performance. Comput. 12(3): 42 (2024) - [c7]Sangam Buddhacharya, Noël Lefevre, Elain S. Fu, Stephen A. Ramsey:
Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoring. BCB 2024: 55:1-55:9 - 2023
- [j9]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:
ARAX: a graph-based modular reasoning tool for translational biomedicine. Bioinform. 39(3) (2023) - 2022
- [j8]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:
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. BMC Bioinform. 23(1): 400 (2022) - [j7]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:
The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren. Frontiers Artif. Intell. 5 (2022) - [i1]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:
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR abs/2203.13906 (2022) - 2021
- [j6]Qi Wei, Stephen A. Ramsey:
Predicting chemotherapy response using a variational autoencoder approach. BMC Bioinform. 22(1): 453 (2021) - [c6]Meghamala Sinha, Stephen A. Ramsey:
Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning. AAAI Spring Symposium: Combining Machine Learning with Knowledge Engineering 2021 - [c5]Yodsawalai Chodpathumwan, Arash Termehchy, Stephen A. Ramsey, Aayam Shrestha, Amy Glen, Zheng Liu:
Structural Generalizability: The Case of Similarity Search. SIGMOD Conference 2021: 326-338 - 2020
- [c4]Yao Yao, Stephen A. Ramsey:
CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs. PSB 2020: 535-546
2010 – 2019
- 2019
- [j5]Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey:
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. BMC Bioinform. 20(1): 63 (2019) - [c3]Zheng Liu, Yao Yao, Qi Wei, Benjamin Weeder, Stephen A. Ramsey:
Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions. PSB 2019: 76-87 - 2017
- [c2]Yao Yao, Zheng Liu, Satpreet Singh, Qi Wei, Stephen A. Ramsey:
CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome. BCB 2017: 79-88 - 2016
- [c1]Tanjin Xu, Stephen A. Ramsey:
Exploration of regression models for cancer noncoding mutation recurrence. BCB 2016: 546-553 - 2015
- [j4]Jichen Yang, Stephen A. Ramsey:
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. Bioinform. 31(21): 3445-3450 (2015) - 2010
- [j3]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:
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinform. 26(17): 2071-2075 (2010) - [j2]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:
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinform. 11: 377 (2010)
2000 – 2009
- 2008
- [j1]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:
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. PLoS Comput. Biol. 4(3) (2008)
Coauthor Index
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