Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. - 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; et al. (PLoS Comput. Biol., 2008)

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. - 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; et al. (Bioinform., 2010)

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. - 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 (BMC Bioinform., 2010)

A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites. - Jichen Yang; Stephen A. Ramsey (Bioinform., 2015)

Exploration of regression models for cancer noncoding mutation recurrence. - Tanjin Xu; Stephen A. Ramsey (BCB, 2016)

CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome. - Yao Yao 007; Zheng Liu; Satpreet Singh; Qi Wei 006; Stephen A. Ramsey (BCB, 2017)

Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions. - Zheng Liu; Yao Yao 007; Qi Wei 006; Benjamin Weeder; Stephen A. Ramsey (PSB, 2019)

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. - Yao Yao 007; Zheng Liu; Qi Wei 006; Stephen A. Ramsey (BMC Bioinform., 2019)

CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs. - Yao Yao 007; Stephen A. Ramsey (PSB, 2020)

Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning. - Meghamala Sinha; Stephen A. Ramsey (AAAI Spring Symposium: Combining Machine Learning with Knowledge Engineering, 2021)

Structural Generalizability: The Case of Similarity Search. - Yodsawalai Chodpathumwan; Arash Termehchy; Stephen A. Ramsey; Aayam Shrestha; Amy Glen; Zheng Liu (SIGMOD Conference, 2021)

Predicting chemotherapy response using a variational autoencoder approach. - Qi Wei 006; Stephen A. Ramsey (BMC Bioinform., 2021)

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. - 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; et al. (BMC Bioinform., 2022)

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. - 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; et al. (CoRR, 2022)

The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren. - 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; et al. (Frontiers Artif. Intell., 2022)

ARAX: a graph-based modular reasoning tool for translational biomedicine. - 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; et al. (Bioinform., 2023)

Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoring. - Sangam Buddhacharya; Noël Lefevre; Elain S. Fu; Stephen A. Ramsey (BCB, 2024)

Predicting Time-to-Healing from a Digital Wound Image: A Hybrid Neural Network and Decision Tree Approach Improves Performance. - Aravind Kolli; Qi Wei 006; Stephen A. Ramsey (Comput., 2024)

Using AI to Improve Diagnosis and Treatment of Rare Diseases: A Chat Agent for Equitable and Accessible Healthcare. - Frank M. Hodges; Sundareswar Pullela; Guy Cohen; Akshay Mulgund; Jared C. Roach; Stephen A. Ramsey (AIME (2), 2025)

Causal analysis for multivariate integrated clinical and environmental exposures data. - Meghamala Sinha; Perry Haaland; Ashok K. Krishnamurthy 001; Bo Lan; Stephen A. Ramsey; Patrick L. Schmitt; Priya Sharma; Hao Xu 006; Karamarie Fecho (BMC Medical Informatics Decis. Mak., 2025)

Correction: Causal analysis for multivariate integrated clinical and environmental exposures data. - Meghamala Sinha; Perry Haaland; Ashok K. Krishnamurthy 001; Bo Lan; Stephen A. Ramsey; Patrick L. Schmitt; Priya Sharma; Hao Xu 006; Karamarie Fecho (BMC Medical Informatics Decis. Mak., 2025)