Stephen A. Ramsey

According to our database, Stephen A. Ramsey authored at least 16 papers between 2008 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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, Eric W. Deutsch, Stephen A. Ramsey, David Koslicki

Bioinform., March, 2023

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, John D. Osborne, Matthew Might

Frontiers Artif. Intell., 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, 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

CoRR, 2022

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, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey

BMC Bioinform., 2022

2021

Predicting chemotherapy response using a variational autoencoder approach.

Qi Wei, Stephen A. Ramsey

BMC Bioinform., 2021

Structural Generalizability: The Case of Similarity Search.

Yodsawalai Chodpathumwan, Arash Termehchy, Stephen A. Ramsey, Aayam Shrestha, Amy Glen, Zheng Liu

Proceedings of the SIGMOD '21: International Conference on Management of Data, 2021

Using a General Prior Knowledge Graph to Improve Data-Driven Causal Network Learning.

Meghamala Sinha, Stephen A. Ramsey

Proceedings of the AAAI 2021 Spring Symposium on Combining Machine Learning and Knowledge Engineering (AAAI-MAKE 2021), 2021

2020

CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs.

Yao Yao, Stephen A. Ramsey

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.

Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey

BMC Bioinform., December, 2019

Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.

Zheng Liu, Yao Yao, Qi Wei, Benjamin Weeder, Stephen A. Ramsey

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

2017

CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome.

Yao Yao, Zheng Liu, Satpreet Singh, Qi Wei, Stephen A. Ramsey

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

Exploration of regression models for cancer noncoding mutation recurrence.

Tanjin Xu, Stephen A. Ramsey

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.

Jichen Yang, Stephen A. Ramsey

Bioinform., 2015

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

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, Ilya Shmulevich

Bioinform., 2010

2008

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, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich

PLoS Comput. Biol., 2008