Stephen A. Ramsey

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 14

Top Topics

Geometric Features

Weight Matrices

Transcription Factor Binding Sites

Similarity Search

Top Venues

Publications

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) (2024)
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)
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) (2022)
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 T. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR (2022)
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 Osborne, Matthew Might
The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren. Frontiers Artif. Intell. 5 (2022)
Qi Wei, Stephen A. Ramsey
Predicting chemotherapy response using a variational autoencoder approach. BMC Bioinform. 22 (1) (2021)
Yodsawalai Chodpathumwan, Arash Termehchy, Stephen A. Ramsey, Aayam Shrestha, Amy Glen, Zheng Liu
Structural Generalizability: The Case of Similarity Search. SIGMOD Conference (2021)
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)
Yao Yao, Stephen A. Ramsey
CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Predictionof Functional Noncoding SNPs. PSB (2020)
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)
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) (2019)
Yao Yao, Zheng Liu, Satpreet Singh, Qi Wei, Stephen A. Ramsey
CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome. BCB (2017)
Tanjin Xu, Stephen A. Ramsey
Exploration of regression models for cancer noncoding mutation recurrence. BCB (2016)
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) (2015)
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 (2010)
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) (2010)
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)