Stephen A. Ramsey

发表

Exploration of regression models for cancer noncoding mutation recurrence

Tanjin Xu, Stephen A. Ramsey, S. Ramsey, 2016, BCB.

An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters

Stephen A. Ramsey, S. Ramsey, 2015, Bioinformatics and biology insights.

CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs

Stephen A. Ramsey, Yao Yao, S. Ramsey, 2019, PSB.

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

Zheng Liu, Stephen A. Ramsey, Qi Wei, 2019, PSB.

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Bin Li, Jared C. Roach, Alistair G. Rust, 2008, PLoS Comput. Biol..

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

Stephen A. Ramsey, Jichen Yang, S. Ramsey, 2015, Bioinform..

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

Stephen A. Ramsey, Ilya Shmulevich, Vladimir Litvak, 2010, Bioinform..

CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome

Zheng Liu, Stephen A. Ramsey, Qi Wei, 2017, BCB.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

Stephen A. Ramsey, Ilya Shmulevich, John Boyle, 2009, BMC Bioinformatics.

Voting-based integration algorithm improves causal network learning from interventional and observational data: an application to cell signaling network inference

Prasad Tadepalli, Stephen A. Ramsey, Meghamala Sinha, 2020, bioRxiv.

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

Stephen A. Ramsey, Meghamala Sinha, S. Ramsey, 2021, AAAI Spring Symposium: Combining Machine Learning with Knowledge Engineering.

Structural Generalizability: The Case of Similarity Search

Stephen A. Ramsey, Arash Termehchy, Yodsawalai Chodpathumwan, 2021, SIGMOD Conference.

An approach for open multivariate analysis of integrated clinical and environmental exposures data

Karamarie Fecho, Stephen A. Ramsey, Ashok Krishnamurthy, 2021, Informatics in Medicine Unlocked.

Predicting chemotherapy response using a variational autoencoder approach

Stephen A. Ramsey, Qi Wei, 2021, BMC Bioinform..

Multiscale Representation of Genomic Signals

Peter W. Laird, Stephen A. Ramsey, Ilya Shmulevich, 2014, Nature Methods.

Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway

Stephen A. Ramsey, Elizabeth S. Gold, Yuliya Vengrenyuk, 2014, PLoS genetics.

ATF3, an adaptive-response gene, enhances TGFβ signaling and cancer-initiating cell features in breast cancer cells

Stephen A. Ramsey, Alan Aderem, S. Ramsey, 2010, Journal of Cell Science.

A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease

Stephen A. Ramsey, S. Ramsey, A. Yu, 2018, Interdisciplinary Sciences: Computational Life Sciences.

Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals

Alistair G. Rust, Stephen A. Ramsey, Ilya Shmulevich, 2009, Nature Immunology.