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Author Details

Stephen A Ramsey
Oregon State University
2004
68
26
PMIDPaper TitleJournal TitlePublished Year
36752514ARAX: a graph-based modular reasoning tool for translational biomedicine.Bioinformatics2023
36125173Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.Clin Transl Sci2022
36214558Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution.Infect Immun2022
36248623The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren.Front Artif Intell2022
36175836RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.BMC Bioinformatics2022
33933069Exosomal proteomic signatures correlate with drug resistance and carboplatin treatment outcome in a spontaneous model of canine osteosarcoma.Cancer Cell Int2021
35875189An approach for open multivariate analysis of integrated clinical and environmental exposures data.Inform Med Unlocked2021
33720008Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis.Elife2021
33573233Vitamin E Deficiency Disrupts Gene Expression Networks during Zebrafish Development.Nutrients2021
33556096Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference.PLoS One2021
34551729Predicting chemotherapy response using a variational autoencoder approach.BMC Bioinformatics2021
32926463Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane.J Vet Intern Med2020
32050897Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.BMC Genomics2020
31797625CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.Pac Symp Biocomput2020
31849009Combining eQTL and SNP Annotation Data to Identify Functional Noncoding SNPs in GWAS Trait-Associated Regions.Methods Mol Biol2020
30567482Loss of 2 Akt (Protein Kinase B) Isoforms in Hematopoietic Cells Diminished Monocyte and Macrophage Survival and Reduces Atherosclerosis in Ldl Receptor-Null Mice.Arterioscler Thromb Vasc Biol2019
31437674Analysis of Staphylococcus infections in a veterinary teaching hospital from 2012 to 2015.Comp Immunol Microbiol Infect Dis2019
30864312Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.Pac Symp Biocomput2019
30947707Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach.BMC Cancer2019
30830865Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression.JCI Insight2019
30727967CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.BMC Bioinformatics2019
27778232A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease.Interdiscip Sci2018
30053712A Preliminary Proteomic Investigation of Circulating Exosomes and Discovery of Biomarkers Associated with the Progression of Osteosarcoma in a Clinical Model of Spontaneous Disease.Transl Oncol2018
29769607FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb.Sci Rep2018
29119511A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.Methods Mol Biol2018
29018868Differential gene regulatory networks in development and disease.Cell Mol Life Sci2018
28052524Cross-species analysis of the canine and human bladder cancer transcriptome and exome.Genes Chromosomes Cancer2017
28650342Inflammatory Ly6Chi monocytes and their conversion to M2 macrophages drive atherosclerosis regression.J Clin Invest2017
28922390Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.PLoS One2017
26835721Investigation of Reagent Delivery Formats in a Multivalent Malaria Sandwich Immunoassay and Implications for Assay Performance.Anal Chem2016
28008225Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.Gene Regul Syst Bio2016
27812284An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.Bioinform Biol Insights2016
25573853Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype.Arterioscler Thromb Vasc Biol2015
26130577A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.Bioinformatics2015
25983554Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.Bioinform Biol Insights2015
25755249An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux.EMBO J2015
24727652Multiscale representation of genomic signals.Nat Methods2014
25474352Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway.PLoS Genet2014
23536772Urokinase plasminogen activator induces pro-fibrotic/m2 phenotype in murine cardiac macrophages.PLoS One2013
22473958ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation.J Exp Med2012
22531117Asymmetric positive feedback loops reliably control biological responses.Mol Syst Biol2012
21536666Mechanisms of urokinase plasminogen activator (uPA)-mediated atherosclerosis: role of the uPA receptor and S100A8/A9 proteins.J Biol Chem2011
22140373Transport in two-dimensional paper networks.Microfluid Nanofluidics2011
21936486Enhanced sensitivity of lateral flow tests using a two-dimensional paper network format.Anal Chem2011
21877294Mathematical modeling of biomolecular network dynamics.Methods Mol Biol2011
20201031A systems biology approach to understanding atherosclerosis.EMBO Mol Med2010
20930144ATF3, an adaptive-response gene, enhances TGF{beta} signaling and cancer-initiating cell features in breast cancer cells.J Cell Sci2010
20663846Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.Bioinformatics2010
20630057SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.BMC Bioinformatics2010
19223588Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform.Proc Natl Acad Sci U S A2009
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Collaborators

Alan Aderem
Seattle Children's Research Institute
Co-authored papers 10
Elizabeth S Gold
Seattle Children's Research Institute
Co-authored papers 8
Ilya Shmulevich
Institute for Systems Biology
Co-authored papers 7
John D Aitchison
Center for Global Infectious Disease Research, Seattle Children's Research Institute
Co-authored papers 7
Jennifer J Smith
Institute for Systems Biology
Co-authored papers 5
Daehee Hwang
Co-authored papers 3
Vladimir Litvak
Co-authored papers 3
Leroy Hood
Center for Phenomic Health, The Buck Institute for Research on Aging
Co-authored papers 3
Theo A Knijnenburg
Allen Institute for Cell Science
Co-authored papers 3
Jared C Roach
Institute for Systems Biology
Co-authored papers 3
Garnet Navarro
Universidad Antonio Narino
Co-authored papers 2
Eric W Deutsch
Institute for Systems Biology
Co-authored papers 2
Matti Nykter
Prostate Cancer Research Center, Tampere University and Tays Cancer Center
Co-authored papers 2
Timothy Galitski
Institute for Systems Biology
Co-authored papers 2
Bruz Marzolf
Co-authored papers 2
Andrew F Siegel
University of Washington
Co-authored papers 2
Vesteinn Thorsson
Institute for Systems Biology
Co-authored papers 2
Karamarie Fecho
Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill
Co-authored papers 2
David Koslicki
and the Huck Institutes of the Life Sciences, Penn State University, University Park
Co-authored papers 2
Marcello Marelli
AstraZeneca Oncology R&D
Co-authored papers 2
Kathryn J Moore
Co-authored papers 2
Alan H Diercks
Seattle Children's Research Institute
Co-authored papers 1
Jesper Gromada
Co-authored papers 1
Nathan D Price
Institute for Systems Biology
Co-authored papers 1
Peter S Askovich
Center for Infectious Disease Research
Co-authored papers 1
John T Berger
4Children's National Hospital
Co-authored papers 1
Matthew Might
Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham
Co-authored papers 1
Kent Shefchek
University of Colorado Anschutz Medical Campus
Co-authored papers 1
Jeffrey A Ranish
Institute for Systems Biology
Co-authored papers 1
Nomi L Harris
Lawrence Berkely National Laboratory, Massachusetts Institute of Technology, Princeton University
Co-authored papers 1
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