Carlson College of Veterinary Medicine

M. Sinha, Tadepalli, P., and Ramsey, S. A., “Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference.”, PLoS One, vol. 16, no. 2, p. e0245776, 2021.

Y. Yao and Ramsey, S. A., “CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.”, Pac Symp Biocomput, vol. 25, pp. 535-546, 2020.

S. A. Ramsey, Liu, Z., Yao, Y., and Weeder, B., “Combining eQTL and SNP Annotation Data to Identify Functional Noncoding SNPs in GWAS Trait-Associated Regions.”, Methods Mol Biol, vol. 2082, pp. 73-86, 2020.

A. Kashyap, Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E. W., Finnegan, M. V., Geniza, M., Hendrix, D. A., Löhr, C. V., Petro, V. M., Sharpton, T. J., Wells, J., Epps, C. W., Jaiswal, P., Tyler, B. M., and Ramsey, S. A., “Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.”, BMC Genomics, vol. 21, no. 1, p. 153, 2020.

C. Parachini-Winter, Bracha, S., Ramsey, S. A., Yang, L., Ho, E., Leeper, H., and Curran, K. M., “Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane.”, J Vet Intern Med, vol. 34, no. 5, pp. 2036-2047, 2020.

H. R. C. Shoen, Rose, S. J., Ramsey, S. A., de Morais, H. Autran, and Bermudez, L. E., “Analysis of Staphylococcus infections in a veterinary teaching hospital from 2012 to 2015.”, Comp Immunol Microbiol Infect Dis, vol. 66, p. 101332, 2019.

“The Biomedical Data Translator Program: Conception, Culture, and Community.”, Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 2019.

Y. Yao, Liu, Z., Wei, Q., and Ramsey, S. A., “CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.”, BMC Bioinformatics, vol. 20, no. 1, p. 63, 2019.

Q. Wei, Ramsey, S. A., Larson, M. K., Berlow, N. E., Ochola, D., Shiprack, C., Kashyap, A., Séguin, B., Keller, C., and Löhr, C. V., “Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach.”, BMC Cancer, vol. 19, no. 1, p. 311, 2019.

V. R. Babaev, Ding, L., Zhang, Y., May, J. M., Ramsey, S. A., Vickers, K. C., and Linton, M. R. F., “Loss 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 Biol, vol. 39, no. 2, pp. 156-169, 2019.

Z. Liu, Yao, Y., Wei, Q., Weeder, B., and Ramsey, S. A., “Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.”, Pac Symp Biocomput, vol. 24, pp. 76-87, 2019.

J. - Da Lin, Nishi, H., Poles, J., Niu, X., Mccauley, C., Rahman, K., Brown, E. J., Yeung, S. T., Vozhilla, N., Weinstock, A., Ramsey, S. A., Fisher, E. A., and Loke, P. 'ng, “Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression.”, JCI Insight, vol. 4, no. 4, 2019.

“Toward A Universal Biomedical Data Translator.”, Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.

A. Z. Yu and Ramsey, S. A., “A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease.”, Interdiscip Sci, vol. 10, no. 2, pp. 449-454, 2018.

A. J. Singh, Ramsey, S. A., Filtz, T. M., and Kioussi, C., “Differential gene regulatory networks in development and disease.”, Cell Mol Life Sci, vol. 75, no. 6, pp. 1013-1025, 2018.

A. J. Singh, Chang, C. - N., Ma, H. - Y., Ramsey, S. A., Filtz, T. M., and Kioussi, C., “FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb.”, Sci Rep, vol. 8, no. 1, p. 7670, 2018.

S. A. Ramsey, “A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.”, Methods Mol Biol, vol. 1702, pp. 291-305, 2018.

J. V. Brady, Troyer, R. M., Ramsey, S. A., Leeper, H., Yang, L., Maier, C. S., Goodall, C. P., Ruby, C. E., Albarqi, H. A. M., Taratula, O., and Bracha, S., “A Preliminary Proteomic Investigation of Circulating Exosomes and Discovery of Biomarkers Associated with the Progression of Osteosarcoma in a Clinical Model of Spontaneous Disease.”, Transl Oncol, vol. 11, no. 5, pp. 1137-1146, 2018.

S. A. Ramsey, Xu, T., Goodall, C., Rhodes, A. C., Kashyap, A., He, J., and Bracha, S., “Cross-species analysis of the canine and human bladder cancer transcriptome and exome.”, Genes Chromosomes Cancer, vol. 56, no. 4, pp. 328-343, 2017.

P. S. Askovich, Ramsey, S. A., Diercks, A. H., Kennedy, K. A., Knijnenburg, T. A., and Aderem, A., “Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.”, PLoS One, vol. 12, no. 9, p. e0184850, 2017.

K. Rahman, Vengrenyuk, Y., Ramsey, S. A., Vila, N. Rotllan, Girgis, N. M., Liu, J., Gusarova, V., Gromada, J., Weinstock, A., Moore, K. J., Loke, P. 'ng, and Fisher, E. A., “Inflammatory Ly6Chi monocytes and their conversion to M2 macrophages drive atherosclerosis regression.”, J Clin Invest, vol. 127, no. 8, pp. 2904-2915, 2017.

M. Choudhury and Ramsey, S. A., “Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.”, Gene Regul Syst Bio, vol. 10, pp. 105-110, 2016.

T. Liang, Robinson, R., Houghtaling, J., Fridley, G., Ramsey, S. A., and Fu, E., “Investigation of Reagent Delivery Formats in a Multivalent Malaria Sandwich Immunoassay and Implications for Assay Performance.”, Anal Chem, vol. 88, no. 4, pp. 2311-20, 2016.

Y. Vengrenyuk, Nishi, H., Long, X., Ouimet, M., Savji, N., Martinez, F. O., Cassella, C. P., Moore, K. J., Ramsey, S. A., Miano, J. M., and Fisher, E. A., “Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype.”, Arterioscler Thromb Vasc Biol, vol. 35, no. 3, pp. 535-46, 2015.

J. Yang and Ramsey, S. A., “A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.”, Bioinformatics, vol. 31, no. 21, pp. 3445-50, 2015.