Found 18 results
Author Title [ Type(Asc)] Year
Filters: Keyword is Computational Biology  [Clear All Filters]
Journal Article
A. Yambartsev, Perlin, M. A., Kovchegov, Y., Shulzhenko, N., Mine, K. L., Dong, X., and Morgun, A., “Unexpected links reflect the noise in networks.”, Biol Direct, vol. 11, no. 1, p. 52, 2016.
R. R. Rodrigues, Shulzhenko, N., and Morgun, A., “Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions.”, Methods Mol Biol, vol. 1849, pp. 227-242, 2018.
“Toward A Universal Biomedical Data Translator.”, Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.
D. B. Burdick, Cavnor, C. C., Handcock, J., Killcoyne, S., Lin, J., Marzolf, B., Ramsey, S. A., Rovira, H., Bressler, R., Shmulevich, I., and Boyle, J., “SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.”, BMC Bioinformatics, vol. 11, p. 377, 2010.
J. P. Bannantine, Griffiths, R. S., Viratyosin, W., Brown, W. J., and Rockey, D. D., “A secondary structure motif predictive of protein localization to the chlamydial inclusion membrane.”, Cell Microbiol, vol. 2, no. 1, pp. 35-47, 2000.
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.
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.
S. A. Ramsey, “A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.”, Methods Mol Biol, vol. 1702, pp. 291-305, 2018.
S. Tripathi, Pohl, M. O., Zhou, Y., Rodriguez-Frandsen, A., Wang, G., Stein, D. A., Moulton, H. M., DeJesus, P., Che, J., Mulder, L. C. F., Yángüez, E., Andenmatten, D., Pache, L., Manicassamy, B., Albrecht, R. A., Gonzalez, M. G., Nguyen, Q., Brass, A., Elledge, S., White, M., Shapira, S., Hacohen, N., Karlas, A., Meyer, T. F., Shales, M., Gatorano, A., Johnson, J. R., Jang, G., Johnson, T., Verschueren, E., Sanders, D., Krogan, N., Shaw, M., König, R., Stertz, S., García-Sastre, A., and Chanda, S. K., “Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.”, Cell Host Microbe, vol. 18, no. 6, pp. 723-35, 2015.
A. V. Ratushny, Ramsey, S. A., and Aitchison, J. D., “Mathematical modeling of biomolecular network dynamics.”, Methods Mol Biol, vol. 781, pp. 415-33, 2011.
R. Greer, Dong, X., Morgun, A., and Shulzhenko, N., “Investigating a holobiont: Microbiota perturbations and transkingdom networks.”, Gut Microbes, vol. 7, no. 2, pp. 126-35, 2016.
W. Viratyosin, Campbell, L. Ann, Kuo, C. - C., and Rockey, D. D., “Intrastrain and interstrain genetic variation within a paralogous gene family in Chlamydia pneumoniae.”, BMC Microbiol, vol. 2, p. 38, 2002.
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.
A. V. Ratushny, Ramsey, S. A., Roda, O., Wan, Y., Smith, J. J., and Aitchison, J. D., “Control of transcriptional variability by overlapping feed-forward regulatory motifs.”, Biophys J, vol. 95, no. 8, pp. 3715-23, 2008.
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.
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.
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.
“The Biomedical Data Translator Program: Conception, Culture, and Community.”, Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 2019.