Found 18 results
Author Title Type [ Year(Desc)]
Filters: Keyword is Computational Biology  [Clear All Filters]
2000
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.
2002
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.
2008
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.
2010
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.
2011
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.
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.
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.
2016
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.
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.
2018
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, “A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.”, Methods Mol Biol, vol. 1702, pp. 291-305, 2018.
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.
2019
“The Biomedical Data Translator Program: Conception, Culture, and Community.”, Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 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.
“Toward A Universal Biomedical Data Translator.”, Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.
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.
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.