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Publications

To see the scholarly work done by the Bioinformatics and Medical Informatics program:

Recent publications from BMI students and faculty affiliates (non-exhaustive – please see individual Google Scholar links for full lists, BMI students in boldface):

Ang, Gavrila, et al. “A High-quality Genome of the convergent lady beetle, Hippodamia convergens.” G3: Genes, Genomes, Genetics (2024): jkae083.

Ortiz-Velez, Adrian, and Scott T. Kelley. “Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA).” NAR Genomics and Bioinformatics 6.1 (2024): lqad110.

Ortiz-Velez, Adrian N., et al. “AutoPhy: Automated phylogenetic identification of novel protein subfamilies.” Plos one 19.1 (2024): e0291801.

Ortiz-Velez, Adrian, and Jeet Sukumaran. “Information theoretic inference of magnitude and direction of gene flow in metapopulation networks using nyemtaay, with potential for applications in metastasizing cancer clonal cell origin analysis.” bioRxiv (2024): 2024-06.

Sisk-Hackworth, Laura, Ortiz-Velez, Adrian et al. “Compositional data analysis of periodontal disease microbial communities.” Frontiers in microbiology 12 (2021): 617949.

Anais Aoki, Arun Sethuraman. Accurate predictive modeling of conservation status in animal species using supervised learning, 24 October 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-3471388/v1]

Canto-Encalada, G., Armstrong, J., Focil-Espinosa, C., Adekunle-Fiyin, A., Peeler, I., Gebbie, W. R., … & Zuniga, C. (2023). Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models.

Conkle-Gutierrez, D., Ramirez-Busby, S. M., Gorman, B. M., Elghraoui, A., Hoffner, S., Elmaraachli, W., & Valafar, F. (2024). Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks. Frontiers in Microbiology, 14, 1265390.

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A.,…, Fouquier, J., … & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8), 852-857.

Fouquier, Jennifer, Tara Schwartz, and Scott T. Kelley. “Rapid assemblage of diverse environmental fungal communities on public restroom floors.” Indoor air 26.6 (2016): 869-879.

Fouquier, J., Rideout, J. R., Bolyen, E., Chase, J., Shiffer, A., McDonald, D., … & Kelley, S. T. (2016). Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome, 4, 1-10.

Chase, J., Fouquier, J., Zare, M., Sonderegger, D. L., Knight, R., Kelley, S. T., … & Caporaso, J. G. (2016). Geography and location are the primary drivers of office microbiome composition. MSystems, 1(2), 10-1128.

Torres, J. N., Paul, L. V., Rodwell, T. C., Victor, T. C., Amallraja, A. M., Elghraoui, A., … & Valafar, F. (2015). Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerging microbes & infections, 4(1), 1-9.

Hester, Eric R., Katie L. Barott, Jim Nulton, Mark JA Vermeij, and Forest L. Rohwer. “Stable and sporadic symbiotic communities of coral and algal holobionts.” The ISME Journal 10, no. 5 (2016): 1157-1169.

Ramirez-Busby, Sarah M., and Faramarz Valafar. “A Systematic Review of Mutations in Pyrazinamidase Associated with Pyrazinamide 1.” BMC Infect Dis 1.4 (2012): 692.

Modlin, S. J., Conkle-Gutierrez, D., Kim, C., Mitchell, S. N., Morrissey, C., Weinrick, B. C., … & Valafar, F. (2020). Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. Elife, 9, e58542.

Modlin, S. J., Robinhold, C., Morrissey, C., Mitchell, S. N., Ramirez-Busby, S. M., Shmaya, T., & Valafar, F. (2021). Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases. Microbial Genomics, 7(3), 000465.