Travis Wheeler

Interests

Teaching

Computation (introductory, through advanced algorithms)BioinformaticsMachine LearningProbabilistic ModelingDrug Discovery

Research

Computational biology: - Algorithms, Machine Learning, Software engineering- Genomics, proteomics, drug discovery, animal tracking/behavior

Courses

Scholarly Contributions

Journals/Publications

• Roy, A., Ward, E., Choi, I., Cosi, M., Edgin, T., Hughes, T. S., Islam, M. S., Khan, A. M., Kolekar, A., Rayl, M., & others, . (2025). MDRepo -- an open data warehouse for community-contributed molecular dynamics simulations of proteins. Nucleic Acids Research, 53(D1), D477--D486.
• Anderson, T., & Wheeler, T. (2024). An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models. BMC Bioinformatics.
• Clements, A. N., Casillas, A. L., Flores, C. E., Liou, H., Toth, R. K., Chauhan, S. S., Sutterby, K., Deshmukh, S. K., Wu, S., Xiu, J., & others, . (2024). Inhibition of PIM kinase in tumor associated macrophages suppresses inflammasome 1 activation and sensitizes prostate cancer to immunotherapy. bioRxiv, 2024--10.
• Copeland, C. J., Roddy, J. W., Schmidt, A. K., Secor, P. R., & Wheeler, T. J. (2024). VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes [EDITOR'S CHOICE]. NAR Genomics and Bioinformatics, 6(2).
• Geller-McGrath, D., Konwar, K. M., Edgcomb, V. P., Pachiadaki, M., Roddy, J. W., Wheeler, T. J., & McDermott, J. E. (2024). Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict. eLife, 13.
• Glidden-Handgis, G., & Wheeler, T. J. (2024). WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences. Bioinformatics Advances.
• Groza, C., Chen, X., Wheeler, T. J., Bourque, G., & Goubert, C. (2024). A unified framework to analyze transposable element insertion polymorphisms using graph genomes. Nature Communications, 15(1).
• Khajouei, E., Ghisays, V., Piras, I. S., Martinez, K. L., Naymik, M., Ngo, P., Tran, T. C., Denny, J. C., Wheeler, T. J., Huentelman, M. J., & others, . (2024). Phenome-Wide Association of APOE Alleles in the All of Us Research Program. medRxiv.
• Krause, G. R., Shands, W., & Wheeler, T. J. (2024). Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinformatics Advances.
• Marbut, A. C., Chandler, J. W., & Wheeler, T. J. (2024). Exploring the Impact of a Transformer's Latent Space Geometry on Downstream Task Performance. arXiv.
• Nord, A. J., & Wheeler, T. J. (2024). Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins. bioRxiv.
• Olson, D. R., & Wheeler, T. J. (2024). ULTRA-Effective labeling of tandem repeats in genomic sequence. Bioinformatics Advances.
• Olson, D. R., Demekas, D., Colligan, T., & Wheeler, T. (2024). NEAR: Neural Embeddings for Amino acid Relationships. bioRxiv.
• Roddy, J. W., Rich, D. H., & Wheeler, T. J. (2024). nail: software for high-speed, high-sensitivity protein sequence annotation. bioRxiv.
• Venkatraman, V., Gaiser, J., Demekas, D., Roy, A., Xiong, R., & Wheeler, T. J. (2024). Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No). Pharmaceuticals, 17(8), 992.
• Colligan, T., Irish, K., Emlen, D. J., & Wheeler, T. J. (2023). DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals. PLOS ONE, 18(7), 1-20.
• Nord, A. J., & Wheeler, T. J. (2023). Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. PLOS ONE, 18(5), e0285225.
• Schimunek, J., Seidl, P., Elez, K., Hempel, T., Le, T., No\'{e}, F., Olsson, S., Raich, L., Winter, R., Gokcan, H., Gusev, F., Gutkin, E. M., Isayev, O., Kurnikova, M. G., Narangoda, C. H., Zubatyuk, R., Bosko, I. P., Furs, K. V., Karpenko, A. D., , Kornoushenko, Y. V., et al. (2023). A community effort in SARS-CoV-2 drug discovery. Molecular Informatics.
• Storer, J. M., Walker, J. A., Baker, J. N., Hossain, S., Roos, C., Wheeler, T. J., & Batzer, M. A. (2023). Framework of the Alu Subfamily Evolution in the platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae. Genes, 14(2), 249.
• Brodie, J. F., Henao-Diaz, L. F., Pratama, B., Copeland, C., Wheeler, T., & Helmy, O. E. (2022). Fruit size in Indo-Malayan island plants is more strongly influenced by filtering than by in situ evolution. The American Naturalist.
• Hubley, R., Wheeler, T. J., & Smit, A. F. (2022). Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. NAR Genomics and Bioinformatics, 4(2), lqac040.
• Nord, A. J., & Wheeler, T. J. (2022). Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms. bioRxiv.
• Roddy, J. W., Lesica, G. T., & Wheeler, T. J. (2022). SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation. NAR Genomics and Bioinformatics, 4(4).

Proceedings Publications

• Marbut, A., McKinney-Bock, K., & Wheeler, T. (2023). Reliable measures of spread in high dimensional latent spaces. In International Conference on Machine Learning.