Publications
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For a complete and up-to-date list of publications, please visit this link.
Selected publications:
- Smith, D., Sadler, M., & Altman, R. (2023). Promises and challenges in pharmacoepigenetics. Cambridge Prisms: Precision Medicine, 1(1), E18. https://doi.org/https://doi.org/10.1017/pcm.2023.6
- Yang, L., Wang, S., & Altman, R. (2023). POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study. Journal of the American Medical Informatics Association: JAMIA, 30(2), 245-255. https://doi.org/10.1093/jamia/ocac226
- Carpenter, K., & Altman, R. (2023). Using GPT-3 to Build a Lexicon of Drugs of Abuse Synonyms for Social Media Pharmacovigilance. Biomolecules, 13(2), 387. https://doi.org/10.3390/biom13020387
- Cousins, H., Taryn, H., Guo, Y., Tzeng, K., Cong, L., & Altman, R. (2023). Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. Bioinformatics, 39(1), btac735. https://doi.org/10.1093/bioinformatics/btac735
- Derry, A., & Altman, R. (2022). COLLAPSE: A representation learning framework for identification and characterization of protein structural sites. Protein Science, 32(2), e4541. https://doi.org/10.1002/pro.4541
- Cousins, H., Kline, A., Wang, C., Qu, Y., Wang, M., Altman, R., Luo, Y., & Cong, L. (2021). Integrative analysis of viral entry networks and clinical outcomes identifies a protective role for spironolactone in severe COVID-19. medRxiv. https://doi.org/10.1101/2022.07.02.22277
- Wang, C., Dinesh, R., Qu, Y., Rustagi, A., Cousins, H., Zengel, J., Guo, Y., Hall, T., Beck, A., Tso, L., Erdemic, E., Tanudtanud, K., Ren, S., Tzeng, K., Wilk, A., Wang, M., Carette, J., Altman, R., Blish, C., & Cong, L. (2021). CRISPRa screening with real world evidence identifies potassium channels as neuronal entry factors and druggable targets for SARS-CoV-2. bioRxiv. https://doi.org/10.1101/2021.07.01
- Townshend, R., Vögele, M., Suriana, P., Derry, A., Powers, A., Laloudakis, Y., Balachandar, S., Jing, B., Anderson, B., Eismann, S., Kondor, R., Altman, R., & Dror, R. (2021). ATOM3D: Tasks On Molecules in Three Dimensions. NeurIPS 2021 Datasets and Benchmarks Track. https://arxiv.org/abs/2012.04035
- Derry, A., Carpenter, K., & Altman, R. (2021). Training data composition affects performance of structure analysis algorithms.. Pacific Symposium on Biocomputing 2022, 10-22. https://doi.org/10.1101/2021.09.30.462647v2
- Sosa, D., Derry, A., Guo, M., Wei, E., Brinton, C., & Altman, R. (2019). A literature-based knowledge graph embedding method for identifying drug repurposing opportunities in rare diseases. Pacific Symposium on Biocomputing 2020, 463-474. https://doi.org/10.1142/9789811215636_0041