Publications

Carpenter, K., & Altman, R. (2024). Databases of ligand-binding pockets and protein-ligand interactions. Computational and Structural Biotechnology Journal, 23, 1320-1338. https://doi.org/10.1016/j.csbj.2024.03.015

Nayar, G., & Altman, R. (2024). Heterogeneous network approaches to protein pathway prediction. Computational and Structural Biotechnology Journal, 23, 2727-2739. https://doi.org/10.1016/j.csbj.2024.06.022

Cousins, H., Nayar, G., & Altman, R. (2024). Computational Approaches to Drug Repurposing: Methods, Challenges, and Opportunities. Annu Rev Biomed Data Sci. https://doi.org/10.1146/annurev-biodatasci-110123-025333

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