Papers:
R. Orenbuch, C. Shearer, A. Kollasch, A. Spinner, T. Hopf, L. van Niekerk, D. Franceschi, M. Dias, J. Frazer, D.S. Marks (2025). Proteome-wide model for human disease genetics. Nature Genetics. doi:10.1038/s41588-025-02400-1
M.C. Angelo*, R. Orenbuch*, D.S. Marks (2025). RNA thermodynamics can be replaced with learnable representations. MLSB Workshop.
M.A. Khan [et al., including R. Orenbuch] (2025). AI-Driven Risk Stratification is Essential for Affordable Early Detection of Cancer. GenAI4Health at NeurIPS, San Diego Convention Center, California, USA.
C. Shearer, R. Orenbuch, F. Teufel, C. Steinmetz, D. Ritter, E. Xie, A. Gazizov, A. Spinner, J. Frazer, M. Dias, P. Notin, D.S. Marks (2024). A Genomic Language Model for Zero-Shot Prediction of Promoter Variant Effects. bioRxiv. doi:10.1101/2024.11.11.623015
B.J. Livesey [et al., including R. Orenbuch] (2025). Guidelines for releasing a variant effect predictor. Genome Biology, Vol. 26. doi:10.1186/s13059-025-03572-z
C. Shearer, R. Orenbuch, F. Teufel, D. Ritter, A. Spinner, E. Xie, J. Frazer, M. Dias, P. Notin, D.S. Marks (2024). LOL-EVE: Predicting Promoter Variant Effects from Evolutionary Sequences. bioRxiv. doi:10.1101/2024.11.11.623015
M. Dias, R. Orenbuch, D.S. Marks, J. Frazer (2024). Toward trustable use of machine learning models of variant effects in the clinic. The American Journal of Human Genetics, Vol. 111.
P. Notin [et al., including R. Orenbuch] (2023). Proteingym: Large-scale benchmarks for protein fitness prediction and design. Advances in Neural Information Processing Systems, Vol. 36.
I. Filip*, Anqi Wang*, Oleksandr Kravtes*, R. Orenbuch*, J. Zhao, G. Manji, N. Malats, K. Olive, R. Rabadan (2023). Pervasiveness of HLA allele-specific expression loss across tumor types. Genome medicine 15, 8. doi.org:10.1186/s13073-023-01154-x
R. Orenbuch, I. Filip, R. Rabadan (2020). HLA Typing from RNA Sequencing and Applications to Cancer. Bioinformatics for Cancer Immunotherapy. Methods Molecular Biology, Vol. 2120.
R. Orenbuch, I. Filip, D. Comito, J. Shaman, I. Pe’er, R. Rabadan (2019). arcasHLA: high resolution HLA typing from RNA seq. Bioinformatics doi:10.1093/bioinformatics/btz474
J. Zhao, A. Chen, [et al., including R. Orenbuch] (2019). Immune and genomic correlates of response to anti-PD-immunotherapy in glioblastoma. Nature Medicine. doi:10.1038/s41591-019-0349-y.