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2026 Other Outputs Know your alphabet: conformational noise, latent-space encodings, and the future of structural phylogeneticsSchmid, Madeline, Liu, Yixiao, Malik, Ashar J. and Ascher, David B. (2026). Know your alphabet: conformational noise, latent-space encodings, and the future of structural phylogenetics. doi: 10.64898/2026.05.06.722973 |
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2026 Other Outputs The duplicate monophyly criterion: an empirical approach to bootstrapping distance-based structural phylogeniesMalik, Ashar J. and Ascher, David B. (2026). The duplicate monophyly criterion: an empirical approach to bootstrapping distance-based structural phylogenies. doi: 10.64898/2026.03.25.713827 |
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2025 Other Outputs Quantome: a quantum surrogate model for biophysical landscapesMalik, Ashar J. and Ascher, David B. (2025). Quantome: a quantum surrogate model for biophysical landscapes. doi: 10.1101/2025.08.06.668871 |
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2025 Other Outputs On a quantum-inspired kernel for classifying protein torsion anglesMalik, Ashar and Ascher, David (2025). On a quantum-inspired kernel for classifying protein torsion angles. doi: 10.1101/2025.08.05.668681 |
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2025 Other Outputs On interactive spatial visualisation of pathogenicity predictionsXu, Junjie, Kovacs, Aaron S., Portelli, Stephanie, Malik, Ashar J. and Ascher, David B. (2025). On interactive spatial visualisation of pathogenicity predictions. doi: 10.1101/2025.03.19.644131 |
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2024 Other Outputs On use of tertiary structure characters in hidden Markov models for protein fold predictionMalik, Ashar J., Puente-Lelièvre, Caroline, Matzke, Nicholas J. and Ascher, David B. (2024). On use of tertiary structure characters in hidden Markov models for protein fold prediction. doi: 10.1101/2024.04.08.588419 |
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2023 Other Outputs Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zonePuente-Lelièvre, Caroline, Malik, Ashar J., Douglas, Jordan, Ascher, David B., Baker, Matthew A. B., Allison, Jane R., Poole, Anthony M., Lundin, Daniel, Fullmer, Matthew S., Bouckert, Remco, Kim, Hyunbin, Steinegger, Martin and Matzke, Nicholas J. (2023). Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone. doi: 10.1101/2023.12.12.571181 |
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2023 Other Outputs On quantum computing and geometry optimizationMalik, Ashar J. and Verma, Chandra S. (2023). On quantum computing and geometry optimization. doi: 10.1101/2023.03.16.532929 |
