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2026 Journal Article Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3DMalik, Ashar J., Kenanov, Dimitar, Chong, Cheng-Shoong, Ozturk, Mert Burak, Wang, Qiqi, Chang, Hong-Yun, Hebrard, Maxime, Ho, Ying Swan, Wang, Zhenxun, Limviphuvadh, Vachiranee, Miyajima, Jhoann M. T., Kannan, Srinivasaraghavan, Magallanes, Roberto Tirado, Sim, Xueling, Chai, Jin Fang, Davila, Sonia, Yeo, Khung Keong, Leong, Khai Pang, Goh, Liuh Ling, Karnani, Neerja, Eriksson, Johan Gunnar, Cheng, Ching-Yu, Wong, Tien Yin, Loh, Marie, Dalan, Rinkoo, Khor, Chiea Chuen, Chew, Guo-Liang, Lim, Weng Khong, Ngeow, Joanne ... Maurer-Stroh, Sebastian (2026). Genomic landscape of drug binding and pharmacogenetic variation across diverse populations using SNPdrug3D. Nature Communications. doi: 10.1038/s41467-026-73816-4 |
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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 Journal Article Transformers as a substrate for structural biologyMalik, Ashar J., Portelli, Stephanie and Ascher, David B. (2026). Transformers as a substrate for structural biology. Current Opinion in Structural Biology, 97 103218, 1-9. doi: 10.1016/j.sbi.2025.103218 |
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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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2026 Journal Article Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biasesMalik, Ashar J. and Ascher, David B. (2026). Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases. Bioinformatics Advances, 6 (1) vbag035, 1-6. doi: 10.1093/bioadv/vbag035 |
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2026 Journal Article mCSM-metal: A Deep Learning Resource to Predict Effect of Mutations on Metal Ion BindingKumar, Akshita, Malik, Ashar J. and Ascher, David B. (2026). mCSM-metal: A Deep Learning Resource to Predict Effect of Mutations on Metal Ion Binding. Journal of Molecular Biology 169678, 169678. doi: 10.1016/j.jmb.2026.169678 |
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2026 Journal Article Structome-AlignViewer: On Confidence Assessment in Structure-Aware AlignmentsMalik, Ashar J., Mao, Siying, Hugenholtz, Philip and Ascher, David B. (2026). Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments. Genome Biology and Evolution, 18 (1) evag004, 1-8. doi: 10.1093/gbe/evag004 |
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2026 Book Chapter MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular DynamicsLanger, Désirée B., Malik, Ashar J., Klemm, Paul, Allison, Jane R. and Poole, Anthony M. (2026). MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular Dynamics. Methods in Molecular Biology. (pp. 275-290) New York, NY: Springer US. doi: 10.1007/978-1-0716-4836-0_15 |
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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 Journal Article Protein structural phylogeneticsPuente-Lelievre, Caroline, Malik, Ashar and Douglas, Jordan (2025). Protein structural phylogenetics. Genome Biology and Evolution, 17 (8) evaf139, 1-20. doi: 10.1093/gbe/evaf139 |
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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 |
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2023 Journal Article The Singapore National Precision Medicine StrategyWong, Eleanor, Bertin, Nicolas, Hebrard, Maxime, Tirado-Magallanes, Roberto, Bellis, Claire, Lim, Weng Khong, Chua, Chee Yong, Tong, Philomena Mei Lin, Chua, Raymond, Mak, Kenneth, Lim, Tit Meng, Cheong, Wei Yang, Thien, Kwee Eng, Goh, Khean Teik, Chai, Jin-Fang, Lee, Jimmy, Sung, Joseph Jao-Yiu, Wong, Tien Yin, Chin, Calvin Woon Loong, Gluckman, Peter D., Goh, Liuh Ling, Ban, Kenneth Hon Kim, Tan, Tin Wee, SG10K_Health Consortium, Van Dam, Rob M., Teo, Yik Ying, Loh, Marie, Eillot, Paul, Lee, Eng Sing ... Tan, Patrick (2023). The Singapore National Precision Medicine Strategy. Nature Genetics, 55 (2), 178-186. doi: 10.1038/s41588-022-01274-x |
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2023 Journal Article Structome: a tool for the rapid assembly of datasets for structural phylogeneticsMalik, Ashar J., Langer, Desiree, Verma, Chandra S., Poole, Anthony M. and Allison, Jane R. (2023). Structome: a tool for the rapid assembly of datasets for structural phylogenetics. Bioinformatics Advances, 3 (1) vbad134, vbad134. doi: 10.1093/bioadv/vbad134 |
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2020 Journal Article DStabilize: a web resource to generate mirror images of biomoleculesMalik, Ashar J., Aronica, Pietro G.A. and Verma, Chandra S. (2020). DStabilize: a web resource to generate mirror images of biomolecules. Structure, 28 (12), 1358-1360.e2. doi: 10.1016/j.str.2020.07.014 |
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2020 Journal Article Erratum: DStabilize: A Web Resource to Generate Mirror Images of Biomolecules (Structure (2020) 28(12) (1358–1360.e2), (S0969212620302471), (10.1016/j.str.2020.07.014))Malik, Ashar J., Aronica, Pietro G.A. and Verma, Chandra S. (2020). Erratum: DStabilize: A Web Resource to Generate Mirror Images of Biomolecules (Structure (2020) 28(12) (1358–1360.e2), (S0969212620302471), (10.1016/j.str.2020.07.014)). Structure, 28 (12), 1376-1378. doi: 10.1016/j.str.2020.11.010 |
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2020 Journal Article Structural phylogenetics with confidenceMalik, Ashar J., Poole, Anthony M. and Allison, Jane R. (2020). Structural phylogenetics with confidence. Molecular Biology and Evolution, 37 (9), 2711-2726. doi: 10.1093/molbev/msaa100 |
