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2026 Journal Article SGGly: a web server for whole-protein, structure-guided analysis of candidate N-linked glycosylation sitesGu, Xiaotong, Zhou, Yunzhuo, Myung, Yoochan and Ascher, David (2026). SGGly: a web server for whole-protein, structure-guided analysis of candidate N-linked glycosylation sites. Nucleic Acids Research, 54 (W1) gkag507, W314-W320. doi: 10.1093/nar/gkag507 |
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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 Multi-omics dataset of TGF-β-induced EMT in breast cancerZhang, Zhen, Ahmed, Emtiaz, Constantin, Nicholas, Lu, Jennifer, Portelli, Stephanie, Ascher, David, Korbie, Darren, Wuethrich, Alain, Sina, Abu and Trau, Matt (2026). Multi-omics dataset of TGF-β-induced EMT in breast cancer. The University of Queensland. (Dataset) doi: 10.48610/954d1e6 |
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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 A three generation family with VACTERL association is found to have a rare form of diamond-blackfan anaemiaLeshchynska, Iryna, Das, Debjani, O’Reilly, Victoria, Sipka, Alena, Iyer, Kavitha, Alankarage, Dimuthu, Rath, Emma, Kumar, Akshita, Kurt, Beth A., Voydanoff, Maria E., The Congenital Heart Disease Synergy Study group, Winlaw, David, Nassar, Natasha, Kirk, Edwin, Stevenson, Roger E., Winlaw, David S., Ascher, David B., Giannoulatou, Eleni, Mark, Paul R., Dunwoodie, Sally L. and Chapman, Gavin (2026). A three generation family with VACTERL association is found to have a rare form of diamond-blackfan anaemia. European Journal of Human Genetics, 34 (5), 619-629. doi: 10.1038/s41431-026-02076-z |
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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 Exploring a genetic basis for the metabolic perturbations in ME/CFS using UK BiobankHuang, Katherine, Muneeb, Muhammad, Thomas, Natalie, Schneider-Futschik, Elena K., Gooley, Paul R., Ascher, David B. and Armstrong, Christopher W. (2026). Exploring a genetic basis for the metabolic perturbations in ME/CFS using UK Biobank. iScience, 29 (1) 114316, 1-13. doi: 10.1016/j.isci.2025.114316 |
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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 Journal Article Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structuresPan, Qisheng, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B. (2026). Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structures. Briefings in Bioinformatics, 27 (1) bbag035, 1-17. doi: 10.1093/bib/bbag035 |
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2026 Journal Article kinCSM-RTK: machine learning-based screening of receptor tyrosine kinase inhibitors in drug discoverySerghini, Adam, Zhou, Yunzhuo, Myung, Yoochan, de Sá, Alex G. C., Portelli, Stephanie and Ascher, David B. (2026). kinCSM-RTK: machine learning-based screening of receptor tyrosine kinase inhibitors in drug discovery. Journal of Chemical Information and Modeling, 66 (1) acs.jcim.5c01677, 61-73. doi: 10.1021/acs.jcim.5c01677 |
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2025 Conference Publication UPF1 variants cause syndromic intellectual disability with a transcriptome profile convergent with fragile X syndrome (Award Candidate)Tan, Natalie B., Jolly, Lachlan, Nawaz, Urwah, Zhao, Sarah F., Gyurkovska, Valeriya, Silk, Michael, Montazaribarforoushi, Saba, Nicolas-Martinez, Emmylou, Carroll, Renee, van Eyk, Clare, Baer, Lachlan, Ascher, David B., Christodoulou, John, Segev, Nava, Gecz, Jozef and White, Susan M. (2025). UPF1 variants cause syndromic intellectual disability with a transcriptome profile convergent with fragile X syndrome (Award Candidate). 58th European Society of Human Genetics (ESHG) Conference, Milan, Italy, 24–27 May 2025. London, United Kingdom: Nature Publishing Group. |
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2025 Conference Publication Integrating genetic datasets to improve Genotype-Phenotype predictionMuneeb, Muhammad and Ascher, David (2025). Integrating genetic datasets to improve Genotype-Phenotype prediction. 58th European Society of Human Genetics (ESHG) Conference, Milan, Italy, 24 - 27 May 2025. London, United Kingdom: Nature Publishing Group. |
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2025 Journal Article Haploinsufficient variants in SMAD5 are associated with isolated congenital heart diseaseAlankarage, Dimuthu, Leshchynska, Iryna, Portelli, Stephanie, Sipka, Alena, Blue, Gillian M., O'Reilly, Victoria, Das, Debjani, Rath, Emma M., Enriquez, Annabelle, Troup, Michael, Fine, Miriam, Poplawski, Nicola, Verlee, Maxim, Humphreys, David T., Harvey, Richard P., Chapman, Gavin, Kirk, Edwin P., Winlaw, David S., Callewaert, Bert, Chung, Wendy K., Ascher, David, Giannoulatou, Eleni and Dunwoodie, Sally L. (2025). Haploinsufficient variants in SMAD5 are associated with isolated congenital heart disease. Human Genetics and Genomics Advances, 6 (4) 100478, 100478. doi: 10.1016/j.xhgg.2025.100478 |
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2025 Journal Article Combinatorial discovery of RAFT cationic polymers for mRNA delivery: structure–function insights from high-throughput screening and machine learningYang, Wenting, Li, Shangqian, Yu, Siqi, de Sá, Alex G. C., Ita, Tanmayee Sai Sivani, Liang, Tian, Forgham, Helen, Qiao, Ruirui, Li, Jiulong, Stayton, Patrick S., Ascher, David B., Meng, Huan, Whittaker, Andrew K. and Fu, Changkui (2025). Combinatorial discovery of RAFT cationic polymers for mRNA delivery: structure–function insights from high-throughput screening and machine learning. Biomacromolecules, 26 (11), 7724-7738. doi: 10.1021/acs.biomac.5c01236 |
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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 Conference Publication Interpreting machine learning pipelines produced by evolutionary AutoML for biochemical property predictionde Sá, Alex G. C., Pappa, Gisele L., Freitas, Alex A. and Ascher, David B. (2025). Interpreting machine learning pipelines produced by evolutionary AutoML for biochemical property prediction. 2025 Genetic and Evolutionary Computation Conference Companion-GECCO, Malaga, Spain, 14-18 July 2025. New York, NY United States: Association for Computing Machinery. doi: 10.1145/3712255.3734339 |
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2025 Journal Article Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challengesTurina, Paola, Petrosino, Maria, Enriquez Sandoval, Carlos A., Novak, Leonore, Pasquo, Alessandra, Alexov, Emil, Alladin, Muttaqi Ahmad, Ascher, David B., Babbi, Giulia, Bakolitsa, Constantina, Casadio, Rita, Cheng, Jianlin, Fariselli, Piero, Folkman, Lukas, Kamandula, Akash, Katsonis, Panagiotis, Li, Minghui, Li, Dong, Lichtarge, Olivier, Mahmud, Sajid, Martelli, Pier Luigi, Pal, Debnath, Panday, Shailesh Kumar, Pires, Douglas E. V., Portelli, Stephanie, Pucci, Fabrizio, Rodrigues, Carlos H. M., Rooman, Marianne, Savojardo, Castrense ... Capriotti, Emidio (2025). Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges. Human Genetics, 144 (2-3) 245403, 265-280. doi: 10.1007/s00439-024-02724-8 |
