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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, 438 (18) 169678, 1-12. doi: 10.1016/j.jmb.2026.169678 |
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2026 Journal Article LDLR Variant Classification Through Activity-Normalized Prime Editing ScreeningZhou, Phillip J., Velimirovic, Minja, Yu, Tian, Gligorovski, Vojislav, Mathis, Nicolas, Zhao, Jing, Phan, Quang Vinh, Vogd, Felicitas, Ryu, Jayoung, Pan, Qisheng, Tyagi, Atharva, Ascher, David B., Schwank, Gerald, Pinello, Luca, Cassa, Christopher A. and Sherwood, Richard I. (2026). LDLR Variant Classification Through Activity-Normalized Prime Editing Screening. Circulation CIRCULATIONAHA.125.078585. doi: 10.1161/circulationaha.125.078585 |
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2026 Journal Article Tracking breast cancer progression using MethylscapeZhang, Zhen, Ahmed, Emtiaz, Constantin, Nicolas, Lu, Jennifer, Portelli, Stephanie, Ascher, David B., Korbie, Darren, Wuethrich, Alain, Sina, Abu Ali Ibn and Trau, Matt (2026). Tracking breast cancer progression using Methylscape. Science Advances, 12 (35) eaeb6556. doi: 10.1126/sciadv.aeb6556 |
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2026 Journal Article Penicillin-resistant <i>Streptococcus dysgalactiae</i> subsp. <i>equisimilis</i> and the association with penicillin-binding protein mutations: a population genotypic and phenotypic studyXie, Ouli, Tan, Aimee, Nguyen, Thanh Binh, Hayes, Andrew J., Dotel, Ravindra, Carter, Glen, O'Sullivan, Matthew V. N., Bond, Katherine, McDevitt, Christopher A., Korman, Tony M., Currie, Bart J., Ascher, David B., Tong, Steven Y. C., van Hal, Sebastiaan J. and Davies, Mark R. (2026). Penicillin-resistant Streptococcus dysgalactiae subsp. equisimilis and the association with penicillin-binding protein mutations: a population genotypic and phenotypic study. Antimicrobial Agents and Chemotherapy, 70 (9) e00137-26, e0013726-e0013726. doi: 10.1128/aac.00137-26 |
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2026 Journal Article A reproducible nine-step protocol for fine-tuning large language models on heterogeneous bioinformatics knowledge sourcesMuneeb, Muhammad and Ascher, David B. (2026). A reproducible nine-step protocol for fine-tuning large language models on heterogeneous bioinformatics knowledge sources. Artificial Intelligence in the Life Sciences, 10 100179, 100179-100179. doi: 10.1016/j.ailsci.2026.100179 |
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2026 Journal Article G2DR: a genotype-first framework for genetics-informed target prioritization and drug repurposingMuneeb, Muhammad and Ascher, David B. (2026). G2DR: a genotype-first framework for genetics-informed target prioritization and drug repurposing. Briefings in Bioinformatics, 27 (4) bbag427, 1-16. doi: 10.1093/bib/bbag427 |
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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 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 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 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 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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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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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 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 |
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2025 Journal Article Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sitesBezawork-Geleta, Ayenachew, Devereux, Camille J., Keenan, Stacey N., Lou, Jieqiong, Cho, Ellie, Nie, Shuai, De Souza, David P., Narayana, Vinod K., Siddall, Nicole A., Rodrigues, Carlos H. M., Portelli, Stephanie, Zheng, Tenghao, Nim, Hieu T., Ramialison, Mirana, Hime, Gary R., Dodd, Garron T., Hinde, Elizabeth, Ascher, David B., Stroud, David A. and Watt, Matthew J. (2025). Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sites. Nature Communications, 16 (1) 2135, 2135. doi: 10.1038/s41467-025-57405-5 |
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2025 Journal Article Drug resistance-associated mutations in Plasmodium UBP-1 disrupt its essential deubiquitinating activitySmith, Cameron J., Eavis, Heledd, Briggs, Carla, Henrici, Ryan, Karpiyevich, Maryia, Ansbro, Megan R., Hoshizaki, Johanna, van der Heden van Noort, Gerbrand J., Ascher, David B., Sutherland, Colin J., Lee, Marcus C.S. and Artavanis-Tsakonas, Katerina (2025). Drug resistance-associated mutations in Plasmodium UBP-1 disrupt its essential deubiquitinating activity. Journal of Biological Chemistry, 301 (3) 108266, 108266. doi: 10.1016/j.jbc.2025.108266 |
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2025 Journal Article Definition and validation of prognostic phenotypes in moderate aortic stenosisSen, Jonathan, Wahi, Sudhir, Vollbon, William, Prior, Marcus, de Sá, Alex G.C., Ascher, David B., Huynh, Quan and Marwick, Thomas H. (2025). Definition and validation of prognostic phenotypes in moderate aortic stenosis. JACC: Cardiovascular Imaging, 18 (2), 133-149. doi: 10.1016/j.jcmg.2024.06.013 |
