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2024 Journal Article PRIMITI: a computational approach for accurate prediction of miRNA-target mRNA interactionUthayopas, Korawich, de Sá, Alex G.C., Alavi, Azadeh, Pires, Douglas E.V. and Ascher, David B. (2024). PRIMITI: a computational approach for accurate prediction of miRNA-target mRNA interaction. Computational and Structural Biotechnology Journal, 23, 3030-3039. doi: 10.1016/j.csbj.2024.06.030 |
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2024 Journal Article DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learningZhou, Yunzhuo, Myung, YooChan, Rodrigues, Carlos H.M. and Ascher, David B. (2024). DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning. Nucleic Acids Research, 52 (W1), W207-W214. doi: 10.1093/nar/gkae412 |
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2024 Journal Article Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptidesKing, Harry R., Bycroft, Mark, Nguyen, Thanh-Binh, Kelly, Geoff, Vinogradov, Alexander A., Rowling, Pamela J E, Stott, Katherine, Ascher, David B., Suga, Hiroaki, Itzhaki, Laura S. and Artavanis-Tsakonas, Katerina (2024). Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides. Proceedings of the National Academy of Sciences of the United States of America, 121 (21) e2322923121, e2322923121. doi: 10.1073/pnas.2322923121 |
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2024 Journal Article Engineering G protein‐coupled receptors for stabilizationVelloso, João Paulo L., de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2024). Engineering G protein‐coupled receptors for stabilization. Protein Science, 33 (6) e5000, 1-13. doi: 10.1002/pro.5000 |
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2024 Journal Article Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantificationRyu, Jayoung, Barkal, Sam, Yu, Tian, Jankowiak, Martin, Zhou, Yunzhuo, Francoeur, Matthew, Phan, Quang Vinh, Li, Zhijian, Tognon, Manuel, Brown, Lara, Love, Michael I., Bhat, Vineel, Lettre, Guillaume, Ascher, David B., Cassa, Christopher A., Sherwood, Richard I. and Pinello, Luca (2024). Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature Genetics, 56 (5), 925-937. doi: 10.1038/s41588-024-01726-6 |
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2024 Journal Article Mutations in glycosyltransferases and glycosidases: implications for associated diseasesGu, Xiaotong, Kovacs, Aaron S., Myung, Yoochan and Ascher, David B. (2024). Mutations in glycosyltransferases and glycosidases: implications for associated diseases. Biomolecules, 14 (4) 497. doi: 10.3390/biom14040497 |
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2024 Journal Article Are manufacturing patents to blame for biosimilar market launch delays?Williamson, Rhys, Munro, Trent, Ascher, David, Robertson, Avril and Pregelj, Lisette (2024). Are manufacturing patents to blame for biosimilar market launch delays?. Value in Health, 27 (3), 287-293. doi: 10.1016/j.jval.2023.12.005 |
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2024 Journal Article A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorderSzot, Justin O., Cuny, Hartmut, Martin, Ella M.M.A., Sheng, Delicia Z., Iyer, Kavitha, Portelli, Stephanie, Nguyen, Vivien, Gereis, Jessica M., Alankarage, Dimuthu, Chitayat, David, Chong, Karen, Wentzensen, Ingrid M., Vincent-Delormé, Catherine, Lermine, Alban, Burkitt-Wright, Emma, Ji, Weizhen, Jeffries, Lauren, Pais, Lynn S., Tan, Tiong Y., Pitt, James, Wise, Cheryl A., Wright, Helen, Andrews, Israel D., Pruniski, Brianna, Grebe, Theresa A., Corsten-Janssen, Nicole, Bouman, Katelijne, Poulton, Cathryn, Prakash, Supraja ... Dunwoodie, Sally L. (2024). A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder. Journal of Clinical Investigation, 134 (4) 174824. doi: 10.1172/jci174824 |
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2024 Journal Article AI-driven GPCR analysis, engineering, and targetingVelloso, João P.L., Kovacs, Aaron S., Pires, Douglas E.V. and Ascher, David B. (2024). AI-driven GPCR analysis, engineering, and targeting. Current Opinion in Pharmacology, 74 102427, 102427. doi: 10.1016/j.coph.2023.102427 |
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2024 Journal Article A broad-spectrum α-glucosidase of glycoside hydrolase family 13 from Marinovum sp., a member of the Roseobacter cladeLi, Jinling, Mui, Janice W.-Y., da Silva, Bruna M., Pires, Douglas E.V., Ascher, David B., Madiedo Soler, Niccolay, Goddard-Borger, Ethan D. and Williams, Spencer J. (2024). A broad-spectrum α-glucosidase of glycoside hydrolase family 13 from Marinovum sp., a member of the Roseobacter clade. Applied Biochemistry and Biotechnology, 196 (9), 6059-6071. doi: 10.1007/s12010-023-04820-3 |
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2024 Journal Article Characterization on the oncogenic effect of the missense mutations of p53 via machine learningPan, Qisheng, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B. (2024). Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. Briefings in Bioinformatics, 25 (1) bbad428, 1-13. doi: 10.1093/bib/bbad428 |
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2024 Book Chapter AI-driven enhancements in drug screening and optimizationSerghini, Adam, Portelli, Stephanie and Ascher, David B. (2024). AI-driven enhancements in drug screening and optimization. Computational drug discovery and design. (pp. 269-294) edited by Mohini Gore and Umesh B. Jagtap. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-3441-7_15 |
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2024 Journal Article Lipid sulfoxide polymers as potential inhalable drug delivery platforms with differential albumin binding affinityEdiriweera, Gayathri R., Butcher, Neville J., Kothapalli, Ashok, Zhao, Jiacheng, Blanchfield, Joanne T., Subasic, Christopher N., Grace, James L., Fu, Changkui, Tan, Xiao, Quinn, John F., Ascher, David B., Whittaker, Michael R., Whittaker, Andrew K. and Kaminskas, Lisa M. (2024). Lipid sulfoxide polymers as potential inhalable drug delivery platforms with differential albumin binding affinity. Biomaterials Science, 12 (11), 2978-2992. doi: 10.1039/d3bm02020g |
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2023 Journal Article Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau diseaseSerghini, Adam, Portelli, Stephanie, Troadec, Guillaume, Song, Catherine, Pan, Qisheng, Pires, Douglas E. V. and Ascher, David B. (2023). Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Human Molecular Genetics, 33 (3), 224-232. doi: 10.1093/hmg/ddad181 |
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2023 Journal Article CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfacesRodrigues, Carlos H. M. and Ascher, David B. (2023). CSM‐Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces. Proteins: Structure, Function, and Bioinformatics, 93 (1), 209-216. doi: 10.1002/prot.26615 |
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2023 Journal Article Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequencesAl-Jarf, Raghad, Karmakar, Malancha, Myung, Yoochan and Ascher, David B. (2023). Uncovering the molecular drivers of NHEJ DNA repair-implicated missense variants and their functional consequences. Genes, 14 (10) 1890, 1-11. doi: 10.3390/genes14101890 |
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2023 Journal Article Identifying innate resistance hotspots for SARS-CoV-2 antivirals using in silico protein techniquesPortelli, Stephanie, Heaton, Ruby and Ascher, David B. (2023). Identifying innate resistance hotspots for SARS-CoV-2 antivirals using in silico protein techniques. Genes, 14 (9) 1699, 1-13. doi: 10.3390/genes14091699 |
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2023 Journal Article Understanding the complementarity and plasticity of antibody–antigen interfacesMyung, Yoochan, Pires, Douglas E. V. and Ascher, David B (2023). Understanding the complementarity and plasticity of antibody–antigen interfaces. Bioinformatics, 39 (7) btad392, 1-7. doi: 10.1093/bioinformatics/btad392 |
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2023 Journal Article LEGO-CSM: a tool for functional characterization of proteinsNguyen, Thanh Binh, de Sá, Alex G. C., Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2023). LEGO-CSM: a tool for functional characterization of proteins. Bioinformatics, 39 (7) btad402, 1-4. doi: 10.1093/bioinformatics/btad402 |
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2023 Journal Article Identifying the molecular drivers of pathogenic aldehyde dehydrogenase missense mutations in cancer and non-cancer diseasesJessen-Howard, Dana, Pan, Qisheng and Ascher, David B. (2023). Identifying the molecular drivers of pathogenic aldehyde dehydrogenase missense mutations in cancer and non-cancer diseases. International Journal of Molecular Sciences, 24 (12) 10157, 1-18. doi: 10.3390/ijms241210157 |
