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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. doi: 10.1038/s41467-025-57405-5 |
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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 245403, 1-16. doi: 10.1007/s00439-024-02724-8 |
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2024 Journal Article Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycinTurner, Adrianna M., Li, Lucy, Monk, Ian R., Lee, Jean Y. H., Ingle, Danielle J., Portelli, Stephanie, Sherry, Norelle L., Isles, Nicole, Seemann, Torsten, Sharkey, Liam K., Walsh, Calum J., Reid, Gavin E., Nie, Shuai, Eijkelkamp, Bart A., Holmes, Natasha E., Collis, Brennan, Vogrin, Sara, Hiergeist, Andreas, Weber, Daniela, Gessner, Andre, Holler, Ernst, Ascher, David B., Duchene, Sebastian, Scott, Nichollas E., Stinear, Timothy P., Kwong, Jason C., Gorrie, Claire L., Howden, Benjamin P. and Carter, Glen P. (2024). Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin. Nature, 635 (8040), 969-977. doi: 10.1038/s41586-024-08095-4 |
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2024 Journal Article AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure informationPan, Qisheng, Parra, Georgina Becerra, Myung, Yoochan, Portelli, Stephanie, Nguyen, Thanh Binh and Ascher, David B. (2024). AlzDiscovery: A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information. Protein Science, 33 (10) e5147, e5147. doi: 10.1002/pro.5147 |
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2024 Journal Article MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2Kovacs, Aaron S., Portelli, Stephanie, Silk, Michael, Rodrigues, Carlos H. M. and Ascher, David B. (2024). MTR3D‐AF2: Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2. Protein Science, 33 (8) e5112, e5112. doi: 10.1002/pro.5112 |
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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 Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challengesRodrigues, Carlos H. M., Portelli, Stephanie and Ascher, David B. (2024). Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Human Genetics, 1-9. doi: 10.1007/s00439-023-02623-4 |
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2024 Journal Article Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challengesTurina, Paola, Dal Cortivo, Giuditta, Enriquez Sandoval, Carlos A., Alexov, Emil, Ascher, David B., Babbi, Giulia, Bakolitsa, Constantina, Casadio, Rita, Fariselli, Piero, Folkman, Lukas, Kamandula, Akash, Katsonis, Panagiotis, Li, Dong, Lichtarge, Olivier, Martelli, Pier Luigi, Panday, Shailesh Kumar, Pires, Douglas E. V., Portelli, Stephanie, Pucci, Fabrizio, Rodrigues, Carlos H. M., Rooman, Marianne, Savojardo, Castrense, Schwersensky, Martin, Shen, Yang, Strokach, Alexey V., Sun, Yuanfei, Woo, Junwoo, Radivojac, Predrag, Brenner, Steven E. ... Capriotti, Emidio (2024). Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges. Human Genetics 620793. doi: 10.1007/s00439-024-02720-y |
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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 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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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 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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2022 Journal Article Identifying the molecular drivers of ALS-implicated missense mutationsPortelli, Stephanie, Albanaz, Amanda, Pires, Douglas Eduardo Valente and Ascher, David Benjamin (2022). Identifying the molecular drivers of ALS-implicated missense mutations. Journal of Medical Genetics, 60 (5) 108798, 1-7. doi: 10.1136/jmg-2022-108798 |
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2022 Journal Article toxCSM: comprehensive prediction of small molecule toxicity profilesde Sá, Alex G.C., Long, Yangyang, Portelli, Stephanie, Pires, Douglas E.V. and Ascher, David B. (2022). toxCSM: comprehensive prediction of small molecule toxicity profiles. Briefings in Bioinformatics, 23 (5) bbac337, 1-11. doi: 10.1093/bib/bbac337 |
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2021 Journal Article Definition of the immune evasion-replication interface of rabies virus P proteinZhan, Jingyu, Harrison, Angela R., Portelli, Stephanie, Nguyen, Thanh Binh, Kojima, Isshu, Zheng, Siqiong, Yan, Fei, Masatani, Tatsunori, Rawlinson, Stephen M., Sethi, Ashish, Ito, Naoto, Ascher, David B., Moseley, Gregory W. and Gooley, Paul R. (2021). Definition of the immune evasion-replication interface of rabies virus P protein. PLOS Pathogens, 17 (7) e1009729, 1-27. doi: 10.1371/journal.ppat.1009729 |
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2021 Journal Article Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resourcePortelli, Stephanie, Olshansky, Moshe, Rodrigues, Carlos H. M., D’Souza, Elston N., Myung, Yoochan, Silk, Michael, Alavi, Azadeh, Pires, Douglas E. V. and Ascher, David B. (2021). Author Correction: Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 53 (2), 254-254. doi: 10.1038/s41588-020-00775-x |
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2021 Journal Article Distinguishing between PTEN clinical phenotypes through mutation analysisPortelli, Stephanie, Barr, Lucy, de Sá, Alex G.C., Pires, Douglas E.V. and Ascher, David B. (2021). Distinguishing between PTEN clinical phenotypes through mutation analysis. Computational and Structural Biotechnology Journal, 19, 3097-3109. doi: 10.1016/j.csbj.2021.05.028 |
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2021 Book Chapter Identifying genotype-phenotype correlations via integrative mutation analysisAirey, Edward, Portelli, Stephanie, Xavier, Joicymara S, Myung, Yoo Chan, Silk, Michael, Karmakar, Malancha, Velloso, João P L, Rodrigues, Carlos H M, Parate, Hardik H, Garg, Anjali, Al-Jarf, Raghad, Barr, Lucy, Geraldo, Juliana A, Rezende, Pâmela M, Pires, Douglas E V and Ascher, David B (2021). Identifying genotype-phenotype correlations via integrative mutation analysis. Artificial neural networks. (pp. 1-32) edited by Hugh Cartwright. New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0826-5_1 |
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2021 Journal Article Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinaseZhou, Yunzhuo, Portelli, Stephanie, Pat, Megan, Rodrigues, Carlos H.M., Nguyen, Thanh-Binh, Pires, Douglas E.V. and Ascher, David B. (2021). Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Computational and Structural Biotechnology Journal, 19, 5381-5391. doi: 10.1016/j.csbj.2021.09.016 |
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2020 Journal Article ThermoMutDB: a thermodynamic database for missense mutationsXavier, Joicymara S, Nguyen, Thanh-Binh, Karmarkar, Malancha, Portelli, Stephanie, Rezende, Pâmela M, Velloso, João P L, Ascher, David B and Pires, Douglas E V (2020). ThermoMutDB: a thermodynamic database for missense mutations. Nucleic Acids Research, 49 (D1), D475-D479. doi: 10.1093/nar/gkaa925 |
