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2022 Journal Article Known allosteric proteins have central roles in genetic diseaseAbrusán, György, Ascher, David B. and Inouye, Michael (2022). Known allosteric proteins have central roles in genetic disease. PLoS Computational Biology, 18 (2) e1009806, 1-28. doi: 10.1371/journal.pcbi.1009806 |
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2022 Journal Article epitope3D: a machine learning method for conformational B-cell epitope predictionda Silva, Bruna Moreira, Myung, YooChan, Ascher, David B. and Pires, Douglas E. V. (2022). epitope3D: a machine learning method for conformational B-cell epitope prediction. Briefings in Bioinformatics, 23 (1) bbab423, 1-8. doi: 10.1093/bib/bbab423 |
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2022 Journal Article Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteriaSharma, Mahima, Lingford, James P., Petricevic, Marija, Snow, Alexander J. D., Zhang, Yunyang, Järvå, Michael A., Mui, Janice W.-Y., Scott, Nichollas E., Saunders, Eleanor C., Mao, Runyu, Epa, Ruwan, da Silva, Bruna M., Pires, Douglas E. V., Ascher, David B., McConville, Malcolm J., Davies, Gideon J., Williams, Spencer J. and Goddard-Borger, Ethan D. (2022). Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proceedings of the National Academy of Sciences, 119 (4) e2116022119, e2116022119. doi: 10.1073/pnas.2116022119 |
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2022 Journal Article Estimating tuberculosis drug resistance amplification rates in high-burden settingsKarmakar, Malancha, Ragonnet, Romain, Ascher, David B., Trauer, James M. and Denholm, Justin T. (2022). Estimating tuberculosis drug resistance amplification rates in high-burden settings. BMC Infectious Diseases, 22 (1) 82, 1-12. doi: 10.1186/s12879-022-07067-1 |
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2022 Journal Article CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring functionNguyen, Thanh Binh, Pires, Douglas E. V. and Ascher, David B. (2022). CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Briefings in Bioinformatics, 23 (1) bbab512, 1-8. doi: 10.1093/bib/bbab512 |
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2021 Journal Article TSMDA: Target and symptom-based computational model for miRNA-disease-association predictionUthayopas, Korawich, de Sá, Alex G.C., Alavi, Azadeh, Pires, Douglas E.V. and Ascher, David B. (2021). TSMDA: Target and symptom-based computational model for miRNA-disease-association prediction. Molecular Therapy - Nucleic Acids, 26, 536-546. doi: 10.1016/j.omtn.2021.08.016 |
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2021 Journal Article PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitorsRodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2021). PdCSM-PPI: Using graph-based signatures to identify protein-protein interaction inhibitors. Journal of Chemical Information and Modeling, 61 (11), 5438-5445. doi: 10.1021/acs.jcim.1c01135 |
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2021 Journal Article mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinityNguyen, Thanh Binh, Myung, Yoochan, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity. NAR Genomics and Bioinformatics, 3 (4) lqab109, lqab109. doi: 10.1093/nargab/lqab109 |
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2021 Journal Article Assessing the performance of computational predictors for estimating protein stability changes upon missense mutationsIqbal, Shahid, Li, Fuyi, Akutsu, Tatsuya, Ascher, David B., Webb, Geoffrey I. and Song, Jiangning (2021). Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings in Bioinformatics, 22 (6) bbab184, 1-23. doi: 10.1093/bib/bbab184 |
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2021 Journal Article CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring functionMyung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2021). CSM-AB: graph-based antibody–antigen binding affinity prediction and docking scoring function. Bioinformatics, 38 (4), 1141-1143. doi: 10.1093/bioinformatics/btab762 |
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2021 Journal Article A novel deep intronic variant strongly associates with AlkaptonuriaLai, Chien-Yi, Tsai, I-Jung, Chiu, Pao-Chin, Ascher, David B., Chien, Yin-Hsiu, Huang, Yu-Hsuan, Lin, Yi-Lin, Hwu, Wuh-Liang and Lee, Ni-Chung (2021). A novel deep intronic variant strongly associates with Alkaptonuria. npj Genomic Medicine, 6 (1) 89, 89. doi: 10.1038/s41525-021-00252-2 |
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2021 Journal Article The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assayTunes, Luiza G., Ascher, David B., Pires, Douglas E. V. and Monte-Neto, Rubens L. (2021). The mutation G133D on Leishmania guyanensis AQP1 is highly destabilizing as revealed by molecular modeling and hypo-osmotic shock assay. Biochimica et biophysica acta. Biomembranes, 1863 (10) 183682, 1-6. doi: 10.1016/j.bbamem.2021.183682 |
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2021 Journal Article Machine Learning of ECG Waveforms to Improve Selection for Testing for Asymptomatic Left Ventricular DysfunctionPotter, Elizabeth L., Rodrigues, Carlos H. M., Ascher, David B., Abhayaratna, Walter P., Sengupta, Partho P. and Marwick, Thomas H. (2021). Machine Learning of ECG Waveforms to Improve Selection for Testing for Asymptomatic Left Ventricular Dysfunction. JACC. Cardiovascular imaging, 14 (10), 1904-1915. doi: 10.1016/j.jcmg.2021.04.020 |
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2021 Journal Article Deep learning in diabetic foot ulcers detection: A comprehensive evaluationYap, Moi Hoon, Hachiuma, Ryo, Alavi, Azadeh, Brüngel, Raphael, Cassidy, Bill, Goyal, Manu, Zhu, Hongtao, Rückert, Johannes, Olshansky, Moshe, Huang, Xiao, Saito, Hideo, Hassanpour, Saeed, Friedrich, Christoph M., Ascher, David B., Song, Anping, Kajita, Hiroki, Gillespie, David, Reeves, Neil D., Pappachan, Joseph M., O'Shea, Claire and Frank, Eibe (2021). Deep learning in diabetic foot ulcers detection: A comprehensive evaluation. Computers in Biology and Medicine, 135 104596, 1-17. doi: 10.1016/j.compbiomed.2021.104596 |
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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 MTR3D: identifying regions within protein tertiary structures under purifying selectionSilk, Michael, Pires, Douglas E V, Rodrigues, Carlos H M, D’Souza, Elston N, Olshansky, Moshe, Thorne, Natalie and Ascher, David B (2021). MTR3D: identifying regions within protein tertiary structures under purifying selection. Nucleic Acids Research, 49 (W1), W438-W445. doi: 10.1093/nar/gkab428 |
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2021 Journal Article pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer propertiesAl-Jarf, Raghad, de Sá, Alex G. C., Pires, Douglas E. V. and Ascher, David B. (2021). pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties. Journal of Chemical Information and Modeling, 61 (7), 3314-3322. doi: 10.1021/acs.jcim.1c00168 |
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2021 Journal Article SAP domain forms a flexible part of DNA aperture in Ku70/80Hnízda, Aleš, Tesina, Petr, Nguyen, Thanh-Binh, Kukačka, Zdeněk, Kater, Lukas, Chaplin, Amanda K, Beckmann, Roland, Ascher, David B, Novák, Petr and Blundell, Tom L (2021). SAP domain forms a flexible part of DNA aperture in Ku70/80. The FEBS Journal, 288 (14), 4382-4393. doi: 10.1111/febs.15732 |
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2021 Journal Article mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactionsRodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2021). mmCSM-PPI: predicting the effects of multiple point mutations on protein–protein interactions. Nucleic Acids Research, 49 (W1), W417-W424. doi: 10.1093/nar/gkab273 |
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2021 Journal Article Mercury methylation by metabolically versatile and cosmopolitan marine bacteriaLin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E. and Moreau, John W. (2021). Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The ISME Journal, 15 (6), 1810-1825. doi: 10.1038/s41396-020-00889-4 |
