Professor David Ascher
NHMRC Emerging Leadership Fellow & Director, Biotechnology Programs
School of Chemistry and Molecular Biosciences
+61 7 336 53991
Researcher biography
Prof David Ascher is currently an NHMRC Investigator and Director of the Biotechnology Program at the University of Queensland. He is also Head of Computational Biology and Clinical Informatics at the Baker Institute.
David’s research focus is in modelling biological data to gain insight into fundamental biological processes. One of his primary research interests has been developing tools to unravel the link between genotype and phenotype, using computational and experimental approaches to understand the effects of mutations on protein structure and function. His group has developed a platform of over 40 widely used programs for assessing the molecular consequences of coding variants (>7 million hits/year).
Working with clinical collaborators in Australia, Brazil and UK, these methods have been translated into the clinic to guide the diagnosis, management and treatment of a number of hereditary diseases, rare cancers and drug resistant infections.
David has a B.Biotech from the University of Adelaide, majoring in Biochemistry, Biotechnology and Pharmacology and Toxicology; and a B.Sci(Hon) from the University of Queensland, majoring in Biochemistry, where he worked with Luke Guddat and Ron Duggleby on the structural and functional characterization of enzymes in the branched-chain amino acid biosynthetic pathway. David then went to St Vincent’s Institute of Medical Research to undertake a PhD at the University of Melbourne in Biochemistry. There he worked under the supervision of Michael Parker using computational, biochemical and structural tools to develop small molecules drugs to improve memory.
In 2013 David went to the University of Cambridge to work with Sir Tom Blundell on using fragment based drug development techniques to target protein-protein interactions; and subsequently on the structural characterisation of proteins involved in non-homologous DNA repair. He returned to Cambridge in 2014 to establish a research platform to characterise the molecular effects of mutations on protein structure and function- using this information to gain insight into the link between genetic changes and phenotypes. He was subsequently recruited as a lab head in the Department of Biochemistry and Molecular Biology at the University of Melbourne in 2016, before joining the Baker Institute in 2019 and the University of Queensland in 2021.
He is an Associate Editor of PBMB and Fronteirs in Bioinformatics, and holds honorary positions at Bio21 Institute, Cambridge University, FIOCRUZ, and the Tuscany University Network.
Book Chapters
Serghini, 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
Ascher, David B., Kaminskas, Lisa M., Myung, Yoochan and Pires, Douglas E. V. (2022). Using graph-based signatures to guide rational antibody engineering. Computer-aided antibody design. (pp. 375-397) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2609-2_21
Airey, 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
Pires, Douglas E. V., Portelli, Stephanie, Rezende, Pâmela M., Veloso, Wandré N. P., Xavier, Joicymara S., Karmakar, Malancha, Myung, Yoochan, Linhares, João P. V., Rodrigues, Carlos H. M., Silk, Michael and Ascher, David B. (2020). A comprehensive computational platform to guide drug development using graph-based signature methods. Structural bioinformatics: methods and protocols. (pp. 91-106) New York, NY, United States: Humana. doi: 10.1007/978-1-0716-0270-6_7
Pires, Douglas E. V., Rodrigues, Carlos H. M., Albanaz, Amanda T. S., Karmakar, Malancha, Myung, Yoochan, Xavier, Joicymara, Michanetzi, Eleni-Maria, Portelli, Stephanie and Ascher, David B. (2019). Exploring protein supersecondary structure through changes in protein folding, stability, and flexibility. Protein Supersecondary Structures: Methods and Protocols. (pp. 173-185) edited by Alexander E. Kister. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-9161-7_9
Pires, Douglas E. V., Kaminskas, Lisa M. and Ascher, David B. (2018). Prediction and optimization of pharmacokinetic and toxicity properties of the ligand. Computational Drug Discovery and Design. (pp. 271-284) New York, NY United States: Humana Press. doi: 10.1007/978-1-4939-7756-7_14
Ascher, David B., Jubb, Harry C., Pires, Douglas E. V., Ochi, Takashi, Higueruelo, Alicia and Blundell, Tom L. (2015). Protein-protein interactions: structures and druggability. Multifaceted roles of crystallography in modern drug discovery. (pp. 141-163) Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/978-94-017-9719-1_12
Journal Articles
Jewell, Shannon, Nguyen, Thanh Binh, Ascher, David B. and Robertson, Avril A.B. (2024). Insights into the structure of NLR family member X1: Paving the way for innovative drug discovery. Computational and Structural Biotechnology Journal, 23, 3506-3513. doi: 10.1016/j.csbj.2024.09.013
Soh, Cheng Hwee, de Sá, Alex G. C., Potter, Elizabeth, Halabi, Amera, Ascher, David B. and Marwick, Thomas H. (2024). Use of the energy waveform electrocardiogram to detect subclinical left ventricular dysfunction in patients with type 2 diabetes mellitus. Cardiovascular Diabetology, 23 (1) 91. doi: 10.1186/s12933-024-02141-1
AlJarf, Raghad, Rodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2024). piscesCSM: prediction of anticancer synergistic drug combinations. Journal of Cheminformatics, 16 (1) 81. doi: 10.1186/s13321-024-00859-4
Huang, Katherine, G. C. de Sá, Alex, Thomas, Natalie, Phair, Robert D., Gooley, Paul R., Ascher, David B. and Armstrong, Christopher W. (2024). Discriminating Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and comorbid conditions using metabolomics in UK Biobank. Communications Medicine, 4 (1) 248, 248. doi: 10.1038/s43856-024-00669-7
Turner, 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
Pan, 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
Sen, Jonathan, Wahi, Sudhir, Vollbon, William, Prior, Marcus, de Sá, Alex G.C., Ascher, David B., Huynh, Quan and Marwick, Thomas H. (2024). Definition and validation of prognostic phenotypes in moderate aortic stenosis. JACC: Cardiovascular Imaging. doi: 10.1016/j.jcmg.2024.06.013
Gu, Xiaotong, Myung, Yoochan, Rodrigues, Carlos H. M. and Ascher, David B. (2024). EFG‐CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models. Protein Science, 33 (8) e5096, e5096. doi: 10.1002/pro.5096
Kovacs, 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
Craig, Olivia, Lee, Samuel, Pilcher, Courtney, Saoud, Rita, Abdirahman, Suad, Salazar, Carolina, Williams, Nathan, Ascher, David B, Vary, Robert, Luu, Jennii, Cowley, Karla J, Ramm, Susanne, Li, Mark Xiang, Thio, Niko, Li, Jason, Semple, Tim, Simpson, Kaylene J, Gorringe, Kylie L and Holien, Jessica K (2024). A new method for network bioinformatics identifies novel drug targets for mucinous ovarian carcinoma. NAR Genomics and Bioinformatics, 6 (3) lqae096, lqae096. doi: 10.1093/nargab/lqae096
Uthayopas, 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
Zhou, 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
King, 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. doi: 10.1073/pnas.2322923121
Velloso, 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
Ryu, 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
Gu, 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
Myung, Yoochan, de Sá, Alex G C and Ascher, David B (2024). Deep-PK: deep learning for small molecule pharmacokinetic and toxicity prediction. Nucleic Acids Research, 52 (W1), W469-W475. doi: 10.1093/nar/gkae254
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
Szot, 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
Velloso, 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. doi: 10.1016/j.coph.2023.102427
Rodrigues, 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
Li, 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), 1-13. doi: 10.1007/s12010-023-04820-3
Pan, 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
Ediriweera, 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
Serghini, 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
Rodrigues, 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
Al-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
Portelli, 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
Myung, 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
Nguyen, 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
Jessen-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
Zhou, Yunzhuo, Pan, Qisheng, Pires, Douglas E. V., Rodrigues, Carlos H. M. and Ascher, David B. (2023). DDMut: predicting effects of mutations on protein stability using deep learning. Nucleic Acids Research, 51 (W1), W122-W128. doi: 10.1093/nar/gkad472
da Silva, Bruna Moreira, Ascher, David B. and Pires, Douglas E. V. (2023). epitope1D: accurate taxonomy-aware B-cell linear epitope prediction. Briefings in Bioinformatics, 24 (3) bbad114, 1-8. doi: 10.1093/bib/bbad114
Silk, Michael, de Sá, Alex, Olshansky, Moshe and Ascher, David B. (2023). Insights from spatial measures of intolerance to identifying pathogenic variants in developmental and epileptic encephalopathies. International Journal of Molecular Sciences, 24 (6) 5114, 1-9. doi: 10.3390/ijms24065114
Morozov, Vladimir, Rodrigues, Carlos H. M. and Ascher, David B. (2023). CSM-Toxin: a web-server for predicting protein toxicity. Pharmaceutics, 15 (2) 431, 1-8. doi: 10.3390/pharmaceutics15020431
Aljarf, Raghad, Tang, Simon, Pires, Douglas E. V. and Ascher, David B. (2023). embryoTox: using graph-based signatures to predict the teratogenicity of small molecules. Journal of Chemical Information and Modeling, 63 (2), 432-441. doi: 10.1021/acs.jcim.2c00824
Williams, Nathan P., Rodrigues, Carlos H. M., Truong, Jia, Ascher, David B. and Holien, Jessica K. (2023). DockNet: high-throughput protein–protein interface contact prediction. Bioinformatics, 39 (1) btac797, 1-3. doi: 10.1093/bioinformatics/btac797
Xavier, Joicymara S., Moir, Monika, Tegally, Houriiyah, Sitharam, Nikita, Abdool Karim, Wasim, San, James E., Linhares, Joana, Wilkinson, Eduan, Ascher, David B., Baxter, Cheryl, Pires, Douglas E. V. and de Oliveira, Tulio (2022). SARS-CoV-2 Africa dashboard for real-time COVID-19 information. Nature Microbiology, 8 (1), 1-4. doi: 10.1038/s41564-022-01276-9
Boer, Jennifer C., Pan, Qisheng, Holien, Jessica K., Nguyen, Thanh-Binh, Ascher, David B. and Plebanski, Magdalena (2022). A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Frontiers in Immunology, 13 954435, 1-13. doi: 10.3389/fimmu.2022.954435
Parthasarathy, Shridhar, Ruggiero, Sarah McKeown, Gelot, Antoinette, Soardi, Fernanda C, Ribeiro, Bethânia F R, Pires, Douglas E V, Ascher, David B, Schmitt, Alain, Rambaud, Caroline, Represa, Alfonso, Xie, Hongbo M, Lusk, Laina, Wilmarth, Olivia, McDonnell, Pamela Pojomovsky, Juarez, Olivia A, Grace, Alexandra N, Buratti, Julien, Mignot, Cyril, Gras, Domitille, Nava, Caroline, Pierce, Samuel R, Keren, Boris, Kennedy, Benjamin C, Pena, Sergio D J, Helbig, Ingo and Cuddapah, Vishnu Anand (2022). A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. The American Journal of Human Genetics, 109 (12), 2253-2269. doi: 10.1016/j.ajhg.2022.11.002
Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M. ... Beltrao, Pedro (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural and Molecular Biology, 29 (11), 1056-1067. doi: 10.1038/s41594-022-00849-w
Zhou, Yunzhuo, Al‐Jarf, Raghad, Alavi, Azadeh, Nguyen, Thanh Binh, Rodrigues, Carlos H. M., Pires, Douglas E. V. and Ascher, David B. (2022). kinCSM
: Using graph‐based signatures to predict small molecule
CDK2
inhibitors. Protein Science, 31 (11) e4453, 1-11. doi: 10.1002/pro.4453
Iftkhar, Saba, de Sá, Alex G. C., Velloso, João P. L., Aljarf, Raghad, Pires, Douglas E. V. and Ascher, David B. (2022). cardioToxCSM: a web server for predicting cardiotoxicity of small molecules. Journal of Chemical Information and Modeling, 62 (20), 4827-4836. doi: 10.1021/acs.jcim.2c00822
Rodrigues, Carlos H. M., Garg, Anjali, Keizer, David, Pires, Douglas E. V. and Ascher, David B. (2022). CSM‐peptides: A computational approach to rapid identification of therapeutic peptides. Protein Science, 31 (10) e4442, 1-9. doi: 10.1002/pro.4442
Portelli, 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
Tichkule, Swapnil, Myung, Yoochan, Naung, Myo T., Ansell, Brendan R. E., Guy, Andrew J., Srivastava, Namrata, Mehra, Somya, Cacciò, Simone M, Mueller, Ivo, Barry, Alyssa E, van Oosterhout, Cock, Pope, Bernard, Ascher, David B and Jex, Aaron R (2022). VIVID: a web application for variant interpretation and visualisation in multidimensional analyses. Molecular Biology and Evolution, 39 (9) msac196. doi: 10.1093/molbev/msac196
Paiva, Vinícius A., Mendonça, Murillo V., Silveira, Sabrina A., Ascher, David B., Pires, Douglas E. V. and Izidoro, Sandro C. (2022). GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings in Bioinformatics, 23 (5) bbac178, 1-9. doi: 10.1093/bib/bbac178
Ruff, Kiersten M., Choi, Yoon Hee, Cox, Dezerae, Ormsby, Angelique R., Myung, Yoochan, Ascher, David B., Radford, Sheena E., Pappu, Rohit V. and Hatters, Danny M. (2022). Sequence grammar underlying the unfolding and phase separation of globular proteins. Molecular Cell, 82 (17), 3193-3208.e8. doi: 10.1016/j.molcel.2022.06.024
de 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
Sen, J., Pires, D., de Sá, A., Ascher, D., Wahir, S. and Marwick, T. (2022). Use of cluster analysis to characterise aortic stenosis phenotypes with treatable and untreatable risk. Heart, Lung and Circulation, 31, S44-S45. doi: 10.1016/j.hlc.2022.06.016
Karmakar, Malancha, Cicaloni, Vittoria, Rodrigues, Carlos H. M., Spiga, Ottavia, Santucci, Annalisa and Ascher, David B. (2022). HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Current Research in Structural Biology, 4, 271-277. doi: 10.1016/j.crstbi.2022.08.001
Rodrigues, Carlos H. M. and Ascher, David B (2022). CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Research, 50 (W1), W204-W209. doi: 10.1093/nar/gkac381
Rezende, Pâmela M., Xavier, Joicymara S., Ascher, David B., Fernandes, Gabriel R. and Pires, Douglas E. V. (2022). Evaluating hierarchical machine learning approaches to classify biological databases. Briefings in Bioinformatics, 23 (4) bbac216, 1-14. doi: 10.1093/bib/bbac216
Rodrigues, Carlos H. M., Pires, Douglas E. V., Blundell, Tom L. and Ascher, David B. (2022). Structural landscapes of PPI interfaces. Briefings in Bioinformatics, 23 (4) bbac165, 1-10. doi: 10.1093/bib/bbac165
Pires, Douglas E V, Stubbs, Keith A, Mylne, Joshua S and Ascher, David B (2022). cropCSM: designing safe and potent herbicides with graph-based signatures. Briefings in Bioinformatics, 23 (2) bbac042. doi: 10.1093/bib/bbac042
Pan, Qisheng, Nguyen, Thanh Binh, Ascher, David B and Pires, Douglas E V (2022). Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Briefings in Bioinformatics, 23 (2) bbac025. doi: 10.1093/bib/bbac025
Abrusán, 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
da 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
Sharma, 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. doi: 10.1073/pnas.2116022119
Nguyen, 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
Uthayopas, 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
Rodrigues, 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
Nguyen, 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
Myung, 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
Lai, 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
Zhan, 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
Al-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
Silk, 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
Rodrigues, 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
Lin, 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
Portelli, 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
Souza Silva, Juliano A., Tunes, Luiza G., Coimbra, Roney S., Ascher, David B., Pires, Douglas E.V. and Monte-Neto, Rubens L. (2021). Unveiling six potent and highly selective antileishmanial agents via the open source compound collection ‘Pathogen Box’ against antimony-sensitive and -resistant Leishmania braziliensis. Biomedicine and Pharmacotherapy, 133 111049, 111049. doi: 10.1016/j.biopha.2020.111049
Zhou, 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
Velloso, João Paulo L., Ascher, David B. and Pires, Douglas E. V. (2021). pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. Bioinformatics Advances, 1 (1) vbab031, vbab031. doi: 10.1093/bioadv/vbab031
Portelli, 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
Hildebrand, Joanne M., Kauppi, Maria, Majewski, Ian J., Liu, Zikou, Cox, Allison J., Miyake, Sanae, Petrie, Emma J., Silk, Michael A., Li, Zhixiu, Tanzer, Maria C., Brumatti, Gabriela, Young, Samuel N., Hall, Cathrine, Garnish, Sarah E., Corbin, Jason, Stutz, Michael D., Di Rago, Ladina, Gangatirkar, Pradnya, Josefsson, Emma C., Rigbye, Kristin, Anderton, Holly, Rickard, James A., Tripaydonis, Anne, Sheridan, Julie, Scerri, Thomas S., Jackson, Victoria E., Czabotar, Peter E., Zhang, Jian-Guo, Varghese, Leila ... Silke, John (2020). A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nature Communications, 11 (1) 3150, 3150. doi: 10.1038/s41467-020-16819-z
Haque, Shadabul, Pouton, Colin W., McIntosh, Michelle P., Ascher, David B, Keizer, David W, Whittaker, Michael R. and Kaminskas, Lisa M. (2020). The impact of size and charge on the pulmonary pharmacokinetics and immunological response of the lungs to PLGA nanoparticles after intratracheal administration to rats. Nanomedicine: Nanotechnology, Biology, and Medicine, 30 102291, 102291. doi: 10.1016/j.nano.2020.102291
Xavier, 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
Portelli, Stephanie, Myung, Yoochan, Furnham, Nicholas, Vedithi, Sundeep Chaitanya, Pires, Douglas E. V. and Ascher, David B. (2020). Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific Reports, 10 (1) 18120, 1-13. doi: 10.1038/s41598-020-74648-y
Rodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2020). DynaMut2
: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Science, 30 (1), 60-69. doi: 10.1002/pro.3942
Portelli, 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. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52 (10), 999-1001. doi: 10.1038/s41588-020-0693-3
Pires, Douglas E V, Veloso, Wandré N P, Myung, YooChan, Rodrigues, Carlos H M, Silk, Michael, Rezende, Pâmela M, Silva, Francislon, Xavier, Joicymara S, Velloso, João P L, da Silveira, Carlos H and Ascher, David B (2020). EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinformatics, 36 (14), 4200-4202. doi: 10.1093/bioinformatics/btaa480
Pires, Douglas E. V. and Ascher, David B. (2020). mycoCSM: Using graph-based signatures to identify safe potent hits against Mycobacteria. Journal of Chemical Information and Modeling, 60 (7), 3450-3456. doi: 10.1021/acs.jcim.0c00362
Pires, Douglas E V, Rodrigues, Carlos H M and Ascher, David B (2020). mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Research, 48 (W1), W147-W153. doi: 10.1093/nar/gkaa416
Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2020). mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Research, 48 (W1), W125-W131. doi: 10.1093/nar/gkaa389
Myung, Yoochan, Rodrigues, Carlos H. M., Ascher, David B. and Pires, Douglas E. V. (2020). mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinformatics, 36 (5), 1453-1459. doi: 10.1093/bioinformatics/btz779
Karmakar, Malancha, Rodrigues, Carlos H. M., Horan, Kristy, Denholm, Justin T. and Ascher, David B. (2020). Structure guided prediction of Pyrazinamide resistance mutations in pncA. Scientific Reports, 10 (1) 1875, 1875. doi: 10.1038/s41598-020-58635-x
Sui, Xiaojing, Pires, Douglas E V, Ormsby, Angelique R, Cox, Dezerae, Nie, Shuai, Vecchi, Giulia, Vendruscolo, Michele, Ascher, David B, Reid, Gavin E and Hatters, Danny M (2020). Widespread remodeling of proteome solubility in response to different protein homeostasis stresses. Proceedings of the National Academy of Sciences of the United States of America, 117 (5), 2422-2431. doi: 10.1073/pnas.1912897117
Bayley, Jean Pierre, Bausch, Birke, Rijken, Johannes Adriaan, van Hulsteijn, Leonie Theresia, Jansen, Jeroen C., Ascher, David, Pires, Douglas Eduardo Valente, Hes, Frederik J., Hensen, Erik F., Corssmit, Eleonora P. M., Devilee, Peter and Neumann, Hartmut P. H. (2020). Variant type is associated with disease characteristics in SDHB, SDHC and SDHD-linked phaeochromocytoma-paraganglioma. Journal of Medical Genetics, 57 (2), 96-103. doi: 10.1136/jmedgenet-2019-106214
Vedithi, Sundeep Chaitanya, Rodrigues, Carlos H. M., Portelli, Stephanie, Skwark, Marcin J., Das, Madhusmita, Ascher, David B., Blundell, Tom L. and Malhotra, Sony (2020). Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal, 18, 271-286. doi: 10.1016/j.csbj.2020.01.002
Trapero, Ana, Pacitto, Angela, Chan, Daniel Shiu-Hin, Abell, Chris, Blundell, Tom L., Ascher, David B. and Coyne, Anthony G. (2020). Covalent inactivation of Mycobacterium thermoresistibile inosine-5'-monophosphate dehydrogenase (IMPDH). Bioorganic and Medicinal Chemistry Letters, 30 (2) 126792, 126792. doi: 10.1016/j.bmcl.2019.126792
Karmakar, Malancha, Trauer, James M, Ascher, David B and Denholm, Justin T (2019). Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysis. The Journal of Infection, 79 (6), 572-581. doi: 10.1016/j.jinf.2019.09.016
Kaminskas, Lisa M., Pires, Douglas E. V. and Ascher, David B. (2019). dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction. Scientific Reports, 9 (1) 15465, 15465. doi: 10.1038/s41598-019-51789-3
Brown, Peter, Tan, Aik-Choon, El-Esawi, Mohamed A., Liehr, Thomas, Blanck, Oliver, Gladue, Douglas P., Almeida, Gabriel M. F., Cernava, Tomislav, Sorzano, Carlos O., Yeung, Andy W. K., Engel, Michael S., Chandrasekaran, Arun Richard, Muth, Thilo, Staege, Martin S., Daulatabad, Swapna V., Widera, Darius, Zhang, Junpeng, Meule, Adrian, Honjo, Ken, Pourret, Olivier, Yin, Cong-Cong, Zhang, Zhongheng, Cascella, Marco, Flegel, Willy A., Goodyear, Carl S., van Raaij, Mark J., Bukowy-Bieryllo, Zuzanna, Campana, Luca G., Kurniawan, Nicholas A. ... RELISH Consortium (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database-The Journal of Biological Databases and Curation, 2019 ARTN baz085, 1-67. doi: 10.1093/database/baz085
Karpiyevich, Maryia, Adjalley, Sophie, Mol, Marco, Ascher, David B., Mason, Bethany, van der Heden van Noort, Gerbrand J., Laman, Heike, Ovaa, Huib, Lee, Marcus C. S. and Artavanis-Tsakonas, Katerina (2019). Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathogens, 15 (10), e1008086. doi: 10.1371/journal.ppat.1008086
Copoiu, Liviu, Torres, Pedro H M, Ascher, David B, Blundell, Tom L and Malhotra, Sony (2019). ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Research, 48 (D1), D368-D375. doi: 10.1093/nar/gkz860
Sernee, M. Fleur, Ralton, Julie E., Nero, Tracy L., Sobala, Lukasz F., Kloehn, Joachim, Vieira-Lara, Marcel A., Cobbold, Simon A., Stanton, Lauren, Pires, Douglas E. V., Hanssen, Eric, Males, Alexandra, Ward, Tom, Bastidas, Laurence M., van der Peet, Phillip L., Parker, Michael W., Ascher, David B., Williams, Spencer J., Davies, Gideon J. and McConville, Malcolm J. (2019). A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasites. Cell Host and Microbe, 26 (3), 385-399.e9. doi: 10.1016/j.chom.2019.08.009
Singh, Vinayak, Pacitto, Angela, Donini, Stefano, Ferraris, Davide M, Boros, Sándor, Illyés, Eszter, Szokol, Bálint, Rizzi, Menico, Blundell, Tom L, Ascher, David B, Pato, Janos and Mizrahi, Valerie (2019). Synthesis and structure-activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. European Journal of Medicinal Chemistry, 174, 309-329. doi: 10.1016/j.ejmech.2019.04.027
Rodrigues, Carlos H. M., Myung, Yoochan, Pires, Douglas E. V. and Ascher, David B. (2019). mCSM-PPI2: predicting the effects of mutations on protein–protein interactions. Nucleic Acids Research, 47 (W1), W338-W344. doi: 10.1093/nar/gkz383
Silk, Michael, Petrovski, Slavé and Ascher, David B (2019). MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Research, 47 (W1), W121-W126. doi: 10.1093/nar/gkz457
Ascher, David B, Spiga, Ottavia, Sekelska, Martina, Pires, Douglas E V, Bernini, Andrea, Tiezzi, Monica, Kralovicova, Jana, Borovska, Ivana, Soltysova, Andrea, Olsson, Birgitta, Galderisi, Silvia, Cicaloni, Vittoria, Ranganath, Lakshminarayan, Santucci, Annalisa and Zatkova, Andrea (2019). Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. European Journal of Human Genetics : EJHG, 27 (6), 888-902. doi: 10.1038/s41431-019-0354-0
Karmakar, Malancha, Rodrigues, Carlos H M, Holt, Kathryn E, Dunstan, Sarah J, Denholm, Justin and Ascher, David B (2019). Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PloS one, 14 (5) e0217169, e0217169. doi: 10.1371/journal.pone.0217169
Jatana, Nidhi, Ascher, David B., Pires, Douglas E.V., Gokhale, Rajesh S. and Thukral, Lipi (2019). Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy, 16 (2), 239-255. doi: 10.1080/15548627.2019.1606636
Kaminskas, Lisa M., Williams, Charlotte C., Leong, Nathania J., Chan, Linda J., Butcher, Neville J., Feeney, Orlagh M., Porter, Christopher J.H., Tyssen, David, Tachedjian, Gilda and Ascher, David B. (2019). A 30 kDa polyethylene glycol-enfuvirtide complex enhances the exposure of enfuvirtide in lymphatic viral reservoirs in rats. European Journal of Pharmaceutics and Biopharmaceutics, 137, 218-226. doi: 10.1016/j.ejpb.2019.03.008
Portelli, Stephanie, Phelan, Jody E., Ascher, David B., Clark, Taane G. and Furnham, Nicholas (2018). Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific Reports, 8 (1) 15356. doi: 10.1038/s41598-018-33370-6
Abayakoon, Palika, Jin, Yi, Lingford, James P., Petricevic, Marija, John, Alan, Ryan, Eileen, Wai-Ying Mui, Janice, Pires, Douglas E.V., Ascher, David B., Davies, Gideon J., Goddard-Borger, Ethan D. and Williams, Spencer J. (2018). Structural and biochemical insights into the function and evolution of sulfoquinovosidases. ACS Central Science, 4 (9), 1266-1273. doi: 10.1021/acscentsci.8b00453
Karmakar, Malancha, Globan, Maria, Fyfe, Janet A. M., Stinear, Timothy P., Johnson, Paul D. R., Holmes, Natasha E., Denholm, Justin T. and Ascher, David B. (2018). Analysis of a novel pncA mutation for susceptibility to pyrazinamide therapy. American Journal of Respiratory and Critical Care Medicine, 198 (4), 541-544. doi: 10.1164/rccm.201712-2572le
Rodrigues, Carlos H.M., Ascher, David B. and Pires, Douglas E.V. (2018). Kinact: a computational approach for predicting activating missense mutations in protein kinases. Nucleic Acids Research, 46 (W1), W127-W132. doi: 10.1093/nar/gky375
Andrews, Katrina A, Ascher, David B, Pires, Douglas Eduardo Valente, Barnes, Daniel R, Vialard, Lindsey, Casey, Ruth T, Bradshaw, Nicola, Adlard, Julian, Aylwin, Simon, Brennan, Paul, Brewer, Carole, Cole, Trevor, Cook, Jackie A, Davidson, Rosemarie, Donaldson, Alan, Fryer, Alan, Greenhalgh, Lynn, Hodgson, Shirley V, Irving, Richard, Lalloo, Fiona, McConachie, Michelle, McConnell, Vivienne P M, Morrison, Patrick J, Murday, Victoria, Park, Soo-Mi, Simpson, Helen L, Snape, Katie, Stewart, Susan, Tomkins, Susan E ... Maher, Eamonn R (2018). Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes , and . Journal of Medical Genetics, 55 (6), 384-394. doi: 10.1136/jmedgenet-2017-105127
Holt, Kathryn E, McAdam, Paul, Thai, Phan Vuong Khac, Thuong, Nguyen Thuy Thuong, Ha, Dang Thi Minh, Lan, Nguyen Ngoc, Lan, Nguyen Huu, Nhu, Nguyen Thi Quynh, Hai, Hoang Thanh, Ha, Vu Thi Ngoc, Thwaites, Guy, Edwards, David J, Nath, Artika P, Pham, Kym, Ascher, David B, Farrar, Jeremy, Khor, Chiea Chuen, Teo, Yik Ying, Inouye, Michael, Caws, Maxine and Dunstan, Sarah J (2018). Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nature Genetics, 50 (6), 849-856. doi: 10.1038/s41588-018-0117-9
Hnízda, Aleš, Fábry, Milan, Moriyama, Takaya, Pachl, Petr, Kugler, Michael, Brinsa, Vítězslav, Ascher, David B, Carroll, William L, Novák, Petr, Žaliová, Markéta, Trka, Jan, Řezáčová, Pavlína, Yang, Jun J and Veverka, Václav (2018). Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia, 32 (6), 1393-1403. doi: 10.1038/s41375-018-0073-5
Rodrigues, Carlos H.M., Pires, Douglas E.V. and Ascher, David B. (2018). DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Research, 46 (W1), W350-W355. doi: 10.1093/nar/gky300
Trapero, Ana, Pacitto, Angela, Singh, Vinayak, Sabbah, Mohamad, Coyne, Anthony G, Mizrahi, Valerie, Blundell, Tom L, Ascher, David B and Abell, Chris (2018). Fragment-based approach to targeting inosine-5'-monophosphate dehydrogenase (IMPDH) from Mycobacterium tuberculosis. Journal of Medicinal Chemistry, 61 (7), 2806-2822. doi: 10.1021/acs.jmedchem.7b01622
Vedithi, Sundeep Chaitanya, Malhotra, Sony, Das, Madhusmita, Daniel, Sheela, Kishore, Nanda, George, Anuja, Arumugam, Shantha, Rajan, Lakshmi, Ebenezer, Mannam, Ascher, David B, Arnold, Eddy and Blundell, Tom L (2018). Structural implications of mutations conferring rifampin resistance in Mycobacterium leprae. Scientific Reports, 8 (1) 5016. doi: 10.1038/s41598-018-23423-1
Hawkey, Jane, Ascher, David B, Judd, Louise M, Wick, Ryan R, Kostoulias, Xenia, Cleland, Heather, Spelman, Denis W, Padiglione, Alex, Peleg, Anton Y and Holt, Kathryn E (2018). Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. Microbial Genomics, 4 (3) ARTN 000165. doi: 10.1099/mgen.0.000165
Trezza, Alfonso, Bernini, Andrea, Langella, Andrea, Ascher, David B, Pires, Douglas E V, Sodi, Andrea, Passerini, Ilaria, Pelo, Elisabetta, Rizzo, Stanislao, Niccolai, Neri and Spiga, Ottavia (2017). A computational approach from gene to structure analysis of the human ABCA4 transporter involved in genetic retinal diseases. Investigative Ophthalmology and Visual Science, 58 (12), 5320-5328. doi: 10.1167/iovs.17-22158
Traynelis, Joshua, Silk, Michael, Wang, Quanli, Berkovic, Samuel F, Liu, Liping, Ascher, David B, Balding, David J and Petrovski, Slavé (2017). Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. Genome Research, 27 (10), 1715-1729. doi: 10.1101/gr.226589.117
Jubb, Harry C, Pandurangan, Arun P, Turner, Meghan A, Ochoa-Montaño, Bernardo, Blundell, Tom L and Ascher, David B (2017). Mutations at protein-protein interfaces: small changes over big surfaces have large impacts on human health. Progress in Biophysics and Molecular Biology, 128, 3-13. doi: 10.1016/j.pbiomolbio.2016.10.002
Albanaz, Amanda T S, Rodrigues, Carlos H M, Pires, Douglas E V and Ascher, David B (2017). Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opinion on Drug Discovery, 12 (6), 553-563. doi: 10.1080/17460441.2017.1322579
Pandurangan, Arun Prasad, Ochoa-Montaño, Bernardo, Ascher, David B. and Blundell, Tom L. (2017). SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Research, 45 (W1), W229-W235. doi: 10.1093/nar/gkx439
Chirgadze, Dimitri Y, Ascher, David B, Blundell, Tom L and Sibanda, Bancinyane L (2017). DNA-PKcs, allostery, and DNA double-strand break repair: defining the structure and setting the stage. Methods in Enzymology, 592, 145-157. doi: 10.1016/bs.mie.2017.04.001
Ramdzan, Yasmin M., Trubetskov, Mikhail M., Ormsby, Angelique R., Newcombe, Estella A., Sui, Xiaojing, Tobin, Mark J., Bongiovanni, Marie N., Gras, Sally L., Dewson, Grant, Miller, Jason M. L., Finkbeiner, Steven, Moily, Nagaraj S., Niclis, Jonathan, Parish, Clare L., Purcell, Anthony W., Baker, Michael J., Wilce, Jacqueline A., Waris, Saboora, Stojanovski, Diana, Bocking, Till, Ang, Ching-Seng, Ascher, David B., Reid, Gavin E. and Hatters, Danny M. (2017). Huntingtin inclusions trigger cellular quiescence, deactivate apoptosis, and lead to delayed necrosis. Cell Reports, 19 (5), 919-927. doi: 10.1016/j.celrep.2017.04.029
Casey, Ruth T, Ascher, David B, Rattenberry, Eleanor, Izatt, Louise, Andrews, Katrina A, Simpson, Helen L, Challis, Benjamen, Park, Soo-Mi, Bulusu, Venkata R, Lalloo, Fiona, Pires, Douglas E V, West, Hannah, Clark, Graeme R, Smith, Philip S, Whitworth, James, Papathomas, Thomas G, Taniere, Phillipe, Savisaar, Rosina, Hurst, Laurence D, Woodward, Emma R and Maher, Eamonn R (2017). SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. Molecular Genetics and Genomic Medicine, 5 (3), 237-250. doi: 10.1002/mgg3.279
Sharp, Julie A, Brennan, Amelia J, Polekhina, Galina, Ascher, David B, Lefevre, Christophe and Nicholas, Kevin R (2017). Dimeric but not monomeric α-lactalbumin potentiates apoptosis by up regulation of ATF3 and reduction of histone deacetylase activity in primary and immortalised cells. Cellular Signalling, 33, 86-97. doi: 10.1016/j.cellsig.2017.02.007
Pandurangan, Arun Prasad, Ascher, David B., Thomas, Sherine E. and Blundell, Tom L. (2017). Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. Biochemical Society Transactions, 45 (2), 303-311. doi: 10.1042/BST20160422
Pires, Douglas E.V. and Ascher, David B. (2017). mCSM–NA: predicting the effects of mutations on protein–nucleic acids interactions. Nucleic Acids Research, 45 (W1), W241-W246. doi: 10.1093/nar/gkx236
Soardi, Fernanda C, Machado-Silva, Alice, Linhares, Natália D, Zheng, Ge, Qu, Qianhui, Pena, Heloísa B, Martins, Thaís M M, Vieira, Helaine G S, Pereira, Núbia B, Melo-Minardi, Raquel C, Gomes, Carolina C, Gomez, Ricardo S, Gomes, Dawidson A, Pires, Douglas E V, Ascher, David B, Yu, Hongtao and Pena, Sérgio D J (2017). Familial germline mutation defines a new human cohesinopathy. NPJ Genomic Medicine, 2 (1) 7. doi: 10.1038/s41525-017-0009-4
Sibanda, Bancinyane L, Chirgadze, Dimitri Y, Ascher, David B and Blundell, Tom L (2017). DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science, 355 (6324), 520-524. doi: 10.1126/science.aak9654
Jubb, Harry C, Higueruelo, Alicia P, Ochoa-Montaño, Bernardo, Pitt, Will R, Ascher, David B and Blundell, Tom L (2017). Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures. Journal of Molecular Biology, 429 (3), 365-371. doi: 10.1016/j.jmb.2016.12.004
Parker, Lorien J., Bocedi, Alessio, Ascher, David B., Aitken, Jade B., Harris, Hugh H., Lo Bello, Mario, Ricci, Giorgio, Morton, Craig J. and Parker, Michael W. (2017). Glutathione transferase P1-1 as an arsenic drug-sequestering enzyme. Protein Science, 26 (2), 317-326. doi: 10.1002/pro.3084
Park, Yumi, Pacitto, Angela, Bayliss, Tracy, Cleghorn, Laura A T, Wang, Zhe, Hartman, Travis, Arora, Kriti, Ioerger, Thomas R, Sacchettini, Jim, Rizzi, Menico, Donini, Stefano, Blundell, Tom L, Ascher, David B, Rhee, Kyu, Breda, Ardala, Zhou, Nian, Dartois, Veronique, Jonnala, Surendranadha Reddy, Via, Laura E, Mizrahi, Valerie, Epemolu, Ola, Stojanovski, Laste, Simeons, Fred, Osuna-Cabello, Maria, Ellis, Lucy, MacKenzie, Claire J, Smith, Alasdair R C, Davis, Susan H, Murugesan, Dinakaran ... Boshoff, Helena I (2017). Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis. ACS Infectious Diseases, 3 (1), 18-33. doi: 10.1021/acsinfecdis.6b00103
Singh, Vinayak, Donini, Stefano, Pacitto, Angela, Sala, Claudia, Hartkoorn, Ruben C., Dhar, Neeraj, Keri, Gyorgy, Ascher, David B., Mondésert, Guillaume, Vocat, Anthony, Lupien, Andréanne, Sommer, Raphael, Vermet, Hélène, Lagrange, Sophie, Buechler, Joe, Warner, Digby F., McKinney, John D., Pato, Janos, Cole, Stewart T., Blundell, Tom L., Rizzi, Menico and Mizrahi, Valerie (2017). The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis. ACS Infectious Diseases, 3 (1), 5-17. doi: 10.1021/acsinfecdis.6b00102
Liang, S., Esswein, S. R., Ochi, T., Wu, Q., Ascher, D. B., Chirgadze, D., Sibanda, B. L. and Blundell, T. L. (2017). Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached. Structural Chemistry, 28 (1), 161-171. doi: 10.1007/s11224-016-0841-7
Kano, Flora S, Souza-Silva, Flávia A, Torres, Leticia M, Lima, Barbara A S, Sousa, Taís N, Alves, Jéssica R S, Rocha, Roberto S, Fontes, Cor J F, Sanchez, Bruno A M, Adams, John H, Brito, Cristiana F A, Pires, Douglas E V, Ascher, David B, Sell, Ana Maria and Carvalho, Luzia H (2016). The presence, persistence and functional properties of Plasmodium vivax duffy binding protein II antibodies are influenced by HLA class II allelic variants. PLoS Neglected Tropical Diseases, 10 (12) e0005177. doi: 10.1371/journal.pntd.0005177
White, Rhiannon R, Ponsford, Amy H, Weekes, Michael P, Rodrigues, Rachel B, Ascher, David B, Mol, Marco, Selkirk, Murray E, Gygi, Steven P, Sanderson, Christopher M and Artavanis-Tsakonas, Katerina (2016). Ubiquitin-dependent modification of skeletal muscle by the parasitic nematode, Trichinella spiralis. PLoS Pathogens, 12 (11) e1005977, e1005977. doi: 10.1371/journal.ppat.1005977
Coelho, Miguel B, Ascher, David B, Gooding, Clare, Lang, Emma, Maude, Hannah, Turner, David, Llorian, Miriam, Pires, Douglas E V, Attig, Jan and Smith, Christopher W J (2016). Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins. Biochemical Society Transactions, 44 (4), 1058-1065. doi: 10.1042/BST20160080
Silvino, Ana Carolina Rios, Costa, Gabriel Luiz, Araújo, Flávia Carolina Faustino de, Ascher, David Benjamin, Pires, Douglas Eduardo Valente, Fontes, Cor Jesus Fernandes, Carvalho, Luzia Helena, Brito, Cristiana Ferreira Alves de and Sousa, Tais Nobrega (2016). Variation in human cytochrome P-450 drug-metabolism genes: a gateway to the understanding of Plasmodium vivax relapses. PLoS One, 11 (7) ARTN e0160172, e0160172. doi: 10.1371/journal.pone.0160172
Pires, Douglas E. V. and Ascher, David B. (2016). mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures. Nucleic Acids Research, 44 (W1), W469-W473. doi: 10.1093/nar/gkw458
Pires, Douglas E. V. and Ascher, David B (2016). CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Research, 44 (W1), W557-W561. doi: 10.1093/nar/gkw390
Pires, Douglas E. V., Blundell, Tom L. and Ascher, David B. (2016). mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Scientific Reports, 6 (1) 29575, 29575. doi: 10.1038/srep29575
Phelan, Jody, Coll, Francesc, McNerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin L., Pain, Arnab, Rigouts, Leen and Clark, Taane G. (2016). Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Medicine, 14 (1) 31, 31. doi: 10.1186/s12916-016-0575-9
Chan, Linda J., Ascher, David B., Yadav, Rajbharan, Bulitta, Jürgen B., Williams, Charlotte C., Porter, Christopher J. H., Landersdorfer, Cornelia B. and Kaminskas, Lisa M. (2016). Conjugation of 10 kDa Linear PEG onto Trastuzumab Fab′ Is Sufficient to Significantly Enhance Lymphatic Exposure while Preserving in Vitro Biological Activity. Molecular Pharmaceutics, 13 (4), 1229-1241. doi: 10.1021/acs.molpharmaceut.5b00749
Andrews, Katrina A, Vialard, Lindsey, Ascher, David B, Pires, Douglas E V, Bradshaw, Nicola, Cole, Trevor, Cook, Jackie, Irving, Richard, Kumar, Ajith, Lalloo, Fiona, Izatt, Louise, Goudie, David, Woodward, Emma R and Maher, Eamonn R (2016). Tumour risks and genotype–phenotype–proteotype analysis of patients with germline mutations in the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD. The Lancet, 387, S19-S19. doi: 10.1016/s0140-6736(16)00406-2
Pires, Douglas E. V., Chen, Jing, Blundell, Tom L. and Ascher, David B. (2016). In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Scientific Reports, 6 (1) 19848. doi: 10.1038/srep19848
Nemethova, Martina, Radvanszky, Jan, Kadasi, Ludevit, Ascher, David B., Pires, Douglas E. V., Blundell, Tom L., Porfirio, Berardino, Mannoni, Alessandro, Santucci, Annalisa, Milucci, Lia, Sestini, Silvia, Biolcati, Gianfranco, Sorge, Fiammetta, Aurizi, Caterina, Aquaron, Robert, Alsbou, Mohammed, Lourenço, Charles Marques, Ramadevi, Kanakasabapathi, Ranganath, Lakshminarayan R., Gallagher, James A., van Kan, Christa, Hall, Anthony K., Olsson, Birgitta, Sireau, Nicolas, Ayoob, Hana, Timmis, Oliver G., Sang, Kim-Hanh Le Quan, Genovese, Federica, Imrich, Richard ... Zatkova, Andrea (2016). Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy. European Journal of Human Genetics, 24 (1), 66-72. doi: 10.1038/ejhg.2015.60
Landersdorfer, Cornelia B., Caliph, Suzanne M., Shackleford, David M., Ascher, David B. and Kaminskas, Lisa M. (2015). PEGylated interferon displays differences in plasma clearance and bioavailability between male and female mice and between female immunocompetent C57Bl/6J and athymic nude mice. Journal of Pharmaceutical Sciences, 104 (5), 1848-1855. doi: 10.1002/jps.24412
Pacitto, Angela, Ascher, David B, Wong, Louise H, Blaszczyk, Beata K, Nookala, Ravi K, Zhang, Nianshu, Dokudovskaya, Svetlana, Levine, Tim P and Blundell, Tom L (2015). Lst4, the yeast Fnip1/2 orthologue, is a DENN-family protein. Open Biology, 5 (12) 150174. doi: 10.1098/rsob.150174
Sigurdardottir, A G, Winter, A, Sobkowicz, A, Fragai, M, Chirgadze, D, Ascher, D B, Blundell, T L and Gherardi, E (2015). Exploring the chemical space of the lysine-binding pocket of the first kringle domain of hepatocyte growth factor/scatter factor (HGF/SF) yields a new class of inhibitors of HGF/SF-MET binding. Chemical Science, 6 (11), 6147-6157. doi: 10.1039/c5sc02155c
Jubb, Harry, Blundell, Tom L. and Ascher, David B. (2015). Flexibility and small pockets at protein-protein interfaces: new insights into druggability. Progress in Biophysics and Molecular Biology, 119 (1), 2-9. doi: 10.1016/j.pbiomolbio.2015.01.009
Blaszczyk, Michal, Harmer, Nicholas J., Chirgadze, Dimitri Y., Ascher, David B. and Blundell, Tom L. (2015). Achieving high signal-to-noise in cell regulatory systems: spatial organization of multiprotein transmembrane assemblies of FGFR and MET receptors. Progress in Biophysics and Molecular Biology, 118 (3), 103-11. doi: 10.1016/j.pbiomolbio.2015.04.007
Jafri, Mariam, Wake, Naomi C, Ascher, David B, Pires, Douglas E V, Gentle, Dean, Morris, Mark R, Rattenberry, Eleanor, Simpson, Michael A, Trembath, Richard C, Weber, Astrid, Woodward, Emma R, Donaldson, Alan, Blundell, Tom L, Latif, Farida and Maher, Eamonn R (2015). Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma. Cancer Discovery, 5 (7), 723-729. doi: 10.1158/2159-8290.CD-14-1096
Pires, Douglas E V, Blundell, Tom L and Ascher, David B (2015). pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58 (9), 4066-72. doi: 10.1021/acs.jmedchem.5b00104
Usher, Jeannette L, Ascher, David B, Pires, Douglas E V, Milan, Anna M, Blundell, Tom L and Ranganath, Lakshminarayan R (2015). Analysis of HGD gene mutations in patients with Alkaptonuria from the United Kingdom: identification of novel mutations. JIMD Reports, 24, 3-11. doi: 10.1007/8904_2014_380
Chan, Linda J., Bulitta, Jürgen B., Ascher, David B., Haynes, John Michael, McLeod, Victoria M., Porter, Christopher J. H., Williams, Charlotte C. and Kaminskas, Lisa M. (2015). PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats but increases plasma clearance after subcutaneous administration. Molecular Pharmaceutics, 12 (3), 794-809. doi: 10.1021/mp5006189
Kaminskas, Lisa M., McLeod, Victoria M., Ascher, David B., Ryan, Gemma M., Jones, Seth, Haynes, John M., Trevaskis, Natalie L., Chan, Linda J., Sloan, Erica K., Finnin, Benjamin A., Williamson, Mark, Velkov, Tony, Williams, Elizabeth D., Kelly, Brian D., Owen, David J. and Porter, Christopher J. H. (2015). Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumor-burdened lymph nodes after intravenous and subcutaneous administration in rats. Molecular Pharmaceutics, 12 (2), 432-443. doi: 10.1021/mp500531e
Hermans, Stefan J, Ascher, David B, Hancock, Nancy C, Holien, Jessica K, Michell, Belinda J, Chai, Siew Yeen, Morton, Craig J and Parker, Michael W (2015). Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides. Protein Science, 24 (2), 190-199. doi: 10.1002/pro.2604
Pires, Douglas E V, Blundell, Tom L and Ascher, David B (2015). Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Research, 43 (D1), D387-D391. doi: 10.1093/nar/gku966
Caliph, Suzanne M., Shackleford, David M., Ascher, David B. and Kaminskas, Lisa M. (2014). Practical lessons in murine thoracic lymph duct cannulations: Observations in female and male mice across four different strains that impact on cannulatability. Journal of Pharmaceutical Sciences, 104 (3), 1207-1209. doi: 10.1002/jps.24312
Watt, Andrew D, Crespi, Gabriela A N, Down, Russell A, Ascher, David B, Gunn, Adam, Perez, Keyla A, McLean, Catriona A, Villemagne, Victor L, Parker, Michael W, Barnham, Kevin J and Miles, Luke A (2014). Anti-Aβ antibody target engagement: a response to Siemers et al.. Acta Neuropathologica, 128 (4), 611-4. doi: 10.1007/s00401-014-1333-8
Pires, Douglas E. V., Ascher, David B. and Blundell, Tom L. (2014). DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42 (Web Server issue), W314-W319. doi: 10.1093/nar/gku411
Watt, Andrew D, Crespi, Gabriela A N, Down, Russell A, Ascher, David B, Gunn, Adam, Perez, Keyla A, McLean, Catriona A, Villemagne, Victor L, Parker, Michael W, Barnham, Kevin J and Miles, Luke A (2014). Do current therapeutic anti-Aβ antibodies for Alzheimer's disease engage the target?. Acta Neuropathologica, 127 (6), 803-810. doi: 10.1007/s00401-014-1290-2
Ascher, David B., Wielens, Jerome, Nero, Tracy L., Doughty, Larissa, Morton, Craig J. and Parker, Michael W. (2014). Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA. Scientific Reports, 4 (1) 4765. doi: 10.1038/srep04765
Crespi, Gabriela A N, Ascher, David B, Parker, Michael W and Miles, Luke A (2014). Crystallization and preliminary X-ray diffraction analysis of the Fab portion of the Alzheimer's disease immunotherapy candidate bapineuzumab complexed with amyloid-β. Acta Crystallographica. Section F, Structural Biology Communications, 70 (Pt 3), 374-7. doi: 10.1107/S2053230X14001642
Feil, Susanne C, Ascher, David B, Kuiper, Michael J, Tweten, Rodney K and Parker, Michael W (2014). Structural studies of Streptococcus pyogenes streptolysin O provide insights into the early steps of membrane penetration. Journal of Molecular Biology, 426 (4), 785-792. doi: 10.1016/j.jmb.2013.11.020
Pires, Douglas E V, Ascher, David B and Blundell, Tom L (2014). mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics, 30 (3), 335-42. doi: 10.1093/bioinformatics/btt691
Kaminskas, Lisa M., Ascher, David B., McLeod, Victoria M., Herold, Marco J., Le, Caroline P., Sloan, Erica K. and Porter, Christopher J. H. (2013). PEGylation of interferon α2 improves lymphatic exposure after subcutaneous and intravenous administration and improves antitumour efficacy against lymphatic breast cancer metastases. Journal of Controlled Release, 168 (2), 200-208. doi: 10.1016/j.jconrel.2013.03.006
Polekhina, Galina, Ascher, David Benjamin, Kok, Shie Foong, Beckham, Simone, Wilce, Matthew and Waltham, Mark (2013). Structure of the N-terminal domain of human thioredoxin-interacting protein. Acta Crystallographica. Section D: Structural Biology, 69 (Pt 3), 333-344. doi: 10.1107/S0907444912047099
Parker, Lorien J, Ascher, David B, Gao, Chen, Miles, Luke A, Harris, Hugh H and Parker, Michael W (2012). Structural approaches to probing metal interaction with proteins. Journal of Inorganic Biochemistry, 115, 138-47. doi: 10.1016/j.jinorgbio.2012.02.015
Ascher, David B, Polekhina, Galina and Parker, Michael W (2012). Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2. Acta Crystallographica. Section F: Structural Biology Communications, 68 (Pt 4), 468-71. doi: 10.1107/S1744309112006963
Parker, Lorien J., Italiano, Louis C., Morton, Craig J., Hancock, Nancy C., Ascher, David B., Aitken, Jade B., Harris, Hugh H., Campomanes, Pablo, Rothlisberger, Ursula, De Luca, Anastasia, Lo Bello, Mario, Ang, Wee Han, Dyson, Paul J. and Parker, Michael W. (2011). Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation. Chemistry-A European Journal, 17 (28), 7806-7816. doi: 10.1002/chem.201100586
Polekhina, Galina, Ascher, David Benjamin, Kok, Shie Foong and Waltham, Mark (2011). Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein. Acta Crystallographica. Section F: Structural Biology Communications, 67 (Pt 5), 613-617. doi: 10.1107/S1744309111010347
Ascher, David B, Cromer, Brett A, Morton, Craig J, Volitakis, Irene, Cherny, Robert A, Albiston, Anthony L, Chai, Siew Yeen and Parker, Michael W (2011). Regulation of insulin-regulated membrane aminopeptidase activity by its C-terminal domain. Biochemistry, 50 (13), 2611-22. doi: 10.1021/bi101893w
Chai, Siew Yeen, Yeatman, Holly R., Parker, Michael W., Ascher, David B., Thompson, Philip E., Mulvey, Hayley T. and Albiston, Anthony L. (2008). Development of cognitive enhancers based on inhibition of insulin-regulated aminopeptidase. BMC Neuroscience, 9 Suppl 2 (Supplement 2) S14. doi: 10.1186/1471-2202-9-S2-S14
Albiston, Anthony L, Morton, Craig J, Ng, Hooi Ling, Pham, Vi, Yeatman, Holly R, Ye, Siying, Fernando, Ruani N, De Bundel, Dimitri, Ascher, David B, Mendelsohn, Frederick A O, Parker, Michael W and Chai, Siew Yeen (2008). Identification and characterization of a new cognitive enhancer based on inhibition of insulin-regulated aminopeptidase. FASEB Journal, 22 (12), 4209-17. doi: 10.1096/fj.08-112227
Ye, Siying, Chai, Siew Yeen, Lew, Rebecca A, Ascher, David B, Morton, Craig J, Parker, Michael W and Albiston, Anthony L (2008). Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase. Biochemistry and Cell Biology, 86 (3), 251-61. doi: 10.1139/o08-037
Conference Paper
de Sá, Alex G. C. and Ascher, David B. (2024). Towards evolutionary-based automated machine learning for small molecule pharmacokinetic prediction. GECCO '24 Companion, Melbourne, VIC, Australia, 14-18 July 2024. New York, NY, United States: ACM. doi: 10.1145/3638530.3664166