Bauer, D.C., Wilson, L.O.W., Twine, N.A. (2022). Artificial Intelligence in Medicine: Applications, Limitations and Future Directions. In: Raz, M., Nguyen, T.C., Loh, E. (eds) Artificial Intelligence in Medicine. Springer, Singapore.Artificial Intelligence in Medicine. Springer, 2022 | DOI: doi.org/10.1007/978-981-19-1223-8_5
Priya Ramarao-Milne*, Yatish Jain*, Letitia M.F. Sng, Brendan Hosking, Carol Lee, Arash Bayat, Michael Kuiper, Laurence O.W. Wilson, Natalie A. Twine, Denis C. Bauer, Data-driven platform for identifying variants of interest in COVID-19 virus, Computational and Structural Biotechnology Journal, 2022 | DOI: doi.org/10.1016/j.csbj.2022.06.005
Scott, S., Hallwirth, C. V., Hartkopf, F., Grigson, S., Jain, Y., Alexander, I. E., Bauer, D. C., and Wilson, L. O. W., Isling: A Tool for Detecting Integration of Wild-Type Viruses and Clinical Vectors, Journal of Molecular Biology, 2022 | DOI: doi.org/10.1016/j.jmb.2021.167408


Fatwa Adikusuma, Caleb Lushington, Jayshen Arudkumar, Gelshan I Godahewa, Yu C J Chey, Luke Gierus, Sandra Piltz, Ashleigh Geiger, Yatish Jain, Daniel Reti, Laurence O W Wilson, Denis C Bauer, Paul Q Thomas, Optimized nickase- and nuclease-based prime editing in human and mouse cells, Nucleic Acids Research, Sept 2021 | DOI: doi.org/10.1093/nar/gkab792
Arash Bayat, Brendan Hosking, Yatish Jain, Cameron Hosking, Milindi Kodikara, Daniel Reti, Natalie A. Twine, Denis C. Bauer, Fast and accurate exhaustive higher-order epistasis search with BitEpi, Scientific Reports, August 2021 | DOI: doi.org/10.1038/s41598-021-94959-y
Aidan P. Tay, Brendan Hosking, Cameron Hosking, Denis C. Bauer, Laurence O.W. Wilson, INSIDER: alignment-free detection of foreign DNA sequences, Computational and Structural Biotechnology Journal, 2021 | DOI: doi.org/10.1016/j.csbj.2021.06.045
Lorenzi, L., Chiu, HS., Avila Cobos, F. et al., The RNA Atlas expands the catalog of human non-coding RNAs, Nature Biotechnology, 2021 | DOI: doi.org/10.1038/s41587-021-00936-1
Daniel Reti, Aidan O'Brien, Pascal Wetzel, Aidan Tay, Denis C. Bauer, Laurence O.W. Wilson, GOANA: A Universal High-Throughput Web Service for Assessing and Comparing the Outcome and Efficiency of Genome Editing Experiments, The CRISPR Journal, April 2021 | DOI: doi.org/10.1089/crispr.2020.0068
Marti Cabanes-Creus, Renina Gale Navarro, Sophia H.Y. Liao, Grober Baltazar, Matthieu Drouyer, Erhua Zhu, Suzanne Scott, Clement Luong, Laurence O.W. Wilson, Ian E. Alexander, Leszek Lisowski, Single amino acid insertion allows functional transduction of murine hepatocytes with human liver tropic AAV capsids, Molecular Therapy. Methods & Clinical Development, 2021 | DOI: doi.org/10.1016/j.omtm.2021.04.0108


Natalie A Twine, Lyndal Henden, Piotr Szul et al., Identity by descent analysis identifies founder events and links SOD1 familial and sporadic ALS cases, npj Genomic Medicine 5, Article number:32 (2020) | DOI: doi.org/10.1038/s41525-020-00139-8
Denis C. Bauer, Laurence O.W. Wilson, A Navigation System for Base Editing: Are We There Yet?, The CRISPR Journal, Volume 3, No 4, August 2020 | DOI: doi.org/10.1089/crispr.2020.29097.dcb
Arash Bayat, Piotr Szul, Aidan R O’Brien, Robert Dunne, Brendan Hosking, Yatish Jain, Cameron Hosking, Oscar J Luo, Natalie Twine, Denis C Bauer, VariantSpark: Cloud-based machine learning for association study of complex phenotype and large-scale genomic data, GigaScience, Volume 9, Issue 8, August 2020 | DOI: doi.org/10.1093/gigascience/giaa077
Denis Bauer, Alejandro Metke-Jimenez, Sebastian Maurer-Stroh, et al. Interoperable medical data: the missing link for understanding COVID-19. Transbound Emerg Dis. 23 October 2020. | DOI: 10.1111/tbed.13892
Bauer, DC, Tay, AP, Wilson, LOW, et al. Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak. Transbound Emerg Dis. 2020; 67: 1453– 1462. | DOI: 10.1111/tbed.13588 | blog
O'Brien et al. Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing Briefings in Bioinformatics 2020. | DOI: doi.org/10.1093/bib/bbz145 blog | press
Marti Cabanes-Creus, Claus V. Hallwirth, Adrian Westhaus, Boaz Ng, Sophia H.Y. Liao, Renina Gale Navarro, Grober Baltazar, Matthieu Drouyer, Suzanne Scott, Grant J. Logan, Giorgia Santilli, Antonette Bennett, Samantha L. Ginn, Geoff McCaughan, Adrian J. Thrasher, Mavis Agbandje-McKenna, Ian E. Alexander, Leszek Lisowski, Single amino acid insertion allows functional transduction of murine hepatocytes with human liver tropic AAV capsids, Science Translational Medicine 9 Spetember 2020 | DOI: doi.org/10.1126/scitranslmed.aba3312
Patricia P. Wright, Suzanne Scott, Sowmya Shetty, Bill Kahler, Laurence J. Walsh, Resistance to compressive force in continuous chelation, Australian Endodontic Journal 9 Spetember 2020 | DOI: doi.org/110.1111/aej.12440
Marti Cabanes-Creus, Adrian Westhaus, Renina Gale Navarro, Grober Baltazar, Erhua Zhu, Anais K. Amaya, Sophia H.Y. Liao, Suzanne Scott, Erwan Sallard, Kimberley L. Dilworth, Arkadiusz Rybicki, Matthieu Drouyer, Claus V. Hallwirth, Antonette Bennett, Giorgia Santilli, Adrian J. Thrasher, Mavis Agbandje-McKenna, Ian E. Alexander, Leszek Lisowski, Attenuation of Heparan Sulfate Proteoglycan Binding Enhances In Vivo Transduction of Human Primary Hepatocytes with AAV2, Molecular Therapy. Methods & Clinical Development 12 June 2020 | DOI: doi.org/10.1016/j.omtm.2020.05.004
Patricia P. Wright, Suzanne Scott, Bill Kahler, Laurence J. Walsh, Organic Tissue Dissolution in Clodronate and Etidronate Mixtures with Sodium Hypochlorite, Journal of Endodontics 2 February 2020 | DOI: doi.org/10.1016/j.joen.2019.10.020


Bayat et al. BitEpi: A Fast and Accurate Exhaustive Higher-Order Epistasis Search BioRxiv 2019
Sathyanarayanan et al. A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping Briefings in Bioinformatics 2019 | DOI: doi.org/10.1093/bib/bbz121
Bayat et al. VariantSpark, A Random Forest Machine Learning Implementation for Ultra High Dimensional Data BioRxiv 2019
Twine et al. TRIBES: A user-friendly pipeline for relatedness detection and disease gene discovery, BioArchive, 2019
Henden and Twine et al. IBD analysis of Australian amyotrophic lateral sclerosis SOD1-mutation carriers identifies five founder events and links sporadic cases to existing ALS families, BioArchive, 2019
Wilson et al. VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9. BMC Biotechnology 2019 | DOI: 10.1186/s12896-019-0535-5 | blog
O'Brien et al. Unlocking HDR-mediated Nucleotide Editing by identifying high-efficiency target sites using machine learning Scientific Reports 2019 | DOI: 10.1038/s41598-019-39142-0 | blog | press


Wilson et al. High Activity Target-Site Identification Using Phenotypic Independent CRISPR-Cas9 Core Functionality The CRISPR Journal 2018
Wilson et al. The current state and future of CRISPR-Cas9 gRNA design tools Frontiers in Pharmacology 2018


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