2020

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. Authorea. July 13, 2020. DOI: 10.22541/au.159467800.05802032
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 blog | press

2019

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
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 | blog
O'Brien et al. Unlocking HDR-mediated Nucleotide Editing by identifying high-efficiency target sites using machine learning Scientific Reports 2019 | blog | press

2018

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

2015

O'Brien et al. VariantSpark: population scale clustering of genotype information BMC Genomics 2015

2014

O'Brien et al. GT-Scan: Identifying unique genomic targets Bioinformatics 2014