Andrew Lonie

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Alexander E Ostrovsky, Alexandru Mahmoud, Andrew J Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anton Nekrutenko, Anup Kumar, Arthur C Eschenlauer, Assunta D DeSanto, Aysam Guerler, Beatriz Serrano-Solano, Berenice Batut, Bjoern A Gruening, Bradley W Langhorst, Bridget Carr, Bryan A Raubenolt, Cameron J Hyde, Catherine J Bromhead, Christopher B Barnett, et al.

Journal article  |  2022  |  NUCLEIC ACIDS RESEARCH

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize t..

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Wolfgang Maier, Simon Bray, Marius van den Beek, Dave Bouvier, Nathan Coraor, Milad Miladi, Babita Singh, Jordi Rambla De Argila, Dannon Baker, Nathan Roach, Simon Gladman, Frederik Coppens, Darren P Martin, Andrew Lonie, Bjoern Gruening, Sergei L Kosakovsky Pond, Anton Nekrutenko

Journal article  |  2021  |  NATURE BIOTECHNOLOGY

Application of a bioinformatics training delivery method for reaching dispersed and distant trainees

Christina R Hall, Philippa C Griffin, Andrew J Lonie, Jeffrey H Christiansen

Journal article  |  2021  |  PLOS COMPUTATIONAL BIOLOGY

Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not uni..

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Bjoern Gruening, Nicholas Keener, Delphine Lariviere, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver

Journal article  |  2020  |  PLOS PATHOGENS

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research sho..

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.

Farah Zaib Khan, Stian Soiland-Reyes, Richard O Sinnott, Andrew Lonie, Carole Goble, Michael R Crusoe

Journal article  |  2019  |  GigaScience

BACKGROUND: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many field..

Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening

Fleur Hammet, Khalid Mahmood, Thomas R Green, Nguyen-Dumont Tu, Melissa C Southey, Daniel D Buchanan, Andrew Lonie, Katherine L Nathanson, Fergus J Couch, Bernard J Pope, Daniel J Park

Journal article  |  2019  |  BIOTECHNIQUES

We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-..

CloudLaunch: Discover and deploy cloud applications

Enis Afgan, Andrew Lonie, James Taylor, Nuwan Goonasekera

Journal article  |  2019  |  FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE

Cloud computing is a common platform for delivering software to end users. However, the process of making complex-to-deploy applic..

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Maria Victoria Schneider, Philippa C Griffin, Sonika Tyagi, Madison Flannery, Saravanan Dayalan, Simon Gladman, Nathan Watson-Haigh, Philipp E Bayer, Michael Charleston, Ira Cooke, Rob Cook, Richard J Edwards, David Edwards, Dominique Gorse, Malcolm McConville, David Powell, Marc R Wilkins, Andrew Lonie

Journal article  |  2019  |  BRIEFINGS IN BIOINFORMATICS

EMBL Australia Bioinformatics Resource (EMBL-ABR) is a developing national research infrastructure, providing bioinformatics resou..

Is RNASEL:p.Glu265*a modifier of early-onset breast cancer risk for carriers of high-risk mutations?

Tu Nguyen-Dumont, Zhi L Teo, Fleur Hammet, Alexis Roberge, Maryam Mahmoodi, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Andrew Lonie, Miroslav K Kapuscinski, Khalid Mahmood, David E Goldgar, Graham G Giles, Ingrid Winship, John L Hopper, Melissa C Southey

Journal article  |  2018  |  BMC CANCER

BACKGROUND: Breast cancer risk for BRCA1 and BRCA2 pathogenic mutation carriers is modified by risk factors that cluster in famili..

Investigating reproducibility and tracking provenance - A genomic workflow case study

Sehrish Kanwal, Farah Zaib Khan, Andrew Lonie, Richard O Sinnott

Journal article  |  2017  |  BMC BIOINFORMATICS

BACKGROUND: Computational bioinformatics workflows are extensively used to analyse genomics data, with different approaches availa..