My name is Michael Roach; I’m a Research Associate (bioinformatician) at the new Flinders Accelerator for Microbiome Exploration at Flinders University (oPiNiOnS aRe My oWn).
I previously worked at the Australian Wine Research Institute where I assembled the Chardonnay genome and developed a new gold standard for grapevine clonal marker discovery. I wrote the pipeline Purge Haplotigs for heterozygous diploid assembly cleanup, and contributed to many other various yeast genomics projects etc.
My Honours and PhD was in drug discovery, not genomics, and involved identifying and testing candidate structural inhibitors of malarial enzymes which required a lot of protein homology modelling and in silico screening.
The transition from protein to DNA bioinformatics was equal parts challenging and rewarding, and I’m excited about the new move from genomics to metagenomics. My Research interests include all things bioinformatics, data viz and graphic design, software dev, and more recently webapp dev.
Outside of work I’m an enthusiast brewer and BCJP certified beer judge (bjcp.org), but wine is good too. I play video games, am a hockey goalie, and generally have too many interests and too little time.
This site is intended to be a collection of stuff I’ve done, stuff I’m doing, and stuff I think is neat. If you’re interested in what I’m doing then great! If you googled your way here to debug some perl code your supervisor gave you then, good luck!
The rest of this page is for my own reference more than anything else
Australian Bioinformatics And Computational Biology Society (ABACBS)
Australian Society for Biochemistry and Molecular Biology (SA state representative 2023; ASBMB)
Australian Society for Microbiology (ASM)
Adelaide Protein Group (committee member and webmaster; APG)
Michael J Roach, N Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Papudeshi, Scott A Handley, C Titus Brown, Nathan S Watson-Haigh, Robert A Edwards (2022), Ten simple rules and a template for creating workflows-as-applications, Plos Comp. Biol. | DOI
Ryan D Hesse, Michael Roach, Emma N Kerr, Bhavya Papudeshi, Laís FO Lima, Asha Z Goodman, Lisa Hoopes, Mark Scott, Lauren Meyer, Charlie Huveneers, Elizabeth A Dinsdale (2022), Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome, Viruses | DOI
Alyce M Martin, Michael Roach, Lauren A Jones, Daniel Thorpe, Rosemary A Coleman, Caitlin Allman, Robert Edwards, Damien J Keating (2022), Single-cell gene expression links SARS-CoV-2 infection and gut serotonin, Gut | DOI
Michael Roach, Sarah Beecroft, Kathie A Mihindukulasuriya, Leran Wang, Lais Farias Oliveira Lima, Elizabeth A Dinsdale, Robert A Edwards, Scott A Handley (2022), Hecatomb: An End-to-End Research Platform for Viral Metagenomics, BioRxiv | DOI
Sarah K Giles, Uwe H Stroeher, Bhavya Papudeshi, Robert A Edwards, Jessica AP Carlson-Jones, Michael Roach, Melissa H Brown (2022), The StkSR Two-Component System Influences Colistin Resistance in Acinetobacter baumannii, Microorganisms | DOI
MJ Roach, K McNair, SK Giles, LK Inglis, E Pargin, S Roux, P Decewicz, RA Edwards (2021), Philympics 2021: Prophage Predictions Perplex Programs, F1000Research | DOI
M Roach, A Cantu, MK Vieri, M Cotten, P Kellam, M Phan, L Hoek, M Mandro, F Tepage, G Mambandu, G Musinya, A Laudisoit, R Colebunders, R Edwards, JL Mokili (2021), No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study, Pathogens | DOI
C Bartel, M Roach, C Onetto, C Curtin, C Varela, C Borneman (2021), Adaptive evolution of sulfite tolerance in Brettanomyces bruxellensis, FEMS Yeast Research | DOI
CA Onetto, SA Schmidt, MJ Roach, AR Borneman (2020), Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice, FEMS Yeast Research | DOI
MJ Roach, AR Borneman, SA Schmidt (2020), Origin of Chardonnay clones with historical significance in Australia and California, Australian Journal of Grape and Wine Research | DOI
MJ Roach, AR Borneman, (2020), New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species, BMC genomics 21 (1), 1-14 | DOI
AG Cordente, AR Borneman, C Bartel, D Capone, M Solomon, M Roach, C Curtin, Inactivating mutations in Irc7p are common in wine yeasts, attenuating carbon-sulfur β-lyase activity and volatile sulfur compound production, (2019), Appl. Environ. Microbiol. 85 (6), e02684-18 | DOI
C Varela, C Bartel, M Roach, A Borneman, C Curtin, (2019), Brettanomyces bruxellensis SSU1 haplotypes confer different levels of sulfite tolerance when expressed in a Saccharomyces cerevisiae SSU1 null mutant, Appl. Environ. Microbiol. 85 (4), e02429-18 | DOI | JOURNAL COVER
MJ Roach, DL Johnson, J Bohlmann, HJJ van Vuuren, SJM Jones, IS Pretorius, SA Schmidt, AR Borneman, (2018), Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, PLoS genetics 14 (11), e1007807 | DOI
MJ Roach, SA Schmidt, AR Borneman, (2018), Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies, BMC bioinformatics 19 (1), 460 | DOI
What can we learn from the human panvirome?, Australian Genomic Technologies Association (AGTA) Annual Conference, Sunshine coast, 2022 | Slides
Recommendations for workflows as applications, Bioinformatics Workflows community meeting, online, 2022 | Slides
Hecatomb: An End-to-End Bioinformatics Research Platform for Viral Metagenomics, P’Con - PaCER conference, Perth, 2022 | Program, Slides
Hecatomb: An End-to-End Bioinformatics Research Platform for Viral Metagenomics, Australian Society for Microbiology (ASM) Conference, Sydney, 2022 | Program, Slides
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, 17th Australian Wine Industry Technical Conference (AWITC), Adelaide, 2019 | Webcast
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, AGTA, Adelaide, 2018 | Program
Session Co-Chair, Emerging Technology, AGTA, Sunshine coast, 2022 | Program
Session Co-Chair, Terrestrial Microbiology, ASM, Sydney, 2022 | Program
Session Chair, Session 4: Biomedical, Australian Bioinformatics and Computational Biology Society (ABACBS) conference, Online, 2021 | Program
Viral Metagenomics with Hecatomb, AGTA, Sunshine coast, 2022 | Program
FAME Metagenomics Workshop, South Australia Genomics Centre workshop series event, Adelaide, 2022 | Twitter | URL
Introduction to Snakemake (parts 1 and 2), FAME Bioinformatics meeting, Adelaide, 2022 | URL
Data visualisation for Atavide: importing your data into R, FAME Bioinformatics meeting, Adelaide, 2021 | URL
Viral Metagenomics with Hecatomb, ABACBS conference, Online, 2021 | Program
Creating command line tools is easy with Snakemake or Nextflow, ABACBS conference, Melbourne, 2022 | Poster
Hecatomb: Accurately classify your viral metagenome sequences, ASM conference, Online, 2021 | Poster
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, Plant and Animal Genome XXVIII Conference, San Diego, USA, 2020 | Poster
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, 17th AWITC, Adelaide, 2019 | Poster
Curating the FALCON-Unzip Chardonnay de novo genome assembly, ASMI BioInfoSummer, Adelaide, 2016 | Poster
The “Torsten Seemann” Outstanding Bioinformatics software Developer Award, 2022, ABACBS
Coding competition winner, 2016, ASMI BioInfoSummer
AWRI Recognition Award, 2016, AWRI (internal award)
Roach, M., Borneman, A., Schmidt, S., Krstic, M., (2021) Applying genomics to grapevine clones, Wine & Viticulture Journal 36(2): 39-41 | PDF
MJ Roach, DL Johnson, J Bohlmann, HJJ van Vuuren, SJM Jones, IS Pretorius, SA Schmidt, AR Borneman, (2019), Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay, Proceedings of the Seventeenth Australian Wine Industry Technical Conference | PDF
M Roach, S Schmidt, A Borneman, (2019), The origin of Chardonnay clones with historical significance in Australia and California, Webcast presented by Anthony Borneman | URL
