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Helena Cooper

@helena-bethany.bsky.social
56 followers 118 following 0 posts

Bioinformatician @ MDU PHL, Melbourne

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Reposted by Helena Cooper
Paul Gardner @ppgardne.bsky.social · 23/08/2026
New paper day! What started as an overly ambitious summer student project is now published. We asked which genomic signals best distinguish protein-coding, short ncRNA and long ncRNA genes from the genomic background. doi.org/10.1093/g3jo...
doi.org
Genomic indicators of gene function: a systematic assessment of the human genome
Abstract. Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological adv
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Reposted by Helena Cooper
Ben Vezina @bananabenana.bsky.social · 17/12/2025
(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪
nature.com
The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study - Nature Communications
Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...
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Reposted by Helena Cooper
Ben Vezina @bananabenana.bsky.social · 13/12/2025
Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊
journals.plos.org
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
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Reposted by Helena Cooper
Hugh Cottingham @hughcottingham.bsky.social · 30/07/2025
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...
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Reposted by Helena Cooper
Ben Vezina @bananabenana.bsky.social · 29/07/2025
New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites. #IDSky #MicroSky 🧪 www.biorxiv.org/content/10.1...
Graph showing IS loads by Klebsiella sub-lineage
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