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Marcus Stoiber

@stoibs11.bsky.social
182 followers 160 following 11 posts

Associate director of modified base machine learning @nanopore | dad of 3 | amateur farmer | Nationals fan | views are my own

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Reposted by Marcus Stoiber
David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · 22/05/2025
#NanoporeConf Lakmal Jayasinghe ONT is the *only* sequencing technology that detects RNA modifications directly. They're now up to 8 modifications that can be detected simultaneously. [This is something I think ONT should be shouting from the rooftops every day] RNA barcoding is in beta testing.
image showing RNA modification landscape of human ribosomal RNAs for 18S and 28S rRNA; patterns of different modifications are shown throughout the entirety of the sequence. A validation of synthetic constructs demonstrates RNA modification detection accuracies of 95-99%.
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Reposted by Marcus Stoiber
Oxford Nanopore @nanoporetech.com · 21/05/2025
Oxford Nanopore sequencing will be ubiquitous for multiomics….and the next step is proteomics. First panel-based proteomics assays, before driving towards full protein sensing in the future. #nanoporeconf
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
The future of @nanoporetech.com sequencing is here now! #NanoporeConf #Proteomics
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Amazing time to be working with @nanoporetech.com sequencing! The pace of innovation in this network of researchers is astonishing! #NanoporeConf
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Dorado 1.0 🚀release with new RNA modified base models for 2’Ome as well as improvement of all DNA and RNA modified base models including massive improvement in 6mA for open chromatin prediction! Also a lot more non-mods related features😆! #NanoporeConf github.com/nanoporetech...
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Dorado 1.0 🚀release with new RNA modified base models for 2’Ome as well as improvement of all DNA and RNA modified base models including massive improvement in 6mA for open chromatin prediction! Also a lot more non-mods related features😆! #NanoporeConf github.com/nanoporetech...
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Initial release of Pomfret for methylation assisted phase block joining for more contiguous phased assemblies without any additional library prep from @nanoporetech.com data. Such amazing work from Xiaowen Feng! #NanoporeConf github.com/nanoporetech...
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Exciting modkit release with open chromatin prediction support and more! Amazing work from Art Rand! @nanoporetech.com #NanoporeConf github.com/nanoporetech...
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Methylation assists tandem repeat expansion estimation from @nanoporetech.com sequencing using strcount. #NanoporeConf
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Reposted by Marcus Stoiber
Matt Loose @minomatt.bsky.social · 21/05/2025
Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com
academic.oup.com
ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis
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Marcus Stoiber @stoibs11.bsky.social · 21/05/2025
Excited for another London Calling! Incredible updates coming over the next two days! #NanoporeConf @nanoporetech.com
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Reposted by Marcus Stoiber
Randall Munroe @xkcd.com · 26/02/2025
RNA xkcd.com/3056
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Reposted by Marcus Stoiber
Martin Smith @martinalexsmith.bsky.social · 23/02/2025
An overview of nanopore sequencing for pangenomes and hemi-hydroxymethylation in medaka fish brains by @ewanbirney.bsky.social Presenting results showing biased 5hmC/5mC hemimethylation at splice sites, and increased skewed hemimethylation across repetitive sequences.
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Reposted by Marcus Stoiber
Hena Jose @henajose.bsky.social · 27/11/2024
Since Oxford Nanopore sequencing does not require any chemical (bisulfite) conversion to detect methylation. It would mean long-range epigenetic modifications, structural variants (SVs),single nucleotide polymorphisms (SNPs), and repeats can all be identified and phased in a single dataset
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Reposted by Marcus Stoiber
Oxford Nanopore @nanoporetech.com · 27/11/2024
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them. Read more: nanoporetech.com/news/oxford-...
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Reposted by Marcus Stoiber
Gang Fang @gangfang.bsky.social · 21/11/2024
Thank u for this question. Worth another thread as it reflects common confusion that more data & better AI/ML is the solution (newer official @nanopore models & new customer methods are being developed/released). For abundant mods like 5mCpG in human, this strategy works. *BUT* for low abundance 1/5
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Reposted by Marcus Stoiber
Adam Phillippy @aphillippy.bsky.social · 21/11/2024
Long-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data! 📄 genome.cshlp.org/content/34/1... 📖 genome.cshlp.org/content/34/1...
genome.cshlp.org
Table of Contents — November 2024, 34 (11)
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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