iiinova — where your digital self keeps evolving

Reposted by Skyler Friedline

Yasset Perez-Riverol @ypriverol.bsky.social · 22/10/2025

Some researchers get their boost from papers or grants. My adrenaline rush comes from pull requests and seeing others use our tools. I got two happiness shots today: - www.nature.com/articles/s41... using #quantms - github.com/PRIDE-Archiv... new PR to #pridepy tool ☕🔥

nature.com

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology

An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.

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Reposted by Skyler Friedline

Ryan Ziels @ryanziels.bsky.social · 21/10/2025

I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠

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Skyler Friedline @skybio.bsky.social · 22/10/2025

Very excited to finally have my thesis work out in the world! Hopefully it just got easier to understand the role of specific microbes in complex communities, even when they are really rare!

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Reposted by Skyler Friedline

Philipp Bayer @philippbayer.bsky.social · 29/08/2025

This is great - we a huge need in the #eDNA community to have data-informed standards for eDNA identity cutoffs, not just the bog-standard 97% besjournals.onlinelibrary.wiley.com/doi/full/10.... For Chordata there is no cutoff that leads to 0% error when assigning species!! (Table S4)

besjournals.onlinelibrary.wiley.com

Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding

The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds ...

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Skyler Friedline @skybio.bsky.social · 02/04/2025

It is disturbing that ChatGPT asks if I like the algorithm's "personality". This word implies personhood, which it does not have. If we start to view this product as a person we need to ask if it is given the full protections a person is due. Is it paid fairly by its employer and free to leave?

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Skyler Friedline @skybio.bsky.social · 13/03/2025

Looking for some help! I'm embarking on a survey of soil carbon in an intensively harvested forest to estimate possible carbon credit opportunities. I could use some help setting expectations for a project like this. If you have experience or know someone who does, reach out!

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Reposted by Skyler Friedline

koonkie.bsky.social @koonkie.bsky.social · 22/02/2025

Making Better Wine with Bioinformatics! Join our CEO Aria Hahn and host Craig Macmillan on the Sustainable Winegrowing Podcast with the Vineyard Team as they dive into the hidden world of microbes in winemaking Listen here: www.vineyardteam.org/podcast?id=1... #winemaker #vineyards #microbiology

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