iiinova — where your digital self keeps evolving

7/ Recently we and @lucksmith.bsky.social described giant microRNA hairpins. Their repeated emergence across invertebrates also pushed us to improve long-hairpin handling in MirMachine 2: doi.org/10.1016/j.ce... ...and we made it: MirMachine 2 finds those long hairpins!!!

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6/ One consequence: many apparent microRNA “losses” are not be biology at all — they reflect annotation biases and overly conservative thresholds.

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5/ We then specifically focussed on >700 Lepidoptera genomes that we struggled with. By introducing the novel features of seed-search and paralogue expectation we achieved substantial improvements and recover full conserved microRNA complements in such underrepresented lineages.

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The Fromm Lab @frommlab.bsky.social · 23/04/2026

4/ 🦋We applied an early version MirMachine 2 across >3000 animal genomes hosted in @ensembl.org and we annotated >450,000 conserved microRNAs showing that microRNA scores - for deuterostomes - very well correlated with N50 and BUSCO values. ‼️Not so much for protostomes - we saw many absences!

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#Biocuration2026 day 4 ended with this beautiful group picture being released and an amazing conference dinner

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The Fromm Lab @frommlab.bsky.social · 22/04/2026

Given the experience with MirGeneDB we can fully support this list of traits required to become a biocurator by Frederique Lisacek‘s presentation remembering Amos Bairoch at #Biocuration2026.

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The Fromm Lab @frommlab.bsky.social · 22/04/2026

Third day of #Biocuration2026 kicks off after two days with very inspiring workshops. 140 delegates from >20 countries come together for the 19th annual Biocuration conference (fist time in Africa)!

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The Fromm Lab @frommlab.bsky.social · 21/04/2026

Second day of #Biocuration2026 started with workshop on data commons, meshes and Hubs with Gen3

The Fromm Lab @frommlab.bsky.social · 08/04/2026

@pedromartinezserra.bsky.social presenting cool work on tunicate phylogeny and more during the annual seminar in Natural Sciences at the Museum here in Tromsø

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The Fromm Lab @frommlab.bsky.social · 14/12/2025

Awesome two day course on microRNA annotation and differential expression analysis done in Oslo last week (#OsloBioinformaticsweek2025) done. Participants (and tutors!) were so committed that this turned out a microRNA hackathon and we are drafting a paper!!!! Thanks for the invite!!

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The Fromm Lab @frommlab.bsky.social · 08/12/2025

Two days of teaching everything about microRNAs in Oslo (#OsloBioinformaticsWeek) ahead.

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The Fromm Lab @frommlab.bsky.social · 21/10/2025

Super happy to host @lovedalen.bsky.social today talking about deep time genomics!

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The Fromm Lab @frommlab.bsky.social · 17/09/2025

Having a great time at the Friedrich Löffler Institute in Greifswald. Impressive place (850 people work here). Many exciting questions about (viral) microRNAs after my presentation. Thank you for the invitation to Balal Sadeghi!!!

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The Fromm Lab @frommlab.bsky.social · 29/08/2025

#argonautes2025 end (for me) with an amazing dinner. Thank you for organizing @svobodalab.bsky.social

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The Fromm Lab @frommlab.bsky.social · 29/08/2025

#argonautes2025 day3 with amazing talks spanning widely over generegulation to evolution and parasitic interaction (via AGO). A presentation by the Argonautes Syndrom family alliance reminded how relevant research on Argonautes and related mechanisms is

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The Fromm Lab @frommlab.bsky.social · 27/08/2025

#argonautes 2025 starts with a card game including 4 Jokers (Nobellaureates)

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8/9 🔁 These results echo my 2013 study in MBE @official-smbe.bsky.social Parasitic flatworms also show massive microRNA losses (up to ~50%) → Suggesting a general principle in lophotrochozoan parasite evolution: 💥 Regulatory gene loss accompanies simplification. pubmed.ncbi.nlm.nih.gov/24025793/

6/9 Regression in proteins and microRNAs is mirrored by morphology! Losses: ▪️Digestive tract ▪️Ciliated head structures ▪️Protonephridia And just like gene losses, morphological losses track with microRNA and BUSCO reductions. Parasitism = evolutionary pruning. 🪓 However, new features evolve, too!

5/9 🔍 The 280 lost core genes in parasitic lineages are not random. They're enriched for regulatory functions: ⚙️ Transcription factors ⚙️ RNA Pol II complex components ⚙️ Translation regulators → Suggests regulatory collapse as parasitism advances.

4/9 📉 Curiously we find that microRNA loss correlates with other forms of genome simplification. 🔸 Each lost microRNA family ≈ 400 protein-coding genes lost 🔸 Strong correlation with metazoan core gene loss (BUSCO) 🔸 Not explained by genome assembly quality or size Simplification at every level.

3/9 🧬 Figure 1: microRNA losses across Syndermata 🔹Free-living rotifers (Monogononta, Bdelloidea): mild miRNA loss 🔹Seisonidea: ~67% loss 🔹Acanthocephala: a shocking 85% microRNA family loss This is the most extreme microRNA reduction ever reported in bilaterians. 📉🧫