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frommlab.bsky.social
The Fromm Lab
@frommlab.bsky.social
1.3K followers 2.5K following 200 posts
lab at @UiTNorgesarktis studying microRNAs, paleotranscriptomics, biosystematics with a fable for flatworms.

MirGeneDB, MirMachine, MirMiner (soon!)
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frommlab.bsky.social
The Fromm Lab @frommlab.bsky.social · Dec 8
Two days of teaching everything about microRNAs in Oslo (#OsloBioinformaticsWeek) ahead.
frommlab.bsky.social
For the model species for sure!!
January 16, 2026 at 4:23 PM
Reposted by The Fromm Lab
jekely.biologists.social.ap.brid.gy
If you are interested in electron microscopy, registration is still open for the

"Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples"

at Stazione Zoologica in Naples.

WIth great teachers from Naples […]

[Original post on biologists.social]
Poster of the EM course in Naples with marine samples. The Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples arises from a very strong and active collaboration between the Stazione Zoologica Anton Dohrn and the EMBL in Heidelberg. The aim of the course is to provide a theoretical and practical training on electron microscopy starting from the basics to the preparation of samples with high pressure freezing and image acquisition using TEM and SEM.
January 13, 2026 at 7:08 AM
Reposted by The Fromm Lab
adameur.bsky.social
Wow! 167.2 Gb HiFi yield from a PacBio SMRT cell🎉 Are we getting close the record? This run was for the “Genome of Sweden” project, where we're building a national reference dataset from 10 year old biobanked DNA samples🧬🧪
January 12, 2026 at 9:54 AM
Reposted by The Fromm Lab
spaam-community.bsky.social
Dreaming of a de novo assembly of your pesky short ancient sequences? 🧬 A new tool, CarpeDeam, may just help your dreams come true. 🧬🖥️
link.springer.com/article/10.1...
#MetagenomicsMonday #ancientDNA #aDNA #paleogenomics #bioinformatics
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets - Genome Biology
De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools…
link.springer.com
January 12, 2026 at 8:01 AM
frommlab.bsky.social
cool Oleks! Have you tested what those ultra conserved loci are?
January 9, 2026 at 8:28 AM
frommlab.bsky.social
!!!
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · Nov 11
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
December 22, 2025 at 10:49 AM
Reposted by The Fromm Lab
ulrichtechnau.bsky.social
I can only second this. BUT, what people often are not aware of: Frontiers in Zoology does NOT belong to the rest of the Frontiers in journals. It is the official journal of the German Zoological Society, a BMC journal and founded BEFORE the other Front in. We suffer a lot from this hijacking.
December 21, 2025 at 1:50 PM
frommlab.bsky.social
Latest RNAcentral update out!
academic.oup.com/nar/advance-...
Validate User
academic.oup.com
December 21, 2025 at 1:05 PM
Reposted by The Fromm Lab
stamatak.bsky.social
Permanent Research Group Leader Position, Crete, Greece: Interested to assume long-term responsibilities for the Biodiversity Computing Group www.biocomp.gr I have set up in Crete? Apply now via apella.minedu.gov.gr/en/node/5998 (PDF also in English) - for questions email to [email protected]
December 15, 2025 at 7:23 AM
frommlab.bsky.social
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!!
December 14, 2025 at 11:46 AM
frommlab.bsky.social
Check RNA, DNA and disease (separately)
December 12, 2025 at 4:28 PM
frommlab.bsky.social
so what is it??
December 12, 2025 at 3:45 PM
Reposted by The Fromm Lab
jopabinia.bsky.social
Peracarid crustaceans contain multitudes - at least 26000 species. In the open ocean, some have transparent eyes up to half the body size (they see more contrast but less precision). In caves, they lose eyes and enhance their smell processing.

Papers next #Crustmas 🧪🦑
(A) Ventral-lateral view of a gravid female Paraphronima gracilis. Eggs are visible as a white mass in the brood pouch. The white arrow indicates the photosensory portion of an ommatidial group. The red/orange coloration is from screening pigments located within and around the retinula cells contributing to the fused rhabdom of each ommatidia. The scale bar represents 2 mm. Photos by Karen Osborn (B) Lateral view of P. gracilis. Facets and light guides are nearly transparent in live specimens; here, the path of an ommatidium is highlighted in blue. The scale bar represents 1 mm. Photos by Karen Osborn Overview of [two of] the three blind peracarids studied. A, B: Spelaeogriphus lepidops, (Spelaeogriphacea) exhibits an eyeless rudimentary eyestalk (A), a slender antenna 1 and a prominent antenna 2 (dark hue of specimen in A due to artificial staining). B: Courtesy by G. Giribet. C: Mictocaris halope (Mictocarididae) exhibits an eyeless rudimentary eyestalk, and a prominent antenna 1 and 2. D, E: Tethysbaena argentarii (Thermosbaenacea). Confocal micrographs of cuticular autofluorescence. In contrast to the other species, the antenna 1 is more prominent than the slender antenna 2. An eyestalk is absent. Scale bars: 0.5 mm.
December 10, 2024 at 4:37 PM
frommlab.bsky.social
Two days of teaching everything about microRNAs in Oslo (#OsloBioinformaticsWeek) ahead.
December 8, 2025 at 10:04 AM
Reposted by The Fromm Lab
palaeogenomics.bsky.social
WOW❗🤯

The amount and quality of the abstracts we've received have completely blown us away! More than 300 abstracts from researchers at all levels and from 33 countries.

We will communicate the selected talks and open registration soon 👉 icp2026.palaeogenomics.org

#ICP2026 will be UNMISSABLE 😍💪
December 2, 2025 at 9:52 AM
frommlab.bsky.social
@projectpsyche.bsky.social is there a way to get samples of Morpho from you?
November 26, 2025 at 10:31 AM
frommlab.bsky.social
The course is aimed at all levels of researchers with projects and interest in microRNAs and free of charge.
Signup here:

www.mn.uio.no/bils/english...

#check also all the other great courses!! 2/2
Oslo Bioinformatics Workshop Week 2025 - Bioinformatics in Life Science – BiLS
December 8th-12th 2025 will see the fourth edition of the Oslo Bioinformatics Workshop Week at the University of Oslo, Norway. This event is organised by the Trainee Committee of BiLS (Bioinformatics ...
www.mn.uio.no
November 25, 2025 at 10:37 AM
frommlab.bsky.social
#FREECOURSE-announcement
Want to learn about microRNA annotation and differential expression analyses? Within the Oslo Bioinformatics week 2025, we will be teaching a two-day course on the 9th and 10th of December at the University of Oslo. 1/2
November 25, 2025 at 10:37 AM
frommlab.bsky.social
Ever seen priapulids?
November 24, 2025 at 6:33 PM
Reposted by The Fromm Lab
petermulhair.bsky.social
Latest work out today in @currentbiology.bsky.social

We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬

To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).

🔗 tinyurl.com/2vyuevpy
Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair et al. uncover a functional bicoid in non-cyclorrhaphan flies, pushing the gene's origin back by ∼20 million years. Reassessing the Diptera phylogeny using the largest dataset to date permits ...
www.cell.com
October 17, 2025 at 3:14 PM
Reposted by The Fromm Lab
alexdemendoza.bsky.social
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
frommlab.bsky.social
wow! What is this? Salp?
November 15, 2025 at 10:19 PM
Reposted by The Fromm Lab
sciences.skyfleet.blue
Forty-thousand-year-old mammoth mummies yield oldest RNA yet found
Forty-thousand-year-old mammoth mummies yield oldest RNA yet found
Ancient RNA promises to shed light on how genes functioned in extinct animals
www.science.org
November 14, 2025 at 5:55 PM
Reposted by The Fromm Lab
scilifelab.se
The world’s oldest #RNA extracted from #WoollyMammoth: “gives us a completely different picture” ↓ 🧪⚒️

Woolly mammoth preserved in the Siberian permafrost for nearly 40,000 years sequenced. 🖥️ 🧬
www.youtube.com/watch?v=tHQv...

Weekend reading:
www.scilifelab.se/news/worlds-...
The world’s oldest #RNA extracted from #WoollyMammoth: “gives us a completely different picture”
YouTube video by SciLifeLab
www.youtube.com
November 14, 2025 at 4:11 PM