Tommi Mäklin
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themaklin.bsky.social
Tommi Mäklin
@themaklin.bsky.social
1.4K followers 410 following 110 posts
I do statistics, bacterial (meta)genomics and bioinformatics software development.

Researcher @ University of Oslo
Posts Replies Media Videos
Reposted by Tommi Mäklin
hansonmark.bsky.social
The solutions of the past 3 decades have failed to change the incentives of #PublishOrPerish. As a result, researcher funding, time, control, and trust has been lost.

The ONE CONSTANT in the wake of the serial crisis, #PlanS and #OpenAccess reform has been publish profit margins.

2/n
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.
November 11, 2025 at 11:52 AM
Reposted by Tommi Mäklin
hansonmark.bsky.social
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.
November 11, 2025 at 11:52 AM
Reposted by Tommi Mäklin
impvienna.bsky.social
🌍Open call: Junior Group Leader positions!

Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.

Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
November 10, 2025 at 1:26 PM
Reposted by Tommi Mäklin
evolvedbiofilm.bsky.social
Strain displacement in microbiomes via ecological competition

Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster

www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 2:19 PM
Reposted by Tommi Mäklin
samuelhorsfield.bsky.social
If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...
Pangenome graphs as a new paradigm in comparative genomics -
Pangenome graphs as a new paradigm in comparative genomics -
www.ebi.ac.uk
November 6, 2025 at 11:40 AM
Reposted by Tommi Mäklin
sangerinstitute.bsky.social
E. coli can spread as quickly as swine flu, new research reveals. 🦠

For the first time, scientists can predict the rate at which gut bacteria pass between people — a major step towards tackling antibiotic-resistant infections.

Read here ⤵️
sanger.ac.uk/news_item/ad...
Advanced disease modelling shows some gut bacteria can spread as rapidly as viruses
Experts can now predict the transmission rate of a bacterial E. coli infection in the same way as they can for viral pandemics, which can help battling treatment-resistant infections in the future.
sanger.ac.uk
November 4, 2025 at 11:55 AM
Reposted by Tommi Mäklin
kristelzilmer.bsky.social
This. Also: We’ve no idea how much groundbreaking research we might actually be missing out on when core research doesn’t have the opportunity to gradually unfold, take place without being tailored to surface claims about high impact and fantastic deliverables.
statsepi.bsky.social Darren Dahly @statsepi.bsky.social · Sep 12
We need more "unfunded" research, not less. Or rather, we need more "core" funding and much less project based funding. Then universities can *invest* in core research infrastructure (including people), reduce precarity, and focus on growing and retaining talent.
November 5, 2025 at 6:45 AM
Reposted by Tommi Mäklin
magicmicrobe.bsky.social
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications
Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...
www.nature.com
November 5, 2025 at 7:32 AM
Reposted by Tommi Mäklin
sarahmackattack.bsky.social
The amount of AI generated art in slides at this conference, primarily used by older scientists, is killing me. Scientists please. Don’t use these ai platforms to make your figures or slides. They look bad and I have yet to see them meaningfully improve the message of talks.
October 31, 2025 at 3:09 AM
Reposted by Tommi Mäklin
rachelmwheatley.bsky.social
🔊 Applications for the tenure-track illuminate global challenge fellowships at Queen’s are now open!
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!

www.qub.ac.uk/Research/fel...
Our Illuminate Global Challenges Fellowships | Research | Queen's University Belfast
www.qub.ac.uk
October 30, 2025 at 12:19 PM
Reposted by Tommi Mäklin
zachhensel.bsky.social
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?

It said a restriction map was "extremely unlikely to have arisen by random evolution.”

I took its claims seriously.

The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.

arxiv.org/abs/2510.23833
22-Oct 2022 headline from The Economist A new paper claims SARS-CoV-2 bears signs of genetic engineering But it has yet to be peer reviewed. And others strongly disagree
October 29, 2025 at 7:32 AM
Reposted by Tommi Mäklin
pedrobeltrao.bsky.social
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3
OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3
github.com
October 28, 2025 at 9:30 AM
Reposted by Tommi Mäklin
mohsenzakeri.bsky.social
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
Reposted by Tommi Mäklin
binomicalabs.org
This particular figure was quite striking - physical microscopy of the E. coli genome. Somehow we run these tangles mess through pores (often not breaking them over significant distances) and render them into reliable representation of whole genomic compartments.

🧫🦠
October 15, 2025 at 2:25 PM
themaklin.bsky.social
taas ajankohtanen vasemmisto.fi/liity-jasene...
October 14, 2025 at 9:48 AM
Reposted by Tommi Mäklin
thelancet.com
Melioidosis—it's a fatal but preventable infection. Why is it not classed as a Neglected Tropical Disease (NTD)? Sophie Cousins reports in The Lancet.

Read in the latest issue 👉 tinyurl.com/zz65vbup
Cover of The Lancet, Oct 11 issue. The quote, "Melioidosis is a disease so neglected it is not on WHO's list of Neglected Tropical Diseases."
October 10, 2025 at 7:30 AM
Reposted by Tommi Mäklin
robert.bio
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Reposted by Tommi Mäklin
begia.bsky.social
Our new systematic review is now out! Briefly, temporal multi-omic data and analyses are crucially needed to improve our understanding of microbiomes. Also, often the omics layers are not analyzed in an integrative way, even while such methods exist.
academic.oup.com/bib/article/...
Multi-omics time-series analysis in microbiome research: a systematic review
Abstract. Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and cha
academic.oup.com
October 9, 2025 at 9:42 AM
Reposted by Tommi Mäklin
josiebryant.bsky.social
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.

🚨 Submit your abstracts now! 🚨

Please RT

coursesandconferences.wellcomeconnectingscience.org/event/air-20...
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211
Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.
coursesandconferences.wellcomeconnectingscience.org
October 8, 2025 at 2:48 PM
Reposted by Tommi Mäklin
ellinoralseth.bsky.social
Obsessed with this Journal of Immaterial Science article 🔥
October 8, 2025 at 8:56 AM
Reposted by Tommi Mäklin
brockhurstlab.bsky.social
New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
Reposted by Tommi Mäklin
teppo-h.bsky.social
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.

duunitori.fi/tyopaikat/ty...
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
duunitori.fi
September 30, 2025 at 8:37 AM
Reposted by Tommi Mäklin
samuelhorsfield.bsky.social
A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...
GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
github.com
September 24, 2025 at 1:27 PM
Reposted by Tommi Mäklin
brockhurstlab.bsky.social
Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...
September 26, 2025 at 8:26 AM
Reposted by Tommi Mäklin
tiedetati.bsky.social
"Suomen Akatemia varoittaa yli­opistoja perus­suomalaisista
Yliopistoihin lähetetyssä ”varautumisviestissä” annetaan ohjeistusta häirinnän, maalittamisen ja mustamaalauksen kohteeksi joutuneille tutkijoille."
www.is.fi/kotimaa/art-...
Suomen Akatemia varoittaa yliopistoja perussuomalaisista
Yliopistoihin lähetetyssä ”varautumisviestissä” annetaan ohjeistusta häirinnän, maalittamisen ja mustamaalauksen kohteeksi joutuneille tutkijoille.
www.is.fi
September 23, 2025 at 9:03 AM