Applications are open now!
You'll also benefit from the supervisory expertise of the brilliant Dipali Singh and @telatin.bsky.social
#mmbdtp #norwich #uea
Scientists found an unexpected viral hitchhiker lurking inside a common gut bacterium β and it was twice as prevalent in people with colorectal cancer.
BRIG v1.0.0 Released β BLAST Ring Image Generator
This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1.
BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings β [β¦]
Interested in developing your skills in microbial 'omics? Consider joining us in Brest π«π·, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/
Bonus: beautiful seascape and friendly spirit!
A Systematic Benchmark of Antibiotic Resistance Gene Detection Tools for Shotgun Metagenomic Datasets https://www.biorxiv.org/content/10.64898/2026.02.04.703716v1
This is a beautiful case of how real science happens & serious scientists work. Kudos to both set of authors: βThis has been a humbling experience, but one that speaks to the self-correcting nature of the scientific endeavor.β www.science.org/doi/10.1126/...
The preprint is available at www.biorxiv.org/content/10.6...
The bioinformatic method (Nextflow) is available at: workflowhub.eu/workflows/2080
βΉ Takeaway 1: sequencing depth and community complexity matter a lot. At low or uneven coverage, all tools struggle β even the ones we like and use ourselves.
βΉ Takeaway 2: speed vs sensitivity vs precision is a trade-off.
Some tools are fast and conservative.
Others are more sensitive but heavier.
π‘ We also tried to control things that usually get mixed together:
β same unified ARG database for all the tools
β simulated data where we know whatβs present
β coverage and complexity varied one at a time
That lets us see patterns, not absolutes.
Our goal wasnβt to crown a winner.
π We asked a narrower question: how do different approaches behave when coverage and complexity change?
Each tool makes different trade-offs by design.
Metagenomic π AMR detection is a genuinely hard problem.
Low coverage, uneven abundance, similar genes, and complex communities all make βground truthβ slippery.
So if results differ across tools, thatβs often expected, not a failure.
How well do current tools detect antimicrobial resistance genes in metagenomes?
@sumeet-tiwari.bsky.social & team benchmarked 5 widely used methods across different sequencing coverages and community complexities, highlighting trade-offs between accuracy and computational cost.
More on the UKRI/STFC funding squeeze.
Significant quote: βIt is clear that no UK university will want to open lecturer positions in curiosity-driven research if such lecturers would not be able to attract much national funding." KCL's Lucien Heurtier.
www.theguardian.com/science/2026...
Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria
Washington Post lays off hundreds of staff after BEZOS wastes 75 MILLIONS on Melanias flop documentary
Information, gone. π
Important study highlighting the need for rigorous quality control during sequencing and the value of analyzing sequence read depth variation in assemblies.
Accurate plasmid reconstruction from metagenomics data using assemblyβalignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
π» Join us next week for Nextflow Training Week (Feb 9-13) - free online training for those new to @nextflow.io or looking to reinforce the basics.
π Register here: hubs.la/Q041v13y0
A social card with the text, "Senior Research Scientist Microbiome Assay and Metaproteomics, to support with day-to-day running of the Figeys lab, including line management, overseeing budgets and scientific direction. Salary: Β£45,450 to Β£56,750, Contract length: 2 years, Apply by 15 February 2026."
π Vacancy! We are looking for a Senior Research Scientist to support with day-to-day running of @dfigeys.bsky.social lab, including line management of staff, overseeing budgets, and leading the scientific direction.
π· Β£45,450 to Β£56,750
ποΈ Apply by 15 February 2026
β‘οΈ buff.ly/UpcuEPa
1/π§΅
Major milestone unlocked for mycology! π
We just published a massive genomic resource in πππ’ππ§ππ’ππ’π ππππ, releasing 2,695 complete circular mitochondrial species assembled from public data
This single dataset nearly πππππππ πthe known mitochondrial diversity of the Kingdom Fungi
rdcu.be/eYZ2h
Some important new government policy that Native Americans might be interested in:
#Resource
HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.
#MicroSky #MicrobiomeSky π¦ π»
www.nature.com/articles/s41...
@mrclmb.bsky.social alumnus Tony Hyman to become new @embl.org director general
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
The study gave dna and cells to the labs. In both cases library preparation was done and in the latter also extraction. So the variability has multiple sources :)
Ring validations are important. @quadraminstitute.bsky.social took part of this study from dna to analysis
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 publishersβ 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 authorsβ 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 βossificationβ, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchersβ 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 β such as reading, reflecting and engaging with othersβ contributions β 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.
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 𧡠1/n
Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
Quick thread on the BBC and the political and societal significance of recent developments:
One of the main reasons the UK has historically been so much less polarised than the US, is that Britain has a shared source of information, consumed and trusted by most people regardless of their politics.
So it turns out... the US air travel system was incredibly, deeply dependent on federal funding to just run day-to-day all this time, to the benefit of private airline shareholders, when everyone thinks that state-run trains are leeching off the government. Weird!
![SeqFu dev - preview of `seqfu less` [coming with 1.24.0]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:swfodoslus64euo7jd6isxu3/bafkreihnhk4n4rdz6los4xk7hqnzgb6yeuyvyaydfqoaqe7tvxjaynpoxa)