Andrea Telatin

Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, 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

RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

This is a beautiful case of how real science happens & serious scientists work. Kudos to both set of authors: “This has been a humbling experience, but one that speaks to the self-correcting nature of the scientific endeavor.” 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

ℹ Takeaway 1: sequencing depth and community complexity matter a lot. At low or uneven coverage, all tools struggle — even the ones we like and use ourselves.

ℹ Takeaway 2: speed vs sensitivity vs precision is a trade-off.
Some tools are fast and conservative.
Others are more sensitive but heavier.

💡 We also tried to control things that usually get mixed together:
– same unified ARG database for all the tools
– simulated data where we know what’s present
– coverage and complexity varied one at a time

That lets us see patterns, not absolutes.

Our goal wasn’t to crown a winner.

🔍 We asked a narrower question: how do different approaches behave when coverage and complexity change?

Each tool makes different trade-offs by design.

Metagenomic 💊 AMR detection is a genuinely hard problem.
Low coverage, uneven abundance, similar genes, and complex communities all make “ground truth” slippery.

So if results differ across tools, that’s 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.

UK ‘could lose generation of scientists’ with cuts to projects and research facilities UK’s research funding body says best scientists are taking posts overseas due to lack of job stability at home

More on the UKRI/STFC funding squeeze.
Significant quote: “It 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...

Hugging Face – The AI community building the future. We’re on a journey to advance and democratize artificial intelligence through open source and open science.

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. 👋

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 assembly–alignment graphs and contrastive learning - Nature Biotechnology PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

💻 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.

👉 Register here: hubs.la/Q041v13y0

YouTube video by Andrea Telatin SeqFu dev - preview of `seqfu less` [coming with 1.24.0]

Meet seqfu less

youtu.be/e77tXBM6fRs?...

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: £45,450 to £56,750, Contract length: 2 years, Apply by 15 February 2026."

🆕 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.

💷 £45,450 to £56,750
🗓️ Apply by 15 February 2026
➡️ buff.ly/UpcuEPa

1/🧵
Major milestone unlocked for mycology! 🍄

We just published a massive genomic resource in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐃𝐚𝐭𝐚, releasing 2,695 complete circular mitochondrial species assembled from public data

This single dataset nearly 𝐓𝐑𝐈𝐏𝐋𝐄𝐒 📈the known mitochondrial diversity of the Kingdom Fungi
rdcu.be/eYZ2h

Some important new government policy that Native Americans might be interested in:

A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models - Nature Microbiology HRGM2 is 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 micro...

#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 🦠💻

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 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.

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/...

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!

A social card with a digital illustration of of AI and the text "Research Scientist (Bioinformatics) to develop and apply computational methods for metaproteomics and multi-omics to advance precision microbiome research. Salary : £37,500 to £41,500, Contract length: 2 years, Apply by 9 November 2025"

⏰ Closing soon! We’re looking for a Research Scientist (Bioinformatics) to join the Laboratory of Dr Kai Cheng in our Food, Microbiome and Health programme

💷 £37,500 to £41,500
🗓️ Apply by 9 November 2025
➡️ buff.ly/DqLnYek

Escherichia coli with a 57-codon genetic code The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here, we designed and generated Escherichia coli with a 4-megabase synthetic genome in whic...

Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...

I saw you running in Newmarket road :)