Mattias de Hollander

When plotting, LLMs see what they expect to see - Posit Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.

Introducing bluffbench, a new tool to evaluate how well LLMs actually see data plots.

When we trick LLMs with secret #RStats transformations, they can miss the visual contradiction.

bluffbench helps us measure this "blind spot" in AI coding agents. Learn more: posit.co/blog/introdu...

Opening of #PMS2025 by @vcarryon.bsky.social @josraaijmakers.bsky.social @microsos.bsky.social

Check out the quality of segmentation by #OneRosette, even when leaves are dying to DC3000. Come and see nuts and bolts of this deep learning prompt-engineering by PhD candidate Felicià Maviane @lipme-toulouse.bsky.social on the 24/10/2025 13h #Margulis

YouTube video by VPRO Tegenlicht Wat DNA uit slootwater ons vertelt over jouw onbekende voorouders | VPRO Tegenlicht

Hoe is al het complexe leven op aarde eigenlijk ontstaan?

Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH Nature Communications - Rhizosphere microbiomes are shaped by root exudation of diverse organic compounds. Here, the rhizoSMASH algorithm is introduced, which maps microbial genes involved in their...

Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4

rdcu.be/eH8tr

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics www.biorxiv.org/content/10.1... #jcampubs

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes academic.oup.com/bioinformati... #jcampubs

ggplot2 4.0.0 A new major version of ggplot2 has been released on CRAN. Find out what is new here.

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

New sylph pre-built databases + taxonomy available for:

- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )

Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)

New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!

#MicroSky 🖥️🧬🦠

Terrestrial Ecology The department of Terrestrial Ecology studies species, communities & ecosystems in a rapidly changing world.

I am so excited to share that I will be joining the Terrestrial Ecology Department at the Netherlands Institute of Ecology (NIOO-KNAW) as a tenure track senior scientist this Fall! Impossible without the unwavering support and mentorship of Jim Bever, Peggy Schutlz, Evan Gora, and Maggie Wagner.

BugBuster: a novel automatic and reproducible [Nextflow] workflow for metagenomic data analysis academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/gene2dis/Bug...

🔬 24-month postdoc position Opening: "Rice Disease Metagenomics in East Africa"
Join UMR PHIM (Montpellier, France) @phimresearch.bsky.social
🧬 Oxford Nanopore long-read metagenomics
🌍 3-month field mission in Kenya
⚙️ Recent PhDs
Apply: sebastien.cunnac@ird.fr
#PostdocJobs #Metagenomics #Rice

🇳🇱 Galaxy is now available in the SURF Research Cloud.
Dutch researchers can launch Galaxy workspaces with configurable resources, data federation, and support for Pulsar, all in a secure, reproducible environment.
galaxyproject.org/news/2025-07...

OReO: optimizing read order for practical compression AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

Paper alert!
We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ...
TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor!
academic.oup.com/bioinformati...
A thread!

Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequenc....

Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes. #ProtistsOnSky #pacbio
onlinelibrary.wiley.com/doi/10.1111/...

Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypothes...

Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.

www.biorxiv.org/content/10.1...

The team's first preprint is out!

Led by ‪
‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?

A 🧵.

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

📢Our synthesis of current knowledge on the fascinating cell of #arbuscular #mycorrhizal fungi is out @currentbiology.bsky.social, part of the special #fungi issue. With @rachaelcargill.bsky.social @tobykiers.bsky.social @thomasshimizu.bsky.social

Open access link: www.cell.com/current-biol...

1/4

Have you ever heard of the term “dark taxa”?

Published in @currentbiology.bsky.social‬, a new study reveals an astonishing 83% of ectomycorrhizal #fungi are classified as dark taxa, existing only through their DNA sequences and eluding formal classification. 🧵

I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

I am happy to see that this beautiful review about detecting rare organisms in metagenomics is now available: kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F... congrats Marios Valmas and Sotirios Vasileiadis for leading and doing the heavy lifting!

Excited to share the #Snakemake monitoring tool I've been working on:
snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics #workflow #opensource 1/3

Promising toolkit for binning and visualizing assembly graphs. The assembly graph is an underutilized source of binning information IMO
gbintk.readthedocs.io/en/latest/

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes Background Soil ecosystems have long been recognized as hotspots of microbial diversity, but most estimates of their complexity remain speculative, relying on limited data and extrapolation from shall...

New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found…
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

These boxes are not moving. A mind-bending optical illusion by Japanese artist Jagarikin.

What percent reads mapped to MAGs is "good" for soil or sediment samples?

is lower than water samples OK/expected due to more complex communities?

🙏
🖥️🧬 microbiome, metagenomics