Xabier Vázquez-Campos

ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷
🤗 Hugging Face Space: huggingface.co/spaces/pimen...
⚙️ Google Colab: colab.research.google.com/drive/1l_h7c...
🧵👇

Remember! Applied and Environmental Microbiology solicits minireviews. And they are free to publish!

There's 2 more I want to write. Time in my career to summarize and rant.

When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.

Faster science, penalties in evaluation, and concerns on quality and impact: Researchers' use and perceptions of preprints www.biorxiv.org/content/10.6... #jcampubs

The MIBiG 5.0 Annotathon is coming soon, and registration is now open!

🧬 Does your research involve biosynthetic gene clusters? Do you love natural product biosynthesis? Do you have an interest in rare & exotic enzymes? We can use your help & expertise.

Register here 👉 forms.gle/C1cWcLHtrjT2...

🧵 FlashPPI (new model) is live in SeqHub. Proteome-wide PPI prediction in minutes, 2,400x faster than the next best sequence-based method, 4x better predictive performance. How it works: 👇

Check out some of the great work by @cynthiasilveira.bsky.social e.g. looking at Hi-C in marine environments pubmed.ncbi.nlm.nih.gov/39657233/

As Martin mentioned, SPAdes with the --custom-hmm option. THe method was implemented as part of BiosyntheticSPAdes (paper linked). In theory works with any of the assembly methods in SPAdes

genome.cshlp.org/content/29/8...

Carbon monoxide dehydrogenase-encoding microorganisms in volcanic astrobiological analogues: an enzyme system to investigate the evolution of life Abstract. Volcanic environments provide analogues for studying the origin of life and its persistence under extreme conditions on early Earth and other pla

And 2nd, a minireview. Collaboration between @belindaferrari.bsky.social and @matehg.bsky.social labs:
"Carbon monoxide dehydrogenase-encoding microorganisms in volcanic astrobiological analogues: an enzyme system to investigate the evolution of life"

academic.oup.com/femsec/advan...

Two of the coauthors, Bec and Tim, had the luck of flying into Bunger Hills right the next day of the paper release!!

1st paper of the year: "Persistent petroleum pollution shifts soil microbial responses in Bunger Hills, East Antarctica"

Led by Kellynn Tan from @belindaferrari.bsky.social lab in collaboration with the Australian Antarctic Division

www.nature.com/articles/s43...

Quantitative metagenomics using a portable protocol journals.asm.org/doi/full/10.... #jcampubs

😳👀

Have a novel protist's genome or transcriptome and want to predict it's mitochondrial proteome? Look no further than CoMR, this handy bioinformatic workflow to help you: www.biorxiv.org/content/10.6... #phylogenetics

The Origins of Agar First introduced into laboratories in 1881, agar remains indispensable as a culture medium.

The Origins of Agar
open.substack.com/pub/cell/p/a...

#microsky

Giant multicellular magnetotactic prokaryotes in marine sediments academic.oup.com/ismej/advanc... #jcampubs

In this review we map the journey to animal multicellularity and define three extinct ancestral stages:
🔹 LUAA: Last Unicellular Animal Ancestor.
🔹 FACA: First Animal Common Ancestor.
🔹 LACA: Last Animal Common Ancestor.
Check it out: bit.ly/4azuLVY @embojournal.org

The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature – a critical evaluation of Akiyoshi, 2025 Summary:Akiyoshi, 2025 presented a hypothesis with implications for the early evolution of eukaryotes and eukaryotic cell division machinery. In this Correspondence, the authors conclude that this hyp...

Recently, a Hypothesis was posed in @jcellsci.bsky.social in which the root of eukaryotes was placed between kinetoplastids and all other eukaryotes. From this, it was implied that LECA did not have a kinetochore. We argue this is highly unlikely. A 🧵(1/12)

Read our reply here: tinyurl.com/n87myhpr

The second isolate from the bacterial phylum Caldisericota (formerly candidate phylum OP5, first detected in Yellowstone's Obsidian Pool) has been found in a thermal spring on Sakhalin Island: Caldisericum insulae sp. nov. 🦠🌋
#microbiology #taxonomy #bacteria #MicroSky
doi.org/10.1007/s007...

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

A small polymerase ribozyme that can synthesize itself and its complementary strand
#evolution #RNA
www.science.org/doi/10.1126/...

Exploring the microbial "dark matter" just got easier🦠🔬
Most #protists are uncultivated and tiny making electron microscopy a nightmare. A new, low-cost protocol allows single-cell tracking and field prep.
#microbiology #eukaryotes #MicroSky #ProtistsOnSky
doi.org/10.1111/jeu....

The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology

The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.

Our new paper in @natcomms.nature.com is now online-early!

We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.

🔗 doi.org/10.1038/s414...

R Graphics Cookbook, 2nd edition by Winston Chang
#RStats
https://bigbookofr.com/chapters/data%20visualization.html#r-graphics-cookbook-2nd-edition

Reassessing viral origins and evolutionary placement in the tree of life - Antonie van Leeuwenhoek The quest to fit all cellular beings in one picture frame as the universal Tree of Life (ToL) has always been a daunting task for evolutionary biologists. Over the decades, ToL has emerged from a dich...

Reassessing viral origins and evolutionary placement in the tree of life
#OriginofLife #TreeofLife #Evolution #virus #phage #MicroSky
doi.org/10.1007/s104...

Request for public discussion and ballot to add rules on paratypes to the SeqCode and amend recommendations on name formation The “Code of Nomenclature of Prokaryotes Described from Sequence Data” (the SeqCode) was conceived and introduced to address the need to validly publish na

SeqCode recognizes strains and their value for experimental work. However, type material in #SeqCode consists of genome sequence that unambiguously defines a species. The request suggests using strains as paratypes of genomic type material.
doi.org/10.1093/isme...

Thank you @mollyherring.bsky.social for the stunning showcase 😍

Like what you see? Come ExM with us! Let’s flood the internet with microbial marvels 🦠

#ProtistsOnSky #MicroEvoSky 🧪🔬🌍

@dudinlab.bsky.social @centriolelab.bsky.social @moorefound.bsky.social @embl.org @erc.europa.eu @embo.org

We finally have the pre-industrial baseline for #Hydrogen in the atmopshere!
Because H2 is so small, it usually leaks right through ice. But new polar core measurements have successfully reconstructed a millennium of H2 data for the first time.
#ClimateChange #EnergyTransition

FRED: a universal tool to generate FAIR metadata for omics experiments www.biorxiv.org/content/10.6... #jcampubs

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