Xabier Vázquez-Campos
@xabivc.bsky.social
Nearly-dry wet-lab microbiologist 😅
Biologist, (env.) microbiologist, bioinformatician. First gen.
Biologist, (env.) microbiologist, bioinformatician. First gen.
Reposted by Xabier Vázquez-Campos
R Graphics Cookbook, 2nd edition by Winston Chang
#RStats
https://bigbookofr.com/chapters/data%20visualization.html#r-graphics-cookbook-2nd-edition
#RStats
https://bigbookofr.com/chapters/data%20visualization.html#r-graphics-cookbook-2nd-edition
February 9, 2026 at 8:36 PM
R Graphics Cookbook, 2nd edition by Winston Chang
#RStats
https://bigbookofr.com/chapters/data%20visualization.html#r-graphics-cookbook-2nd-edition
#RStats
https://bigbookofr.com/chapters/data%20visualization.html#r-graphics-cookbook-2nd-edition
Reposted by Xabier Vázquez-Campos
Reassessing viral origins and evolutionary placement in the tree of life
#OriginofLife #TreeofLife #Evolution #virus #phage #MicroSky
doi.org/10.1007/s104...
#OriginofLife #TreeofLife #Evolution #virus #phage #MicroSky
doi.org/10.1007/s104...
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...
doi.org
February 8, 2026 at 1:11 PM
Reassessing viral origins and evolutionary placement in the tree of life
#OriginofLife #TreeofLife #Evolution #virus #phage #MicroSky
doi.org/10.1007/s104...
#OriginofLife #TreeofLife #Evolution #virus #phage #MicroSky
doi.org/10.1007/s104...
Reposted by Xabier Vázquez-Campos
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...
doi.org/10.1093/isme...
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
doi.org
February 8, 2026 at 5:34 PM
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...
doi.org/10.1093/isme...
Reposted by Xabier Vázquez-Campos
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
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
February 4, 2026 at 8:43 PM
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
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
Reposted by Xabier Vázquez-Campos
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
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
February 5, 2026 at 12:37 PM
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
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
Reposted by Xabier Vázquez-Campos
FRED: a universal tool to generate FAIR metadata for omics experiments www.biorxiv.org/content/10.6... #jcampubs
February 5, 2026 at 2:31 PM
FRED: a universal tool to generate FAIR metadata for omics experiments www.biorxiv.org/content/10.6... #jcampubs
Reposted by Xabier Vázquez-Campos
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #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.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Reposted by Xabier Vázquez-Campos
Super excited to share my latest publication with Justin Malogan and @suez.bsky.social , my love letter to viromics! 🦠 Here, we discuss computational and wet lab methods to study the gut virome and how they can be used together
But why is this synergy so important?
journals.asm.org/doi/10.1128/...
But why is this synergy so important?
journals.asm.org/doi/10.1128/...
Tools and approaches to study the human gut virome: from the bench to bioinformatics | mSystems
The human gut microbiome is a complex community of bacteria, archaea, fungi, protozoa,
and viruses that reside within the gastrointestinal (GI) tract (1). Notably, much of the literature regarding the...
journals.asm.org
February 4, 2026 at 3:56 PM
Super excited to share my latest publication with Justin Malogan and @suez.bsky.social , my love letter to viromics! 🦠 Here, we discuss computational and wet lab methods to study the gut virome and how they can be used together
But why is this synergy so important?
journals.asm.org/doi/10.1128/...
But why is this synergy so important?
journals.asm.org/doi/10.1128/...
Reposted by Xabier Vázquez-Campos
BactoTraits: a trait database for exploring functional diversity of bacterial communities www.nature.com/articles/s41... #jcampubs
BactoTraits: a trait database for exploring functional diversity of bacterial communities - Scientific Data
Scientific Data - BactoTraits: a trait database for exploring functional diversity of bacterial communities
www.nature.com
February 3, 2026 at 2:14 PM
BactoTraits: a trait database for exploring functional diversity of bacterial communities www.nature.com/articles/s41... #jcampubs
Reposted by Xabier Vázquez-Campos
Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).
Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution
HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...
www.nature.com
February 3, 2026 at 10:52 AM
Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).
Reposted by Xabier Vázquez-Campos
New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis
Abstract. Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fun
academic.oup.com
February 1, 2026 at 10:18 AM
New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
Reposted by Xabier Vázquez-Campos
Workflow graphical editor and translator to Nextflow f1000research.com/articles/15-...
F1000Research Article: Workflow graphical editor and translator to Nextflow.
Read the latest article version by Ilya Kiselev, Anna Ryabova, Fedor Kolpakov, at F1000Research.
f1000research.com
February 2, 2026 at 5:02 PM
Workflow graphical editor and translator to Nextflow f1000research.com/articles/15-...
Reposted by Xabier Vázquez-Campos
Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence academic.oup.com/ismej/advanc... #jcampubs
Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence
Abstract. Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which
academic.oup.com
February 2, 2026 at 2:04 PM
Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence academic.oup.com/ismej/advanc... #jcampubs
Reposted by Xabier Vázquez-Campos
Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes
#microbiology #archaea #MicroSky
link.springer.com/article/10.1...
#microbiology #archaea #MicroSky
link.springer.com/article/10.1...
Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes - Genome Biology
Background Processing of archaeal 16S and 23S rRNAs is believed to involve excision of individual rRNAs from polycistronic precursors, circularization of excised rRNAs, and re-linearization before the...
link.springer.com
February 1, 2026 at 6:49 PM
Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes
#microbiology #archaea #MicroSky
link.springer.com/article/10.1...
#microbiology #archaea #MicroSky
link.springer.com/article/10.1...
Reposted by Xabier Vázquez-Campos
slow5tools v1.4.0 released github.com/hasindu2008/...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB.
guide to lossy archive: hasindu2008.github.io/slow5tools/a...
paper: doi.org/10.1101/gr.2...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB.
guide to lossy archive: hasindu2008.github.io/slow5tools/a...
paper: doi.org/10.1101/gr.2...
Release slow5tools-v1.4.0 · hasindu2008/slow5tools
What's Changed
slow5tools skim supports the new auxiliary field open_pore_level introduced in latest ONT pod5
slow5tools degrade has new profiles added (by @sashajenner and @hiruna72) and are docu...
github.com
January 28, 2026 at 11:46 PM
slow5tools v1.4.0 released github.com/hasindu2008/...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB.
guide to lossy archive: hasindu2008.github.io/slow5tools/a...
paper: doi.org/10.1101/gr.2...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB.
guide to lossy archive: hasindu2008.github.io/slow5tools/a...
paper: doi.org/10.1101/gr.2...
Reposted by Xabier Vázquez-Campos
📢 Rfam 15.1 is here!
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
January 28, 2026 at 11:16 AM
📢 Rfam 15.1 is here!
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
✨ 50 new RNA families including riboswitch candidates, plastid ncRNAs, snoRNAs, plant xrRNAs and more.
🧬 10 families updated with 3D structures
🖥️ Brand new interactive alignment viewer
Take a look xfam.wordpress.com/2026/01/08/r...
#RNA #Bioinformatics #RNAbiology
Reposted by Xabier Vázquez-Campos
A phylogeny of 4'854 #insects --- with structural #genomics shedding light on protein functions & remote homologs www.nature.com/articles/s41... #biodiversity
Structural genomics sheds light on protein functions and remote homologs across the insect tree of life - Cell Research
Cell Research - Structural genomics sheds light on protein functions and remote homologs across the insect tree of life
www.nature.com
January 28, 2026 at 1:19 PM
A phylogeny of 4'854 #insects --- with structural #genomics shedding light on protein functions & remote homologs www.nature.com/articles/s41... #biodiversity
Reposted by Xabier Vázquez-Campos
Photoelectrotrophy: a novel mode of microbial metabolism and its biogeochemical effects. link.springer.com/article/10.1...
Photoelectrotrophy: a novel mode of microbial metabolism and its biogeochemical effects - Reviews in Environmental Science and Bio/Technology
Photoelectrotrophic metabolism (photoelectrotrophy) is an emerging energy-conversion mode in which non-photosynthetic microorganisms harvest light-derived electrons from photosensitizers (e.g., semico...
link.springer.com
January 28, 2026 at 4:16 PM
Photoelectrotrophy: a novel mode of microbial metabolism and its biogeochemical effects. link.springer.com/article/10.1...
Reposted by Xabier Vázquez-Campos
Trait-based meta-analysis of microbial guilds in the iron redox cycle journals.asm.org/doi/full/10.... #jcampubs
January 27, 2026 at 2:27 PM
Trait-based meta-analysis of microbial guilds in the iron redox cycle journals.asm.org/doi/full/10.... #jcampubs
Reposted by Xabier Vázquez-Campos
#NatMicroPicks
Identification of a 5500-year-old Treponema genome from human remains recovered in Colombia uncovers a new subspecies of Treponema pallidum, the cause of syphilis, and provides insights into its evolutionary history. @science.org
www.science.org/doi/10.1126/...
Identification of a 5500-year-old Treponema genome from human remains recovered in Colombia uncovers a new subspecies of Treponema pallidum, the cause of syphilis, and provides insights into its evolutionary history. @science.org
www.science.org/doi/10.1126/...
A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia
Treponematosis, a bacterial infection caused by Treponema pallidum subspecies and T. carateum (yaws, bejel, syphilis, pinta), has afflicted humans for millennia. Despite paleopathological evidence and...
www.science.org
January 26, 2026 at 3:55 PM
#NatMicroPicks
Identification of a 5500-year-old Treponema genome from human remains recovered in Colombia uncovers a new subspecies of Treponema pallidum, the cause of syphilis, and provides insights into its evolutionary history. @science.org
www.science.org/doi/10.1126/...
Identification of a 5500-year-old Treponema genome from human remains recovered in Colombia uncovers a new subspecies of Treponema pallidum, the cause of syphilis, and provides insights into its evolutionary history. @science.org
www.science.org/doi/10.1126/...
Reposted by Xabier Vázquez-Campos
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
January 26, 2026 at 1:27 PM
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
Reposted by Xabier Vázquez-Campos
In this review in Fungal Ecology, Håvard Kauserud (@drhyfe.bsky.social) argues that while the ITS region is by far the best DNA (meta)barcoding marker for fungi, we should not use it naively or simplistically doi.org/10.1016/j.fu...
January 20, 2026 at 1:30 AM
In this review in Fungal Ecology, Håvard Kauserud (@drhyfe.bsky.social) argues that while the ITS region is by far the best DNA (meta)barcoding marker for fungi, we should not use it naively or simplistically doi.org/10.1016/j.fu...
Reposted by Xabier Vázquez-Campos
Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage
Prototaxites reconstruction by Matt Humpage
January 21, 2026 at 7:25 PM
Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage
Prototaxites reconstruction by Matt Humpage
Reposted by Xabier Vázquez-Campos
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
January 20, 2026 at 11:48 AM
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
Reposted by Xabier Vázquez-Campos
Molecular evolution of the Wood-Ljungdahl pathway and the reductive glycine pathway in Desulfobacterota
#microbiology #bacteria #CO2 #MicroSky
doi.org/10.3389/fmic...
#microbiology #bacteria #CO2 #MicroSky
doi.org/10.3389/fmic...
January 18, 2026 at 7:01 PM
Molecular evolution of the Wood-Ljungdahl pathway and the reductive glycine pathway in Desulfobacterota
#microbiology #bacteria #CO2 #MicroSky
doi.org/10.3389/fmic...
#microbiology #bacteria #CO2 #MicroSky
doi.org/10.3389/fmic...