Xabier Vázquez-Campos
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xabivc.bsky.social
Xabier Vázquez-Campos
@xabivc.bsky.social
180 followers 260 following 41 posts
Nearly-dry wet-lab microbiologist 😅

Biologist, (env.) microbiologist, bioinformatician. First gen.
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Reposted by Xabier Vázquez-Campos
biorxiv-bioinfo.bsky.social
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
November 26, 2025 at 2:46 AM
Reposted by Xabier Vázquez-Campos
vijinim.bsky.social
🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106
•
💻 Github: github.com/Vini2/agtools
📄 Preprint: biorxiv.org/content/10.110…
November 25, 2025 at 11:21 PM
Reposted by Xabier Vázquez-Campos
stevenjrobbins.bsky.social
Hey Team! What do you think are the best free digital notebooks these days.

I've used:
Evernote--great, but now it's paid

TiddlyWiki wasn't bad, but got rid of scrollable code blocks

Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki.

Suggestions?
November 26, 2025 at 9:49 PM
Reposted by Xabier Vázquez-Campos
hormiga.bsky.social
You know those labs that keep harming students, again and again? Some reflections on why it's so hard to stop this from happening and where our responsibilities lie.

scienceforeveryone.science/bad-mentors-... 🧪
Bad mentors hurt people
What to do about bad mentors?
scienceforeveryone.science
November 25, 2025 at 6:38 PM
Reposted by Xabier Vázquez-Campos
mkddueholm.bsky.social
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules
Abstract. Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most m
academic.oup.com
November 25, 2025 at 8:56 AM
Reposted by Xabier Vázquez-Campos
hbrappap.bsky.social
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
Reposted by Xabier Vázquez-Campos
bffo.bsky.social
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to
academic.oup.com
November 24, 2025 at 12:56 AM
Reposted by Xabier Vázquez-Campos
isepprotists.bsky.social
New #ISEPpapers! Natural and artificial variations of the standard genetic code www.cell.com/current-biol... #Protists #TreeOfLife #Evolution #Microbes #Genetics
schematic evolutionary tree of eukaryotes with various changes in the genetic code mapped
November 23, 2025 at 6:01 PM
Reposted by Xabier Vázquez-Campos
isme-microbes.bsky.social
The IUCN Microbial Conservation Specialist Group, the first IUCN body focused on protecting microbial life, outlines its goals, framework, and initial action plan in an ISME journal editorial.
Read the editorial: isme-microbes.org/iucn-expands...
#MicrobialEcology #microbes #climatechange
November 20, 2025 at 5:19 PM
Reposted by Xabier Vázquez-Campos
merenbey.bsky.social
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!

Please find more information on the venue, program, and the application form here, and spread the word 😇

anvio.org/workshops/20...
November 20, 2025 at 6:42 PM
Reposted by Xabier Vázquez-Campos
karthik-a.bsky.social
Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org
November 20, 2025 at 9:04 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems
This review synthesises evidence from culture-dependent systems and complex environments, concluding that temperate phages drive microbial adaptation across individual, population and community level...
enviromicro-journals.onlinelibrary.wiley.com
November 17, 2025 at 6:04 PM
Reposted by Xabier Vázquez-Campos
stephenturner.us
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
Reposted by Xabier Vázquez-Campos
phylogenomics.bsky.social
Science is awesome ... www.cell.com/trends/biote... #violacein #pigments
One-pot production of colored bacterial cellulose
Zhou et al. report the one-pot production of colored bacterial cellulose (BC) as a sustainable alternative to petroleum-based fabrics. Metabolic engineering enhanced colorant yields, while co-culture ...
www.cell.com
November 16, 2025 at 5:04 AM
Reposted by Xabier Vázquez-Campos
wentsunghwang.bsky.social
#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages
The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...
www.biorxiv.org
November 13, 2025 at 7:28 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy www.nature.com/articles/s41... #jcampubs
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications
It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...
www.nature.com
November 13, 2025 at 7:40 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Augmenting microbial phylogenomic signal with tailored marker gene sets www.nature.com/articles/s41... #jcampubs
Augmenting microbial phylogenomic signal with tailored marker gene sets - Nature Communications
Marker genes used in microbial phylogenomics are limited to fixed gene sets selected from complete genomes. TMarSel is a flexible yet robust method for selecting any number of markers from genomes or ...
www.nature.com
November 13, 2025 at 8:54 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Assembly, architecture and functional roles of microbial surface layers www.nature.com/articles/s41... #jcampubs
Assembly, architecture and functional roles of microbial surface layers - Nature Reviews Microbiology
Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss rece...
www.nature.com
November 13, 2025 at 7:44 PM
Reposted by Xabier Vázquez-Campos
jlsteenwyk.bsky.social
NEW pub in @science.org 🥳

Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?

For over 15 years, #phylogenomic studies have been divided.

We provide new evidence suggesting that...

🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
Reposted by Xabier Vázquez-Campos
hansonmark.bsky.social
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/...
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.
November 11, 2025 at 11:52 AM
Reposted by Xabier Vázquez-Campos
stevenjrobbins.bsky.social
Metagenomics colleagues!

I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.

Please help and share!
November 11, 2025 at 8:21 PM
Reposted by Xabier Vázquez-Campos
dzunkovam.bsky.social
Our Springer Nature book is just published! Big thanks to the co-editor Chris Rinke
@chrisrinke.bsky.social and to all book contributors, coming from @i2sysbio.es, @jgi.doe.gov and many other institutes I couldn't find on BlueSky
link.springer.com/book/10.1007...
#microsky #singlecell #genomics 🧪🦠
Single-Cell Omics in Microbiome Research
This volume introduces single-cell microbial (gen)omics as an innovative approach to study microbial diversity and symbiosis
link.springer.com
November 10, 2025 at 4:30 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
The cell envelope of diderm bacteria: a unified scaffold, not a stack of layers www.sciencedirect.com/science/arti... #jcampubs
November 10, 2025 at 4:39 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
The Hidden Viral Network: How Viruses Shape Microbial Adaptability and Biogeochemical Cycling in the Polyextreme Mars‐Analog Qaidam Basin Desert enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
The Hidden Viral Network: How Viruses Shape Microbial Adaptability and Biogeochemical Cycling in the Polyextreme Mars‐Analog Qaidam Basin Desert
Our study unveils the largely unexplored soil virosphere and virus-host interactions in the hyperarid Mars-analog desert of the Qaidam Basin. The findings underscore the vital ecological role of viru....
enviromicro-journals.onlinelibrary.wiley.com
November 10, 2025 at 4:40 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes academic.oup.com/femsre/advan... #jcampubs
November 10, 2025 at 4:43 PM