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npariente.bsky.social
Nonia Pariente
@npariente.bsky.social
3.7K followers 2.2K following 490 posts
Editor in Chief of the #NonProfit, #OpenAccess journal @plosbiology.org Former Chief Editor of Nature Microbiology.
#Virologist. #Feminist. #Spaniard in the UK. #Galician. #European always.
Views my own.

https://orcid.org/0000-0002-3666-5683
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npariente.bsky.social
Nonia Pariente @npariente.bsky.social · Nov 22
Hi Bluesky! 👋
Dipping my toes here given the dumpsterfire over at X. I am Editor in Chief of #PLOSBiology, interested in all things #science.
#virologist, passionate about #OpenScience & making #publication process constructive & transparent.
I look forward to rebuilding community here!
Reposted by Nonia Pariente
leonsimons.com
"how can someone not at least find it interesting watching a whole planet shift geological ages in the blink of an eye?"

Hear, hear!
December 20, 2025 at 9:24 AM
Reposted by Nonia Pariente
connorggbamford.bsky.social
2000 yr old rotavirus!
biorxivpreprint.bsky.social bioRxivpreprint @biorxivpreprint.bsky.social · 4d
RNA virus genomes from centuries- to millennia-old Adelie penguin mummies https://www.biorxiv.org/content/10.64898/2025.12.17.693957v1
December 19, 2025 at 7:37 AM
npariente.bsky.social
Thoughtful recap of 2025 by Joanna Clarke, including many discoveries made this year & the editors' picks of those we published in @plosbiology.org

Want to guess? There are bright yellow worms, unusual mycomembranes, human response to avatars, tit learning strategies, soil science & more

🧪
plosbiology.org PLOS Biology @plosbiology.org · 4d
2025 was marked by upheaval and uncertainty for many within the life science community. In this Editorial, we reflect on the past year and highlight some of the many research achievements that give us reasons to be thankful.
🧪 #AcademicSky #biology #EOY #science #roundup
plos.io/4j5T3uh
The text 'A catalyst for better' is shown over a background of blue cells and part of the PLOS logo
December 19, 2025 at 12:42 PM
Reposted by Nonia Pariente
plosbiology.org
2025 was marked by upheaval and uncertainty for many within the life science community. In this Editorial, we reflect on the past year and highlight some of the many research achievements that give us reasons to be thankful.
🧪 #AcademicSky #biology #EOY #science #roundup
plos.io/4j5T3uh
The text 'A catalyst for better' is shown over a background of blue cells and part of the PLOS logo
December 19, 2025 at 10:13 AM
Reposted by Nonia Pariente
roliroberts.bsky.social
Lovely celebration of 2025 for @plosbiology.org by my colleague Jo Clarke. My two nominations for this were journals.plos.org/plosbiology/... (by Chaolun Li &co) about worms turned yellow by orpiment, and journals.plos.org/plosbiology/... about a boom in AI-generated articles (by Matt Spick &co)...
The alvinellid worm Paralvinella hessleri is the only animal that colonizes the hottest part of deep-sea hydrothermal vents in the west pacific. Wang et al. found P. hessleri accumulates exceptionally high level of toxic element arsenic (>1% of wet weight) and tolerates elevated concentrations of hydrogen sulfide. Using advanced microscopy, elementary analysis, and genomics and proteomics approaches, the authors identify a previously unrecognized arsenic-sulfide biomineralization process in P. hessleri. Their data suggest that arsenic accumulates within epithelial cell granules, where it likely reacts with sulfide diffused inward from the hydrothermal vent fluid, resulting in the intracellular formation of orpiment (As2S3) minerals. In this “fighting poison with poison” manner, the highly toxic arsenic and sulfide were simultaneously detoxified in the form of orpiment within intracellular granules of the single layer of epithelial cells. The image shows a lateral view of a P. hessleri specimen with buccal tentacles extroverted; note that the animal has a bright yellow color which derives from the epithelial orpiment crystals. Image Credit: Hao Wang
December 19, 2025 at 11:07 AM
npariente.bsky.social
Just given my annual State of the journal address (thanks to @jkpfeiff.bsky.social for the original idea)

It is always great to compile the year's achievements & what a year it has been for @plosbiology.org! I am immensely proud of my team of enthusiastic & committed editors

🥂 to a great 2026!
Title slide for PLOS Biology State of the journal address 2025
December 18, 2025 at 5:05 PM
npariente.bsky.social
Prestige by association is less beneficial than looking at the impact of individual papers

"Most researchers would receive more recognition if assessed by article-level metrics than by journal-level metrics" @plosbiology.org

Why are we still stuck on #journal impact factors?

#JIF #ALMs
🧪
plosbiology.org PLOS Biology @plosbiology.org · 5d
Are authors fairly judged by assessing the #journals in which their work is published? @bihutchins.bsky.social &co reveal that most influential papers are published in lower tier journals, and more authors would be better recognized with #ArticleLevelMetrics #ALMs @plosbiology.org 🧪 plos.io/4oV58Ed
Standing on the shoulders of giants. Researchers (nodes) at early (red), mid (blue) and late (grey) career stage who have built on one another's work (edges). Large nodes are researchers whose work would not be recognized with journal level metrics but would be recognized with article level metrics. Credit: B. Ian Hutchins
December 18, 2025 at 11:35 AM
Reposted by Nonia Pariente
alanmcn1.bsky.social
AI folks now having to realise what GWAS folks did about studying bacterial genome datasets. Great work by great researchers
plosbiology.org PLOS Biology @plosbiology.org · 5d
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
Bacterial population structure and clade-specific sampling affect machine learning predictions of antimicrobial resistance (AMR). Top: An illustration of defining clades for genomes in one species. R: resistant (triangles), S: susceptible (circles). Bottom left: An example of training scenarios for scheme B based on the clade splitting in shown above. Models were trained on all samples except for resistant or susceptible samples from one clade. The held-out genomes from the same clade were used as the test sets. Bottom right: The precision and recall scores for scheme B; a-random and b-random indicate testing on random train-test splits of the pathological unbalanced data.
December 17, 2025 at 5:41 PM
Reposted by Nonia Pariente
plosbiology.org
#MachineLearning methods are used to predict #AntimicrobialResistance #AMR from genomic data. @lbarquist.bsky.social &co show that sampling biases driven by population structure severely undermine the accuracy of AMR prediction models even with large datasets @plosbiology.org 🧪 plos.io/4iZ0zXQ
Bacterial population structure and clade-specific sampling affect machine learning predictions of antimicrobial resistance (AMR). Top: An illustration of defining clades for genomes in one species. R: resistant (triangles), S: susceptible (circles). Bottom left: An example of training scenarios for scheme B based on the clade splitting in shown above. Models were trained on all samples except for resistant or susceptible samples from one clade. The held-out genomes from the same clade were used as the test sets. Bottom right: The precision and recall scores for scheme B; a-random and b-random indicate testing on random train-test splits of the pathological unbalanced data.
December 18, 2025 at 9:30 AM
Reposted by Nonia Pariente
carlbergstrom.com
Just decline the peer review invitation.

What are you people even doing?
More than half of researchers now use AI for peer review — often against guidance
A survey of 1,600 academics found that more than 50% have used artificial-intelligence tools while peer reviewing manuscripts.
www.nature.com
December 16, 2025 at 10:39 PM
Reposted by Nonia Pariente
harmitmalik.bsky.social
I can't believe this still needs to be said (and more loudly):

Trans rights are human rights.
December 18, 2025 at 12:54 AM
Reposted by Nonia Pariente
npariente.bsky.social
Yearly reminder that the world will not end if that new manuscript or revision sits on your desk for a couple more weeks, or you are realistic about decision times.

Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
a cartoon drawing of minnie mouse talking on a phone
Alt: a cartoon drawing of minnie mouse working intensely
media.tenor.com
December 17, 2025 at 1:02 PM
Reposted by Nonia Pariente
lbarquist.bsky.social
Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
journals.plos.org
December 17, 2025 at 2:55 PM
Reposted by Nonia Pariente
buzzbaum.bsky.social
Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious?

Either way, we have good news.
We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July.

Sign up: meetings.embo.org/event/26-arc...

We look forward to seeing you in Cambridge, UK.

Please repost!
Molecular Biology of Archaea: Life Through the Prism of Archaea
In 1977, Woese and colleagues revealed Archaea as a distinct domain of life. Building on this insight, the discovery of Asgard archaea has strengthened the view that many hallmarks of eukaryotic cell…
meetings.embo.org
December 16, 2025 at 12:00 PM
npariente.bsky.social
I'd generally recommend against submitting anything now to an editorial office.

It's it the easiest way to ensure that it gets buried under a pile of other submissions, and editors/reviewers are frazzled when they get to it
npariente.bsky.social Nonia Pariente @npariente.bsky.social · 6d
Yearly reminder that the world will not end if that new manuscript or revision sits on your desk for a couple more weeks, or you are realistic about decision times.

Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
a cartoon drawing of minnie mouse talking on a phone
Alt: a cartoon drawing of minnie mouse working intensely
media.tenor.com
December 17, 2025 at 1:05 PM
npariente.bsky.social
Yearly reminder that the world will not end if that new manuscript or revision sits on your desk for a couple more weeks, or you are realistic about decision times.

Editors & reviewers are people too, are getting swamped with work just about now, and will likely enjoy a well-deserved break soon
🧪
a cartoon drawing of minnie mouse talking on a phone
Alt: a cartoon drawing of minnie mouse working intensely
media.tenor.com
December 17, 2025 at 1:02 PM
Reposted by Nonia Pariente
npariente.bsky.social
An important reminder that the wild and wonderful are often not recapitulated by model organism biology.

The Rudner lab shows that the biogenesis of #anthrax spores has striking differences with the process in B. subtilis

🧪
plosbiology.org PLOS Biology @plosbiology.org · 7d
Is #Bsubtilis a good model for the spore-forming #anthrax #pathogen B. anthracis? This study identifies >150 B. anthracis #sporulation genes and cytologically phenotypes the mutants, revealing similarities & striking differences between model & pathogen @plosbiology.org 🧪 plos.io/3YsvlyZ
Conserved B. anthracis sporulation genes have mutant phenotypes that are similar, but not identical, to B. subtilis mutants. Top: Representative fluorescence and phase-contrast micrographs of sporulating B. anthracis and B. subtilis. Wild-type strains were induced to sporulate by nutrient exhaustion at 37 °C in PA (B. anthracis) or DSM (B. subtilis). Time after the onset of sporulation is indicated in the top left corner of the B. anthracis images. The membranes were stained (0–5 hour) with TMA-DPH. Bottom: Representative fluorescence images of the indicated B. anthracis mutants at hour 4 of sporulation. All strains harbor forespore (PspoIIQ-yfp) and mother cell (PspoIID-cfp) transcriptional reporters. σF activity in the forespore (SigF) and σE activity in the mother cell (SigE) were visualized with YFP (false-colored green) and CFP (false-colored red), respectively. The membranes were stained with TMA-DPH. Disporic cells in spoIIR::Tn (yellow carets), impaired engulfment in spoIID::Tn and spoIIQ::Tn (white carets), and small forespores in spoIIIAE::Tn (light blue carets) are highlighted. Scale bars indicate 5 μm.
December 16, 2025 at 4:52 PM
npariente.bsky.social
😱
samuelmoore.org Samuel Moore @samuelmoore.org · 6d
"Ask AI to summarize long sections, clarify jargon, or outline the structure. Always verify summaries against the original."

Frontiers guidance on AI in peer review for ECRs optimistically expects them to "verify summaries" of things they couldn't be bothered to read it in the first place.
AI in peer review: what early-career researchers should know (and how to use it wisely)
For early-career researchers, AI has become part of everyday work, whether in drafting manuscripts, organizing ideas, or exploring literature. A survey of 1,645
www.frontiersin.org
December 17, 2025 at 8:17 AM
Reposted by Nonia Pariente
bananabenana.bsky.social
Absolutely stoked to have this published in @plosbiology.org

We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.

journals.plos.org/plosbiology/...

#MicroSky #microbiology 🧬 🧪 💊
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
journals.plos.org
December 13, 2025 at 9:46 AM
Reposted by Nonia Pariente
kelwyres.bsky.social
Ditto, ditto, ditto!

We are thrilled this is now available in @plosbiology.org 🎉🎉🎉

Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠

Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩
December 15, 2025 at 2:45 AM
npariente.bsky.social
An important reminder that the wild and wonderful are often not recapitulated by model organism biology.

The Rudner lab shows that the biogenesis of #anthrax spores has striking differences with the process in B. subtilis

🧪
plosbiology.org PLOS Biology @plosbiology.org · 7d
Is #Bsubtilis a good model for the spore-forming #anthrax #pathogen B. anthracis? This study identifies >150 B. anthracis #sporulation genes and cytologically phenotypes the mutants, revealing similarities & striking differences between model & pathogen @plosbiology.org 🧪 plos.io/3YsvlyZ
Conserved B. anthracis sporulation genes have mutant phenotypes that are similar, but not identical, to B. subtilis mutants. Top: Representative fluorescence and phase-contrast micrographs of sporulating B. anthracis and B. subtilis. Wild-type strains were induced to sporulate by nutrient exhaustion at 37 °C in PA (B. anthracis) or DSM (B. subtilis). Time after the onset of sporulation is indicated in the top left corner of the B. anthracis images. The membranes were stained (0–5 hour) with TMA-DPH. Bottom: Representative fluorescence images of the indicated B. anthracis mutants at hour 4 of sporulation. All strains harbor forespore (PspoIIQ-yfp) and mother cell (PspoIID-cfp) transcriptional reporters. σF activity in the forespore (SigF) and σE activity in the mother cell (SigE) were visualized with YFP (false-colored green) and CFP (false-colored red), respectively. The membranes were stained with TMA-DPH. Disporic cells in spoIIR::Tn (yellow carets), impaired engulfment in spoIID::Tn and spoIIQ::Tn (white carets), and small forespores in spoIIIAE::Tn (light blue carets) are highlighted. Scale bars indicate 5 μm.
December 16, 2025 at 4:52 PM
Reposted by Nonia Pariente
plosbiology.org
Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2
Collapsed phylogenetic tree of the Klebsiella pneumoniae Species Complex (top) and the presence of metabolic capabilities (bottom), leading to lineage-specific metabolic networks and traits
December 16, 2025 at 9:01 AM
Reposted by Nonia Pariente
peterhotezmdphd.bsky.social
Frankenstein
December 13, 2025 at 4:10 PM
Reposted by Nonia Pariente
angierasmussen.bsky.social
Anyone else find it alarming that the FDA Commissioner is sharing deranged conspiracy theories about HIV coming from a lab and Lyme disease being a bioweapon made by Nazi war criminals in a USDA lab during the Cold War? Just me?

rasmussenretorts.substack.com/p/commission...
December 14, 2025 at 10:13 PM
Reposted by Nonia Pariente
mackayim.bsky.social
Gripes about this report:
⚠️It's stupidly hard to see precise detail (the pink bands above🤨) of the virus dominance swap though.🤬
⚠️Why is SARS-CoV-2 getting such clear genomic coverage but not flu? Especially right now. We have the bloody capacity thanks to a ton of COVID $. Come on.
December 13, 2025 at 5:26 AM