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Yifan ZHOU

@yifanzhou.bsky.social
143 followers 360 following 21 posts

Postdoc at NIOZ | Archaeal Viruses | metagenomics/metaviromics | Haloarchaea | DPANN

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Reposted by Yifan ZHOU
Andrew Roger @andrewjroger.bsky.social · 18/03/2026
So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.
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Reposted by Yifan ZHOU
Mart Krupovic @mkrupovic.bsky.social · 11/09/2026
Why did some #viruses evolve to be #giants while others did not? Our perspective piece on this topic with Eugene Koonin. www.pnas.org/doi/10.1073/...
pnas.org
Why did some viruses evolve to be giants while others did not? | PNAS
Viruses are ubiquitous mobile genetic elements that are obligate symbionts of cellular life forms and replicate exclusively within host cells. The ...
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DEEMteam_Orsay @deemteam.bsky.social · 04/09/2026
Databases may contain lots of misannotated 16S rRNA sequences, which can hinder accurate taxonomic assignment in metabarcoding and metagenomic analyses. We have addressed this issue for Asgard archaea and generated a curated set of high-quality 16S rRNA sequences: academic.oup.com/ismecommun/a...
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Waggoner Lab @labwaggoner.bsky.social · 27/08/2026
Bats’ remarkable longevity and immunity are linked through pleiotropic adaptations to viruses and ageing-related disease @nature.com @psudmant.bsky.social @ucberkeleyofficial.bsky.social @lucievirevolte.bsky.social www.nature.com/articles/s41...
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Ryan Cook @ryancook94.bsky.social · 27/08/2026
Happy to see the last parts of my PhD with @milja001.bsky.social now published in @microbiomej.bsky.social (many thanks to all involved!) link.springer.com/article/10.1...
link.springer.com
Distinct gut viral communities across life stages in dairy cattle - Microbiome
Background Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages shape m...
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SILVA @arb-silva.bsky.social · 26/08/2026
📢 We are excited to announce that the new SILVA 144 Release is now live! See more details here: www.arb-silva.de/news/item/si...
arb-silva.de
SILVA Release 144 is here
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Reposted by Yifan ZHOU
Evgenii Protasov @evgenii-protasov.bsky.social · 24/08/2026
The narrowing prokaryote–eukaryote divide reveals a complexity spectrum #microbiology #eukaryote #prokaryote #evolution #MicroSky @cp-trendsmicrobiol.bsky.social www.sciencedirect.com/science/arti...
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Tanmay Bharat @tbharat-lab.bsky.social · 23/08/2026
Molecular architecture of colossal surface layers from hyperthermophilic archaea Led by @idocaspy.bsky.social (Ido) In collaboration with @mkrupovic.bsky.social and @vikramalva.bsky.social labs doi.org/10.64898/202...
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Nature @nature.com · 29/07/2026
Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ
go.nature.com
Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature
Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.
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Yifan ZHOU @yifanzhou.bsky.social · 13/08/2026
Viruses, Proviruses and Satellites from Asgard Archaea Enrichments www.biorxiv.org/content/10.6...
biorxiv.org
Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions
Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Her...
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Reposted by Yifan ZHOU
Rob Edwards @linsalrob.bsky.social · 22/07/2026
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.
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Archaea Biology Vienna @archaea-vienna.bsky.social · 11/05/2026
Do biofilms give an ecological advantage? Yes! A fantastic follow-up to our previous biofilm work in ammonia-oxidizing archaea: "Biofilm Lifestyle Drives Ecophysiological Niche Expansion in an Archaeal Soil Nitrifier" www.biorxiv.org/content/10.6... Congratulations to all authors! #archaea
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Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
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Ed Hutchinson @socialinfluenza.bsky.social · 18/05/2026
Absolutely extraordinary work from Hui Gao, John Briggs and co @mpibiochem.bsky.social on the structure of the influenza matrix protein in situ, particularly in filamentous virions. It's beautiful, and answers questions I've been wondering about for twenty years www.biorxiv.org/content/10.6...
A reconstruction of part of the M1 helix of influenza A virus (looking from the outside of the virion, down onto the top of the N terminal domain of M1), showing a helix of M1 protomers (blue) bound to phosphatidyl inositol (green), and a 'seam' of M1 protomers placed every fourth unit in a distinct conformation (pink) which allows them to bind to the C-terminal domains of the NA tetramer (yellow).
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Reposted by Yifan ZHOU
Rob Edwards @linsalrob.bsky.social · 05/04/2026
Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky
biorxiv.org
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Mart Krupovic @mkrupovic.bsky.social · 03/03/2026
With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268
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Sorek Lab @soreklab.bsky.social · 05/03/2026
Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes www.science.org/doi/10.1126/... Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration! Linking below previous thread on our findings
science.org
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...
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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 08/03/2026
Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics
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Reposted by Yifan ZHOU
Ed Rybicki 🇿🇲🇿🇦🇬🇧🍷🚀 @edrybicki.bsky.social · 21/03/2026
Life's a continuum of organisms - from independently mobile bits of genomes, through viruses, to organelles, to barely non-organellar symbiotes, to cells. That are mostly not independent either.
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Reposted by Yifan ZHOU
Kathryn (Katy) Appler @katyappler.bsky.social · 18/02/2026
Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12
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Buzz Baum @buzzbaum.bsky.social · 16/12/2025
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!
meetings.embo.org
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…
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Reposted by Yifan ZHOU
Phage papers @phagepapers.bsky.social · 20/11/2025
gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research. DOI: 10.1093/nar/gkaf1115 pubmed.ncbi.nlm.nih.gov/41171134
pubmed.ncbi.nlm.nih.gov
gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research - PubMed
The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation …
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Yifan ZHOU @yifanzhou.bsky.social · 13/11/2025
www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Reposted by Yifan ZHOU
DEEMteam_Orsay @deemteam.bsky.social · 02/11/2025
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH
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Fabai Wu @fabaiwu.bsky.social · 21/10/2025
Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky
nature.com
Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution
Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.
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Nature Microbiology @natmicrobiol.nature.com · 20/10/2025
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues. @mkrupovic.bsky.social @yifanzhou.bsky.social @deemteam.bsky.social www.nature.com/articles/s41...
nature.com
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
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Yifan ZHOU @yifanzhou.bsky.social · 20/10/2025
Archaeal symbioses all the way down by Mike Dyall-Smith www.nature.com/articles/s41...
nature.com
Archaeal symbioses all the way down - Nature Microbiology
Ethiopian salt lakes feature unique microbial communities with nesting layers of symbioses, where haloarchaea and their ultra-small archaeal symbionts are prey to viruses, which are in turn hijacked b...
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Reposted by Yifan ZHOU
Frédérique Le Roux @fredoleroux.bsky.social · 12/10/2025
Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
biorxiv.org
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
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Yifan ZHOU @yifanzhou.bsky.social · 17/10/2025
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...
nature.com
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
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Yifan ZHOU @yifanzhou.bsky.social · 02/10/2025
www.science.org/doi/full/10....
science.org
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
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Reposted by Yifan ZHOU
Joe Grove @grovearmada.bsky.social · 26/09/2025
🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
viro3d.cvr.gla.ac.uk
Viro3D
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Cameron Thrash @jcamthrash.bsky.social · 18/08/2025
Computational function prediction of bacteria and phage proteins journals.asm.org/doi/abs/10.1... #jcampubs
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Yifan ZHOU @yifanzhou.bsky.social · 30/06/2025
Thank you❤️❤️
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DEEMteam_Orsay @deemteam.bsky.social · 17/02/2025
(1/2) Preprint alert! In collaboration with @yifanzhou.bsky.social and @mkrupovic.bsky.social we describe host-parasite layers in hypersaline systems of the Danakil Depression. Haloarchaea host nanohaloarchea and both are infected by viruses (12 new families found). www.biorxiv.org/content/10.1...
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Yifan ZHOU @yifanzhou.bsky.social · 16/02/2025
After 3 years of work, we are thrilled to submit this preprint. In collaboration with DEEM Team, we uncovered the complex interactions between haloarchaea, nanohaloarchaea, and their respective viruses and virus satellites. See🧵 www.biorxiv.org/content/10.1... #DPANN #ArchaealViruses #Satellite
biorxiv.org
Nested parasitism in hypersaline environments: viruses and virus satellites of haloarchaea and their nanosized cellular symbionts
It is increasingly recognized that hyperparasitism, whereby a parasite exploits a host which itself is a parasite, is a common phenomenon across ecosystems and domains of life. Here, to explore hyperp...
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Yifan ZHOU @yifanzhou.bsky.social · 02/02/2025
Wish you good fortune in the Year of Snake #archaealvirology
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