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Dominik Lücking

@dominikluecking.bsky.social
137 followers 267 following 15 posts

GVs, Phages, MGEs and Bioinf :)

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Reposted by Dominik Lücking
Lauren Queiss @lqueiss.bsky.social · 24/09/2026
What happens when two viruses coinfect the same host? Check out the first publication of my PhD, where we describe two new viruses from an extremophilic system! www.nature.com/articles/s42...
nature.com
Two coinfecting archaeal viruses provide insights into virus-virus interactions - Communications Biology
Communications Biology - Two coinfecting archaeal viruses provide insights into virus-virus interactions
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Anouk Willemsen @willemsenanouk.bsky.social · 24/09/2026
Why did some #viruses #evolve to be giants while others did not? ".. #giantViruses are typical viruses that evolved from smaller ones via accretion of genes recruited from the hosts." doi.org/10.1073/pnas... @mkrupovic.bsky.social & E. Koonin
doi.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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Alejandro Manzano Marín @amanzanom.bsky.social · 18/09/2026
Please help spread the word! I'm searching for a #PhD student to join my group to work on #Symbiont - #pathogen interactions in #Hemiptera. Fully-funded, 4 years *Full details 👇🏼 besymblab.univie.ac.at/wp-content/u... 🧵 on the project 👇🏼 bsky.app/profile/aman... #ScienceJobs #SymbioSky #MicroSky
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Roland Hatzenpichler @environmicrobio.bsky.social · 17/09/2026
I love me some Fermi problems! However, there are no good instructions on how to use them in classes. So I wrote it up! If you read this it, you will finally learn the answer to the question 'How much phosphorous is released each day by viruses lysing Prochlorococcus cells?' tinyurl.com/2njt9r8h
A manuscript title stating 'Better roughly right than precisely wrong: Fermi problems in biology curricula'
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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European Virus Bioinformatics Center @evbc.bsky.social · 06/07/2026
This comprehensive review synthesises current knowledge on the infection cycles of #Nucleocytoviricota (giant DNA viruses), highlighting shared mechanisms and lineage-specific innovations across diverse #virus families. 🦠🔬 📄 doi.org/10.1038/s41579-026-01319-6 👤 EVBC member: Mart Krupovic
doi.org
Infection cycles of viruses of the phylum Nucleocytoviricota - Nature Reviews Microbiology
In this Review, Abergel et al. overview infection cycles across the Nucleocytoviricota phylum, highlighting shared mechanisms and lineage-specific features spanning viral entry, viral factory formation, genome replication, virion morphogenesis and egress, and discuss key unresolved questions in the field.
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Monir Moniruzzaman @giantvirus.bsky.social · 31/08/2026
New research from our lab revealing pervasive genomic islands (GIs) in giant viruses (GV). Leveraging long-read assembled GV genomes we reveal these GIs, their functional repertiore and roles in GV genome variation. Research led by PhD candidate Benjamin Minch! www.nature.com/articles/s41...
nature.com
Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses - Nature Communications
Researchers analyzed 369 giant virus genomes and identified widespread genomic islands, regions of rapid gene turnover that help these viruses adapt to hosts and even exchange genes with bacteria, rev...
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Anouk Willemsen @willemsenanouk.bsky.social · 17/07/2026
Isolation of a Cohort of #giantViruses From Above the Arctic Circle in Northern Norway doi.org/10.1111/1462...
doi.org
Isolation of a Cohort of Giant Viruses From Above the Arctic Circle in Northern Norway
(1) From July 2021 and May 2025 441 marine, freshwater, and soil samples were collected between longitudes 12.79° W to 23.68° E and latitudes 67.88° N to 83.90° N. (2) All samples were screened for v....
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Dominik Lücking @dominikluecking.bsky.social · 08/07/2026
To add: Lau and Dani are on Wednesday (today!), me and Büsra are on Thursday :).
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Sullivan Lab at OSU @sullivan-lab.bsky.social · 06/07/2026
🚨VIROMICS WORKSHOP 2026🚨 Application is now OPEN for the 8th International Viromics Workshop, Oct. 14-16, 2026, in-person at Ohio State University. Application closes Aug. 7. Apply: forms.gle/pJFLDCNEBvAe... Full details: u.osu.edu/viruslab/vir... #viromics #viruses #ecology #workshop
forms.gle
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Sarah Bagby @scbagby.bsky.social · 29/06/2026
Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
Screenshot of an email header with subject line "Crazy ideas"
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
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Anouk Willemsen @willemsenanouk.bsky.social · 03/06/2026
www.linkedin.com/posts/univer...
linkedin.com
University of Vienna – Anouk Willemsen, Assistant Professor at CeMESS | University of Vienna Philanthropy
When do viruses become a threat? 🧬 Viruses are all around us, and most go unnoticed. With new viral generations emerging daily, just a few mutations under the right conditions can change everything. ...
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Reposted by Dominik Lücking
Joshua Weitz @joshuasweitz.bsky.social · 29/05/2026
Viruses are highly abundant in the oceans, but there is one place you won't typically find them: in global ocean ecosystem models... until now. Introducing "vDarwin", an explicit integration of viruses into the MITgcm/Darwin global ecosystem framework: www.biorxiv.org/content/10.6... a 🧵
Integration of a model of viral lysis, shunt and shuttle in a large scale ocean circulation model. (A) Schematic of the large scale ocean circulation model (MITgcm): major surface ocean circulation patterns and the schematic of the advection/diffusion are represented. Note that vertical grid spacing increases with depth (i.e., layers become thicker). (B) Simplified ecosystem represented in the study. For simplicity nitrogen remineralization to nitrite and nitrate and mortality fluxes to DOM and POM are not represented. (C) Schematic of the vDarwin ecosystem model integrated in the large scale circulation model. It represents a simplification of the ecosystem presented in (B) assuming that N is the limiting nutrient. It includes the growth of a single phytoplankton type, viral lysis, zooplankton grazing, the viral shunt and shuttle and remineralization (note that remineralizing bacteria are not explicitly represented).
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Anouk Willemsen @willemsenanouk.bsky.social · 22/05/2026
New Work out! A multilayered network reveals the centrality of newly discovered #Nucleocytoviricota in wastewater treatment plant communities w/ @dominikluecking.bsky.social & @amanzanom.bsky.social doi.org/10.64898/202... @erc.europa.eu @univie.ac.at @dome-vienna.bsky.social 1/4
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Dominik Lücking @dominikluecking.bsky.social · 22/05/2026
Hey y'all, exciting news! New paper in preprint :). Nucleocytoviricota discovery, virophages, polinton-like viruses with a touch of ecology and evolution! doi.org/10.64898/202... Let me know what you think (scary thing to say online, but well...)
doi.org
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Alejandro Manzano Marín @amanzanom.bsky.social · 18/05/2026
New work out! #Coevolution and synchronized evolutionary rates in #aphid dual #endosymbiot sytems w/ Jess, Emmanuelle, Armelle, & co. doi.org/10.64898/202... @cbgpmontpellier.bsky.social @inrae-france.bsky.social @cemess.bsky.social @dome-vienna.bsky.social @univie.ac.at #SymbioSky #MicroSky
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Isa Wilkie @iwilkie.bsky.social · 14/05/2026
Very proud to announce that I successfully defended my PhD last week!
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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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Cameron Thrash @jcamthrash.bsky.social · 08/05/2026
StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution academic.oup.com/bioinformati... #jcampubs
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Vijini Mallawaarachchi @vijinim.bsky.social · 08/05/2026
🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience
academic.oup.com
agtools: A Software Framework to Manipulate Assembly Graphs
AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info
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Gytis Dudas @evogytis.bsky.social · 22/04/2026
Please share! My lab has an open fully-funded PhD position at Vilnius University's Life Sciences Center in Lithuania. The PhD project will involve identifying missing orthomyxovirus segments from public sequence data. Applicants must hold an MSc by June & have bioinformatics experience. 1/2
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Mart Krupovic @mkrupovic.bsky.social · 22/04/2026
"The selfish ribosome" paper is now published in @plosbiology.org . Have a look! Many thanks to the editors and reviewers! doi.org/10.1371/jour...
journals.plos.org
The selfish ribosome
In this Essay, the evolution of life is construed as a ribosomal takeover, whereby the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensured the propagatio...
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Monir Moniruzzaman @giantvirus.bsky.social · 16/04/2026
Sharing the latest preprint from our lab where we identify pervasive presence of Genomic Islands (GIs) in diverse giant viruses and characterize their functions and origins - leveraging cultured isolate genomes and long-read sequenced giant virus genomes. www.biorxiv.org/content/10.6...
biorxiv.org
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Jim Shaw @jimshaw.bsky.social · 27/03/2026
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj
rdcu.be
High-resolution metagenome assembly for modern long reads with myloasm
Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
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Daan Speth @daanspeth.bsky.social · 25/03/2026
We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵
Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories
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Monir Moniruzzaman @giantvirus.bsky.social · 25/03/2026
Excited to share our lab's new paper in Current Biology featuring MS student Sydney Schultz's work. We show that a polar alga carries large amount of giant viral DNA in its genome, and many of the viral genes respond to stress - with implications for host adaptation. www.cell.com/current-biol...
cell.com
Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress
Schultz et al. show that polar algae harbor extensive endogenous giant virus elements that are transcriptionally active, stress responsive, and integrated into host regulatory networks, highlighting v...
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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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Daan Speth @daanspeth.bsky.social · 02/03/2026
Interested in microbial proteins and their diversity? 🖥️🧬🦠 We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences. AASTK currently consists of 4 tools: - CASM - PASR - CUGO - Meta 1/
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Maria Dzunkova @dzunkovam.bsky.social · 23/02/2026
We had a special speaker today at @i2sysbio.es , Anouk Willemsen @willemsenanouk.bsky.social. I have known her since my PhD and I truly admire her work on giant viruses #viruses #microsky
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Kranzusch Lab @kranzuschlab.bsky.social · 17/02/2026
Max Fels @mfels.bsky.social from our lab discovers giant DNA viruses that infect amoeba encode eIF4E and the entire suite of 4F complex proteins to control mRNA translation, including beautiful crystal structures of viral 4E bound to modified mRNA 5' caps: www.cell.com/cell/fulltex...
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Sofya Garushyants @garushyants.bsky.social · 17/02/2026
Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...
training.nih.gov
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Amanda Moehring @flybehaviour.bsky.social · 13/02/2026
Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself. www.science.org/doi/10.1126/...
science.org
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 ...
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Cluster of Excellence 'MicroPlanet' @microbesplanet.bsky.social · 11/02/2026
Today, for International Day of Women and Girls in Science, we’re celebrating the incredible women driving research and innovation in the @fwf-at.bsky.social CoE Microplanet! @cornelia-cr.bsky.social
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Matthias Wietz @matthiaswietz.bsky.social · 05/02/2026
Music is a big part of my life, and this is my band. open.spotify.com/album/5VxsyC...
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Anouk Willemsen @willemsenanouk.bsky.social · 15/12/2025
On our way to the 6th Ringberg Symposium on Giant Virus Biology #ringbergGV2025
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Anouk Willemsen @willemsenanouk.bsky.social · 10/12/2025
Last week we wrapped up the first edition of the Virus evolution and ecology course under the umbrella of the brand new Master in Microbiome Science offered @univie.ac.at. We learned about viruses, their evolution, and their ecological impact across different ecosystems. 1/2 #VirEvol
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Morten Kam Dahl Dueholm @mkddueholm.bsky.social · 03/12/2025
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...
nature.com
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
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European Virus Bioinformatics Center @evbc.bsky.social · 04/12/2025
📢Join us for the next ECR #Viromics Webinar "Drawing from phage diversity to uncover genomic factors shaping host interaction" ‍🎙️Antônio P. Camargo, Uni São Paulo, Brazil  🗓️10 Dec. 2025, 4 PM CET 📍Online/Zoom (register for login details) 👉 evbc.uni-jena.de/events/ecr-viromic…
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Simon Roux @simrouxvirus.bsky.social · 03/12/2025
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
academic.oup.com
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
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The Banfield Lab @banfieldlab.bsky.social · 28/11/2025
Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses www.nature.com/articles/s41... @luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
nature.com
Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications
Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...
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Mart Krupovic @mkrupovic.bsky.social · 28/11/2025
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
nature.com
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
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Monir Moniruzzaman @giantvirus.bsky.social · 26/11/2025
Our work in collaboration with @jedfuhrman.bsky.social lab on the temporal dynamics of marine giant viruses published in ISME communications. PhD student Benjamin Minch is a co-first author. Please take a look! academic.oup.com/ismecommun/a...
academic.oup.com
Validate User
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PLOS Biology @plosbiology.org · 25/11/2025
#Virus discovery has accelerated but linking viruses to hosts is hard. @sullivan-lab.bsky.social use synthetic #microbiomes to optimize & benchmark #Hi-C for virus-host linkage inference, applying this to existing #soil data to reveal 100s of novel linkages @plosbiology.org 🧪 plos.io/3MlAENO
Comparison of virus-host prediction from Hi-C and in silico tools. Top: Eular plot showing the overlap of viruses with host predictions obtained from the experimental Hi-C linkage approach, or one of two in silico tools (iPHoP and VirMatcher) that use different probabilistic models to aggregate output of various sequence-based features to create host prediction scores. Bottom: Comparison of virus-host predictions across all samples between Hi-C and iPHoP, shown with and without applying a Z-score filter for the Hi-C linkages. Black bars indicate congruent predictions identified from both tools and gray bars indicate non-congruent predictions. Note: Although many viruses had multiple predicted hosts from each tool, only the top-scoring prediction for each virus was considered in this comparison.
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David Karpa @dkarpa.bsky.social · 12/11/2025
In capitalism, we cannot expect companies to do anything else than maximise profits. Doing so is not only naive but harmful
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Alex Crits-Christoph @acritschristoph.bsky.social · 10/11/2025
I think you're thinking of these! graphics.wsj.com/infectious-d...
graphics.wsj.com
Battling Infectious Diseases in the 20th Century: The Impact of Vaccines
The number of infected people, measured over 70-some years and across all 50 states and the District of Columbia, generally declined after vaccines were introduced.
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Dominik Lücking @dominikluecking.bsky.social · 10/11/2025
I'm looking for a specific figure I saw on bsky recently on here: It was a heatmap-like plot showing the effectiveness of vaccines. X axis was time, Y axis was different viruses / diseases and you could easily see how each of them disappeared after a vaccine was developed. Any ideas?
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Patrick Pausch @patrick-pausch.bsky.social · 06/11/2025
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
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Luis Orellana (Coto) @cotoorellana.bsky.social · 30/10/2025
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
nature.com
Average nucleotide identity — the backbone of modern ecological genomics - Nature Reviews Genetics
In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...
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Max Planck Institute for Marine Microbiology @mpimarinemicrobio.bsky.social · 27/10/2025
Congratulations @lqueiss.bsky.social 👏🎉😀 Lauren won the Best Poster Award at the Women in Electron Microscopy (#WeM) – Exchange and Networking event @fz-juelich.de Pic: FZJülich/Kurt Steinhausen www.mpi-bremen.de/en/Lauren-Qu... #WomeninSTEM #marinescience #MachMINT @maxplanck.de #FemaleScience
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