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Xing-Xing Shen

@xingxingshen.bsky.social
182 followers 203 following 11 posts

Evolutionary Biology, Phylogenetics, Comparative genomics, Structural genomics, Collaboratives, Insects. Lab website: shenxlab.com

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Reposted by Xing-Xing Shen
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
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Kranzusch Lab @kranzuschlab.bsky.social · 12/08/2026
The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB
nature.com
Shared principles of human and bacterial antiviral immunity - Nature
The Review describes shared ancient, conserved mechanisms between human antiviral immunity and bacterial anti-phage systems, outlining universal principles of pathogen sensing, signalling and effector...
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Xing-Xing Shen @xingxingshen.bsky.social · 22/05/2026
Ancient wars between microbes gave us key immune defenses | Science | AAAS www.science.org/content/arti...
science.org
Ancient wars between microbes gave us key immune defenses
A better understanding of battles between bacteria and viruses could inspire new medicines
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Andrew Roger @andrewjroger.bsky.social · 06/05/2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
academic.oup.com
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
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Yi-Jyun Luo @yjluo.bsky.social · 07/11/2025
Pleased to share our latest paper led by @tomlewin.bsky.social, now out in @currentbiology.bsky.social! We present the first chromosome-level genome of a phoronid and show that shared chromosomal fusions unite phoronids and bryozoans as sister groups. www.cell.com/current-biol...
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Max Telford @maxjtelford.bsky.social · 24/04/2025
It's publication day of my first book: The Tree of Life. The tree of life is a time machine that can take us back 4 billion years to meet our most distant ancestor. It is the magic that lets us tell the origin stories, beginning with this ancient relative, of everything from mushrooms to man.
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Ana Serra Silva @anaserrasilva.bsky.social · 02/02/2026
New paper on @biorxiv-evobio.bsky.social: Are interphylum spiralian relationships resolvable? doi.org/10.64898/202... @maxjtelford.bsky.social and I tried answering this question with two independent phylogenomic datasets. (1/7) 🧪
doi.org
Are interphylum spiralian relationships resolvable?
The phyla making up the major animal clade of Spiralia have been clear since the advent of molecular phylogenetics; the relationships between these spiralian phyla have not. The lack of consensus over the relationships between these important animal phyla might be a clue implying their emergence in an explosive radiation. Focusing on the five largest spiralian phyla (Annelida, Brachiopoda, Mollusca, Nemertea and Platyhelminthes) and using two phylogenomic datasets, we have applied site-bootstrapping and taxon-jackknifing to explore this example of taxonomic instability. Analyses on the 105 possible rooted trees relating them showed that interphylum branches are very short. Preference for rooting Spiralia on Platyhelminthes is a long-branch artefact. Most analyses on the 15 unrooted trees showed a preference for the same topology but the support over other solutions was non significant. We conclude that the spiralian phyla emerged in rapid succession resulting in a difficult to resolve radiation. The deep history we infer for Spiralia has wide ranging implications for our interpretation of Cambrian fossils and for the evolution of traits such as biomineralization, segmentation and larvae. Impact Statement Analyses of two independent phylogenomic datasets suggest an explosive radiation at the origin of Spiralia, with implications for understanding the group’s evolutionary history. ### Competing Interest Statement The authors have declared no competing interest.
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Kranzusch Lab @kranzuschlab.bsky.social · 06/02/2026
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...
nature.com
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
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National Academy of Sciences @nasonline.org · 22/01/2026
Join us in congratulating Philip J. Kranzusch (@kranzuschlab.bsky.social) of @danafarber.bsky.social and @harvardmed.bsky.social, winner of the 2026 NAS Award in Molecular Biology for his groundbreaking work advancing understanding of innate immunity! www.nasonline.org/award/nas-aw... #NASaward
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Kranzusch Lab @kranzuschlab.bsky.social · 01/02/2026
www.nature.com/articles/s41...
nature.com
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
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Xing-Xing Shen @xingxingshen.bsky.social · 29/01/2026
Excited to share a new piece of work in @embojournal.org Parasitoid wasps hijack a bacterial gene that governs venoms against host. Coauthors include @rokaslab.bsky.social and others. Read more from: link.springer.com/article/10.1...
link.springer.com
A bacterial gene acquired by parasitoid wasps contributes to venom secretion against host defence - The EMBO Journal
Horizontal gene transfer (HGT) is an important source of gene innovation in prokaryotic and eukaryotic organisms. Several genes acquired by hosts of parasitoid wasps via HGT have been reported to prot...
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Kyle T David @kylethedavid.bsky.social · 28/01/2026
Excited to announce our latest publication in reporting evidence for three (3!) new whole genome duplications (WGDs) in yeasts. Scientists have often wondered why WGD is so rare in fungi, it turns out we may just not have been looking hard enough! 🧪 🍄 🧬 www.sciencedirect.com/science/arti...
sciencedirect.com
Discovery of additional ancient genome duplications in yeasts
Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages,1,2 preceding adaptive radiations in vertebrates,3,4,5 t…
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 28/01/2026
Researchers built a massive atlas of 13.3 million predicted protein structures from 824 insect species, revealing that structural analysis detects remote evolutionary relationships invisible to sequence-based methods.
Figure from: Structural genomics sheds light on protein functions and remote homologs across the insect tree of l
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Rob Waterhouse @rmwaterhouse.bsky.social · 28/01/2026
A phylogeny of 4'854 #insects --- with structural #genomics shedding light on protein functions & remote homologs www.nature.com/articles/s41... #biodiversity
nature.com
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
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Xing-Xing Shen @xingxingshen.bsky.social · 28/01/2026
New work in @Cell Research We conducted a large-scale structural genomics analysis of #insects, integrating phylogenomics with protein structure prediction to uncover hidden functions and evolutionary insights across the insect tree of life. Read more from www.nature.com/articles/s41...
nature.com
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
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Steve Haddock @stevehaddock.bsky.social · 09/01/2026
The re-analysis of this #sponge #ctenophore study made me realize how important it is to really *look* at your data. Their filtering pipeline was meant to retain "strong" genes, but many of them had NO ctenophores and most had polyphyletic sponges. Time to put down the pitchforks for a while.
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Casey Dunn @caseywdunn.bsky.social · 09/01/2026
Our eLetter github.com/caseywdunn/s... responding to a recent Science paper was just posted. The paper found more genes with consistent support for sponge-sister than ctenophore-sister. We found several technical issues that, when corrected, reverse the conclusions and recover ctenophore-sister.
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Ming Tommy Tang @tommytang.bsky.social · 04/11/2025
Democratizing protein language model training, sharing and collaboration www.nature.com/articles/s4...
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Aude Bernheim @audeber.bsky.social · 04/11/2025
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79). Update time ! Send me a message to 1) add your lab or others 2) Correct info docs.google.com/spreadsheets... #Phagesky #Microsky
docs.google.com
Labs in bacterial immunity
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Astronomy 🔭 @astronomy.bsky.social · 10/05/2025
"We are like butterflies who flutter for a day and think it is forever." - Carl Sagan, Cosmos
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 25/04/2025
Visit our posters at #RECOMB2025 for: Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis Metagenomics: Classification & Metabuli App GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery & get Marv stickers!
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 29/04/2025
Today @yewonhan.bsky.social will give a flash talk about our metagenomic large-scale protein structure clustering and analysis at #RECOMB2025. Today (April 29) 1 p.m. at Global Lounge in “The Commons”
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Michelle Leger @freejakoba.bsky.social · 13/03/2025
So nice to see this out! Congratulations Kelsey, @lauraeme.bsky.social , @andrewjroger.bsky.social and colleagues! www.nature.com/articles/s41...
nature.com
A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
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Sorek Lab @soreklab.bsky.social · 23/01/2025
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors A 🧵 1/10 www.cell.com/cell/abstrac...
cell.com
Structure-guided discovery of viral proteins that inhibit host immunity
Large-scale, structure-guided computational pipeline sifts through millions of phage proteins to identify those that bind and antagonize host immune proteins. Detected proteins are shown to inhibit no...
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phy_papers @phypapers.bsky.social · 19/01/2025
A critical evaluation of deep-learning based phylogenetic inference programs using simulated data sets pubmed.ncbi.nlm.nih.gov/39824436
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Science Magazine @science.org · 17/01/2025
An #AI model created to design proteins simulates 500 million years of protein evolution in developing a previously unknown bright fluorescent protein. Learn more in a new Science study: scim.ag/40l2z3J
RESEARCH ARTICLE Simulating 500 million years of evolution with a language model.

Figure 1E, shown here, displays unconditional generations from ESM3 98B (colored by sequence identity to the nearest sequence in the training set), embedded by ESM3, and projected by UMAP alongside randomly sampled sequences from UniProt (in gray). Generations are diverse, high quality, and cover the distribution of natural sequences.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/01/2025
The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out! 🌐 search.foldseek.com
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Sina Majidian @sinamajidian.bsky.social · 03/01/2025
FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social
FastOMA retains OMA’s high precision accuracy and even improves upon it in terms of recall, positioning it on the Pareto frontier of orthology inference methods. 
FastOMA is not only fast but also accurate. a, QfO benchmar, agreement with SwissTree reference phylogeny covering manually curated gene trees. The error bars indicate 95% confidence intervals comparing FastOMA with EnsemblCompara, Domainoid, OrthoMCL, Ortholnspector, sonicparanoid, PANTHER, OrthoFinder, Hieranoid26 and the OMA family including OMA pairs, OMA groups and OMA GETHOGs (graph-based efficient technique for HOGs).

c) A computation time comparison of FastOMA and state-of-the-art alternatives.
https://www.nature.com/articles/s41592-024-02552-8
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James Lingford @jameslingford.bsky.social · 13/01/2025
Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work www.biorxiv.org/content/10.1...
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Mario dos Reis @mariodosreis.bsky.social · 06/01/2025
A reminder that we have two open PhD projects on Bayesian phylogenetics in the lab: One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan) And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)
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April Wei @aprilwei.bsky.social · 05/12/2024
Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG
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Emily Troyer @fishfetisher.bsky.social · 29/12/2024
On the 4th day of #Fishmas, my true love gave to me: The Troyer et al. 2022 Tetraodontiformes phylogenetic tree!! www.pnas.org/doi/full/10....
Tetraodontiformes phylogeny from Troyer et al, 2022 etched onto a wooden ornament.
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Joseph W. Brown @josephwb.bsky.social · 28/12/2024
I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪
A cross-stitched logo for the phylogenetic inference program PAUP. In yellow are the letters P-A-U-P, attached at the base in the pattern of a phylogenetic tree. The "tree" is outlines in dark blue, with light blue in the background. The counters in the Ps and A are orange.
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Thorben Danke @sagaoptics.bsky.social · 29/12/2024
Bumblebee, Bombus spec. The wild bees of the genus Bombus, also called bumblebees, can be easily identified by the ocelli between the compound eyes. These are arranged almost in a straight line next to each other and not in a triangle like in other bees genera.
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Roli Roberts @roliroberts.bsky.social · 25/11/2024
What did the Last Eukaryotic Common Ancestor (#LECA) look like? Consensus View in #PLOSBiology; massive authorship including @AncestralState, @lauraeme.bsky.social, John Archbald, @andrewjroger.bsky.social, @dackslabecb.bsky.social, Jeremy Wideman. plos.io/4g0alq4
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Andrew Roger @andrewjroger.bsky.social · 11/12/2024
This looks interesting! Anyone tried it on amino acid alignments?
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 23/12/2024
Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...
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