Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Microbiologist | Molecular Microbiology | Eco-physiology | Microbiome | Co-Evolution 4 Fit |
scholar.google.nl/citations?hl=en&use…
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Photoholes within cyanobacterial mats can account for the origin of #anammox bacteria and ancient #nitrogen loss link.springer.com/article/10.1...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸A must read! The constant and often irrational renaming of microbes is out of control, and bad for microbiology and microbiologists. journals.asm.org/doi/10.1128/...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Visualizing pairwise genome comparisons? No need to run BLAST separately anymore! 🧬 #gbdraw has implemented #LOSAT, a WASM-powered Rust reimplementation of BLASTN/TBLASTX. ✅ No local installation ✅ No data transfer (Serverless) Try it here: gbdraw.app
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41... How bacteria evolved thousands of precision nanoinjectors? Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Very interesting paper. www.science.org/doi/10.1126/...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸The Shingles vaccine has outperformed all expectations. Why? erictopol.substack.com/p/spotlight-...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix github.com/ebiggers/lib...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Do viruses use RNA to rewire bacteria? Yes! In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection. #RNA #Phage doi.org/10.1016/j.mo...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸This is a disaster. I would not be where I am today without the constructive (and yes, sometimes frustrating) reviews my NSF proposals received as a young investigator. This feedback didn't come from the POs but rather the peer reviewers and panelists who saw how I was trying to enter the field
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸🦠🧪🧬🚨 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-...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Need to predict whether a given contig in your assembly was circular in the environment? Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity: anvio.org/help/main/pr...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸#microsky #phagesky Mycobacterium #phage review by Graham Hatfull covering the state of the art www.pnas.org/doi/10.1073/...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true? Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT. We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Genome-wide bacterial genetic interaction mining by dual Tn-seq | Nature Methods nature.com/articles/s41592-025…
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Also, as always, 16S rRNA gene amplicon sequencing != metagenomics
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸case for absolute gene expression estimates in microbiome studies using metatranscriptomics | The ISME Journal | Oxford Academic academic.oup.com/ismej/article/19/1/…
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸3.5-year #Postdoc position on avian microbiomes and reproduction @animalecol-nioo.bsky.social @niooknaw.bsky.social on a fully-funded ERC project focused on understanding the significance of reproductive microbiomes for host biology and fitness. Reach out for more info! nioo.knaw.nl/en/vacancies...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸🚨🚨 New paper in @narjournal.bsky.social! 🍾 Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons). We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín. 👇
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA. #ArchaeaSky #MEvoSky #MicroSky 🔗 doi.org/10.1101/2025... 💻 github.com/stephkoest/w...
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
- Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸[Not loaded yet]
