Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
@alex03-cz.bsky.social
Microbiologist | Microbiology | Virology | Anti-viral | Anti-immune | Co-Evolution 4 Fit |
https://scholar.google.nl/citations?hl=en&user=4cUcmfMAAAAJ
https://scholar.google.nl/citations?hl=en&user=4cUcmfMAAAAJ
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
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
November 20, 2025 at 8:40 PM
🚨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
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)
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Plastic degradation by enzymes from uncultured deep sea microorganisms
Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are
academic.oup.com
November 10, 2025 at 6:04 PM
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)
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 https://www.nature.com/articles/s41592-025-02921-x
November 8, 2025 at 6:44 AM
Genome-wide bacterial genetic interaction mining by dual Tn-seq | Nature Methods https://www.nature.com/articles/s41592-025-02921-x
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...
Pull requests · hadley/genzplyr
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 8, 2025 at 12:29 AM
Y’all these genzplyr PRs are off the hook: github.com/hadley/genzp...
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
🧪Did you know that America is known for its cancer research b/c of the National Cancer Act in 1971 signed by Nixon. Mary Lasker took her cause to congress and the American public as a leading proponent of the National Cancer Act. She said, "If you think research is expensive, try disease!"
September 18, 2025 at 9:53 AM
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Microbiology societies from five continents recently met at @asm.org HQ in DC for the inaugural Global Strategy Meeting on Microbes and Climate Change. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Microbes without borders: uniting societies for climate action | mBio
The climate crisis is one of the most urgent and complex challenges of our time. Although
often overlooked in models and policy, microorganisms play a critical role in climate
dynamics. They are sensi...
journals.asm.org
September 25, 2025 at 5:49 PM
Microbiology societies from five continents recently met at @asm.org HQ in DC for the inaugural Global Strategy Meeting on Microbes and Climate Change. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Also, as always, 16S rRNA gene amplicon sequencing != metagenomics
September 21, 2025 at 2:30 AM
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 https://academic.oup.com/ismej/article/19/1/wraf188/8239678?login=true
A case for absolute gene expression estimates in microbiome studies using metatranscriptomics
Metatranscriptomics is widely used to study the functional dynamics of microbial communities in their natural environment [1–6]. Changes in gene expression
dx.doi.org
September 16, 2025 at 10:22 PM
case for absolute gene expression estimates in microbiome studies using metatranscriptomics | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/article/19/1/wraf188/8239678?login=true
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
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…
September 10, 2025 at 3:40 PM
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...
nioo.knaw.nl/en/vacancies...
Postdoctoral researcher: avian microbiomes and reproduction
We are looking for a postdoctoral researcher to join our team working on avian reproductive microbiomes at the Netherlands Institute of Ecology (NIOO-KNAW) in the group of Dr. Melissah Rowe. The postd...
nioo.knaw.nl
August 12, 2025 at 3:06 PM
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...
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
August 5, 2025 at 12:45 PM
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.
👇
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.
👇
ExcludonFinder: mapping transcriptional overlaps between neighboring genes
Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc
academic.oup.com
July 25, 2025 at 9:26 PM
🚨🚨 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.
👇
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...
🧵 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...
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
www.biorxiv.org
July 20, 2025 at 1:04 PM
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...
🧵 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 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments journals.asm.org/doi/full/10.... #jcampubs
April 18, 2025 at 2:53 PM
Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments journals.asm.org/doi/full/10.... #jcampubs
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Today at #ASMicrobe, 240 early career scientists from around the world gathered to learn about essential tools and insights to successfully launch and develop their professional careers. Looking to unlock your career potential? Explore ASM's resources! asm.social/2t4
June 19, 2025 at 10:17 PM
Today at #ASMicrobe, 240 early career scientists from around the world gathered to learn about essential tools and insights to successfully launch and develop their professional careers. Looking to unlock your career potential? Explore ASM's resources! asm.social/2t4
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Our new paper is online in Genome Biology:
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....
Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology
Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...
genomebiology.biomedcentral.com
June 11, 2025 at 1:43 PM
Our new paper is online in Genome Biology:
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Biofilm architecture determines the dissemination of conjugative plasmids: We measured the spatiotemporal spread of plasmids in biofilms and found that plasmids only spread in some biofilm regions!
Collab with lab of @sbigot.bsky.social & Christian Lesterlin
www.pnas.org/doi/10.1073/...
Collab with lab of @sbigot.bsky.social & Christian Lesterlin
www.pnas.org/doi/10.1073/...
Biofilm architecture determines the dissemination of conjugative plasmids | PNAS
Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that
significantly contributes to the dissemination of antibiotic res...
www.pnas.org
April 28, 2025 at 7:03 AM
Biofilm architecture determines the dissemination of conjugative plasmids: We measured the spatiotemporal spread of plasmids in biofilms and found that plasmids only spread in some biofilm regions!
Collab with lab of @sbigot.bsky.social & Christian Lesterlin
www.pnas.org/doi/10.1073/...
Collab with lab of @sbigot.bsky.social & Christian Lesterlin
www.pnas.org/doi/10.1073/...
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Single-tooth prediction of childhood caries:
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
June 9, 2025 at 9:03 PM
Single-tooth prediction of childhood caries:
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
• Dental plaque microbiota patterns in children are predictive of tooth-specific caries development.
• Spatial-MiC model, integrating microbial and spatial data, improves caries forecasting with 93% accuracy
www.cell.com/cell-host-mi...
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Various classes of riboswitches bind the nitrogen-rich compound guanidine, but its physiological significance remains elusive. In #JBacteriology, discover what we know so far about this important compound and open questions to guide future research: asm.social/2rW
June 6, 2025 at 3:14 PM
Various classes of riboswitches bind the nitrogen-rich compound guanidine, but its physiological significance remains elusive. In #JBacteriology, discover what we know so far about this important compound and open questions to guide future research: asm.social/2rW
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
New paper out! We searched for cargo across thousands of Type 11 Secretion Systems (T11SS) in Proteobacteria and uncovered 2,500+ predicted secreted proteins, including 6 novel cargo types, with experimental verification of a new surface lipoprotein, Pls. doi.org/10.1099/mgen.0.001406
May 21, 2025 at 4:40 PM
New paper out! We searched for cargo across thousands of Type 11 Secretion Systems (T11SS) in Proteobacteria and uncovered 2,500+ predicted secreted proteins, including 6 novel cargo types, with experimental verification of a new surface lipoprotein, Pls. doi.org/10.1099/mgen.0.001406
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere https://journals.asm.org/doi/full/10.1128/msphere.00996-24?af=R
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere
We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in ...
journals.asm.org
June 3, 2025 at 5:44 AM
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria | mSphere https://journals.asm.org/doi/full/10.1128/msphere.00996-24?af=R
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly
#ISMEJournal from Roman Stocker, Mary Ann Moran labs
academic.oup.com/ismej/advanc...
#ISMEJournal from Roman Stocker, Mary Ann Moran labs
academic.oup.com/ismej/advanc...
Validate User
academic.oup.com
May 31, 2025 at 8:21 AM
Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly
#ISMEJournal from Roman Stocker, Mary Ann Moran labs
academic.oup.com/ismej/advanc...
#ISMEJournal from Roman Stocker, Mary Ann Moran labs
academic.oup.com/ismej/advanc...
Reposted by Chen Zhang 🇨🇳 🇯🇵 🇳🇱 🇺🇸
Sequence-based prediction of intermolecular interactions driven by disordered regions | Science https://www.science.org/doi/full/10.1126/science.adq8381?af=R
Sequence-based prediction of intermolecular interactions driven by disordered regions
Intrinsically disordered regions (IDRs) in proteins play essential roles in cellular function. A growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of amino acids but is instead ...
www.science.org
May 22, 2025 at 11:19 PM
Sequence-based prediction of intermolecular interactions driven by disordered regions | Science https://www.science.org/doi/full/10.1126/science.adq8381?af=R