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 🇨🇳 🇯🇵 🇳🇱 🇺🇸
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...
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...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 19, 2025 at 6:43 AM
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...
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
NSF now planning to let POs largely decide what gets funded, and to send PIs reviews that are only 3-5 sentences long. They don't have to use outside reviewers (except maybe 1) and don't have to convene panels. (1/5)
NSF pares down grant-review process, reducing influence of outside scientists
Memo cites overburdened staff, but some say move also aims to elevate White House priorities
www.science.org
December 16, 2025 at 2:12 AM
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...
@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...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
doi.org
December 9, 2025 at 3:25 AM
🧬🦠🚨 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...
@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
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
December 8, 2025 at 3:04 PM
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
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...
www.biorxiv.org/content/10.6...
Systematic discovery of TIR-based immune signaling systems in bacteria
Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...
www.biorxiv.org
December 4, 2025 at 9:25 AM
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...
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-...
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
academic.oup.com
December 3, 2025 at 2:34 AM
🦠🧪🧬🚨 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...
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...
anvi-report-circularity
An anvi'o program. Predict contig circularity from paired-end read alignments in a given BAM file.
anvio.org
November 28, 2025 at 9:11 AM
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...
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/...
Mycobacterium #phage review by Graham Hatfull covering the state of the art
www.pnas.org/doi/10.1073/...
All the world’s a phage | PNAS
A renewed interest in bacteriophages has emerged from the explosive discovery of the
complex pan-immune bacterial defense system and a revival of t...
www.pnas.org
October 31, 2025 at 10:00 AM
#microsky #phagesky
Mycobacterium #phage review by Graham Hatfull covering the state of the art
www.pnas.org/doi/10.1073/...
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.
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.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 24, 2025 at 5:00 PM
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.
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 🇨🇳 🇯🇵 🇳🇱 🇺🇸
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...