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Jess Chen

@drjesschen.bsky.social

Mom, wife, birder, bike commuter, and microbial bioinformatician.

55 Posts431 Follower322 Folgt
Mychal Threets@mychal3ts.bsky.social · last mo.

Vaccines do not cause autism. Autism is not something to be fixed. Autism is not something to be cured. My autistic friends, you are autistic joy. Thank you for being wonderful you ✨ Sincerely, Your Autistic Library Friend 💛

Mychal smiles in a shirt that reads, “Be a buddy not a bully”
Jess Chen@drjesschen.bsky.social · last mo.

Beyond honored to be the recipient of the 2026 Maurice Weber Laboratorian Award. Thanks to Fred Weber for sponsoring this award and for presenting me with this phenomenal Baker microscope from 1860!

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Will Matlock@wtmatlock.bsky.social · 2mo ago

🚨 New preprint with @annadewar.bsky.social 🚨 Do plasmids “ameliorate” towards their hosts? Maybe… We show that the classic plasmid-host GC correlation is confounded by population structure, and argue that plasmid mobility shapes the opportunity for host-associated compositional evolution.

Mobility shapes plasmid GC content evolution

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

doi.org

Thomas House@tah-sci.com · 4mo ago

Regarding Ebola - the best genomic data and estimates we have now suggest a time to most recent common ancestor around the start of April. If we ballpark at 500 cumulative cases 50 days after this, this implies a doubling time of around > virological.org/t/initial-ge...

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda

2026-05-21 Update - Temporal Tree Estimate See the top post for authors, collaborators and acknowledgments. Figure 1 | Temporal phylogenetic reconstruction of the first 10 genomes using BEAST v10....

virological.org

Kai Kupferschmidt@kakape.bsky.social · 4mo ago

While everyone is watching hantavirus I'm actually much more eager to learn more about the Ebola outbreak in DRC's Ituri Province that Africa CDC has confirmed. Early information makes it sound very large for an outbreak that has just been reported: "about 246 suspected cases and 65 deaths"

Steven Robbins@stevenjrobbins.bsky.social · 8mo ago

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments? My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database. Please share around for visibility.

Victor de Lorenzo (CNB, Madrid)@vdlorenzo.bsky.social · 8mo ago

How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio

Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...

journals.asm.org