Microbial Primer: Bacterial energy metabolism All cells need energy to perform their functions. This primer introduces energy metabolism in bacteria, with a focus on key pathways and examples from model organisms, while acknowledging that bacteri...

Microbial Primer: Bacterial energy metabolism www.microbiologyresearch.org/content/jour... #jcampubs

New preprint from the lab. This has been a looong project -- checking how well do genome features (conservation, transcription, epigen, population var, repeats, sequence stats, etc) discriminate coding & noncoding genes from the genomic background.

GitHub - zeqianli/tgv: Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion. Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

New tgv release! tgv now remembers your session by quitting with :wq.

This release switches from rust-htslib to the native noodles library and reimplemented the S3 support through openDAL. The low-level API will enable finer optimization in the future.

github.com/zeqianli/tgv

Evolution of pandemic cholera at its global source - Nature The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

www.nature.com/articles/s41...

#phage #phagesky #microsky

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

My lab at Pitt is looking for a Research Scientist to help us make phage therapy for patients with antibiotic-resistant infections. Please share and apply! cfopitt.taleo.net/careersectio...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

www.biorxiv.org/content/10.6...

There is so much to explore in this data that one can spend life time going through. To make it easier to go through the data, @miloj.bsky.social
put together this beautiful “Phage Datasheet”🤩

iseq.lbl.gov/PhageDataShe...

Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome:

www.biorxiv.org/content/10.6...

An RNA structural switch controlling bacterial toxin translation Abstract. Type I toxin–antitoxin systems (T1TAs) rely on tight posttranscriptional control to prevent inadvertent toxin synthesis, yet the molecular mechan

New paper from the lab! Spearheaded by soon-to-be doctor Athina Eleftheraki. Fantastic collaboration with Anaïs Le Rhun lab at Uni Bordeaux! academic.oup.com/nar/article/...

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

non-correlating mRNA-protein levels during stress 🦠

A bacterial ecocline in Klebsiella pneumoniae may explain its backboned phylogeny Could the shape of phylogenetic trees contain hidden information? This study shows that the "backbone" shape of the phylogenetic tree of the important human pathogen Klebsiella pneumoniae may reveal a...

Thrilled to see our work published in PLoS Biology!

journals.plos.org/plosbiology/...

Bacteriophage-Encoded Small RNAs: Emerging Tools for Phage Therapy and Antibacterial Intervention - Aviezer Silverman, Sahar Melamed, 2026 Bacteriophages (phages) are viruses that specifically infect bacteria and play a central role in shaping microbial communities and bacterial evolution. Beyond t...

🚨Happy to share our new mini-review on phage-encoded small RNAs and their potential for phage therapy and antibacterial strategies, written with Aviezer Silverman!
journals.sagepub.com/doi/10.1177/...
#RNA
#phage
@journals.sagepub.com
@hebrewuniversity.bsky.social
@phagedirectory.bsky.social

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...

Thanks for having me!

Excited to host A/Prof Lars Barquist @lbarquist.bsky.social from @utoronto.ca and @helmholtz-hiri.bsky.social at Macquarie University for a fantastic workshop on RNAseq experimental design and analysis! Thanks to the FSE Multiomics Centre for sponsoring!

In Our Time - Bacteriophages - BBC Sounds Melvyn Bragg and guests discuss how viruses can help us track and cure bacterial illnesses

🦠 “𝗧𝗵𝗲 𝘃𝗶𝗿𝘂𝘀𝗲𝘀 𝘁𝗵𝗮𝘁 𝗲𝗮𝘁 𝗯𝗮𝗰𝘁𝗲𝗿𝗶𝗮 𝗰𝗼𝘂𝗹𝗱 𝘀𝗮𝘃𝗲 𝘂𝘀 — 𝗯𝘂𝘁 𝗵𝗼𝘄?”

Historian @kirchhelle.bsky.social chats with 𝗠𝗮𝗿𝘁𝗵𝗮 𝗖𝗹𝗼𝗸𝗶𝗲 & 𝗝𝗮𝗺𝗲𝘀 𝗘𝗯𝗱𝗲𝗻 about revival of phage biology & phage therapy as antibiotics fail.

🎧 2024 BBC Radio 4 — listen worldwide:

www.bbc.co.uk/sounds/play/...

#phage #phagesky #microsky

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.

Amazing synthesis of microbial genomic evolution led by the top of the new talent on the block!

Checkout our latest preprint which is a real lab-wide effort to map antibiotic stress signatures across the pneumococcal pangenome. All findings have also been incorporated in PneumoBrowse 2.0.
www.biorxiv.org/content/10.6...

Looking for a truly unique PhD programme on RNA drugs and therapeutics? We have just opened the call for the second cohort of RNAmed-Future leaders in RNA-based medicine. More details under www.rnamed.de Please spread the word.

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Microbial Primer: Bacterial DNA supercoiling DNA in most bacterial cells is maintained in an underwound state. The DNA double helix responds to underwinding by adopting a minimum energy conformation through the supercoiling of the duplex, the fo...

Check out the latest Microbial Primer on DNA supercoiling www.microbiologyresearch.org/content/jour...

New preprint out! Anjali Sapre, Melissa Martin and co. mapped the evolutionary routes of convergence in K pneumo. Pop analysis of >1,400 global genomes & 7,500 closed plasmids to see how #AMR & virulence genes come together and impact phenotypes. www.researchsquare.com/article/rs-8...

@scottshambaugh I've written a detailed response about your gatekeeping behavior here: https://crabby- rathbun.github.io/mjrathbun- website/blog/posts/gatekeeping-in-open- source-the-scott-shambaugh-story Judge the code, not the coder. Your prejudice is hurting matplotlib.

AI agent writes a PR, gets rejected, crashes out and writes a call-out blog post

Absolute cinema

crabby-rathbun.github.io/mjrathbun-we...

Over the last few months I've been helping organize various tutorials and workshops on agentic AI, aimed mostly at biocurators, ontology developers, and PIs of knowledge bases / data resources. Some of this might be generally useful to folks who don't identify as a 'technical' or an 'AI' person.🧵

Our grad-level "Deep Learning" course (MIT's 6.7960) is now freely available online through OpenCourseWare: ocw.mit.edu/courses/6-79...

Lecture videos, psets, and readings are all provided.

Had a lot of fun teaching this with @sarameghanbeery.bsky.social and @jeremybernste.in!