Thanks for having me!
09.03.2026 04:59
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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!
๐ฆ โ๐ง๐ต๐ฒ ๐๐ถ๐ฟ๐๐๐ฒ๐ ๐๐ต๐ฎ๐ ๐ฒ๐ฎ๐ ๐ฏ๐ฎ๐ฐ๐๐ฒ๐ฟ๐ถ๐ฎ ๐ฐ๐ผ๐๐น๐ฑ ๐๐ฎ๐๐ฒ ๐๐ โ ๐ฏ๐๐ ๐ต๐ผ๐?โ
Historian @kirchhelle.bsky.social chats with ๐ ๐ฎ๐ฟ๐๐ต๐ฎ ๐๐น๐ผ๐ธ๐ถ๐ฒ & ๐๐ฎ๐บ๐ฒ๐ ๐๐ฏ๐ฑ๐ฒ๐ป about revival of phage biology & phage therapy as antibiotics fail.
๐ง 2024 BBC Radio 4 โ 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
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.
๐จ New pre-print! ๐จ 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)
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.๐งต
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!
Thrilled to announce that Iโve just opened my research lab at @helmholtz-hiri.bsky.social !
A huge thank you to my mentor Roi Avraham (and lab members!) for the incredible training and support that made this possible.
The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.
Our new paper in @natcomms.nature.com is now online-early!
We describe independent evolution of bacterial genomes of only ~50โ52 kb โ the smallest known outside cellular organelles โ revealing striking convergence toward minimal gene sets.
๐ doi.org/10.1038/s414...
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: โWhat are the downstream molecular consequences of early genome erosion?โ
Happy to share a preprintโthe last chapter of my dissertation with @mcsymbiont.bsky.social and Coโon what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
What a beautiful dream.
BackToBack #PhageSky in @nature.com
A pore-forming antiphage defence is activated by oligomeric phage proteins
-from Maxwell & Norris
www.nature.com/articles/s41...
Bacterial immune activation via supramolecular assembly with phage triggers
-from Laub & Ghanbarpour
www.nature.com/articles/s41...
All you want for christmas is.... transposon mutagenesis!
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Still lots of time to apply for this exciting project with us. Please share and encourage interested students to get in touch.
Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...
Always good to start the year with a new preprint. We charted DNA methylation in Salmonella enterica: www.biorxiv.org/content/10.64898/2026.01.27.702048v1.
Why should microbiologists be interested in historical infection remedies, and how can we best investigate them for antimicrobial discovery? Thoroughly enjoyed co-writing this Microbiology Primer with @tosinorababa.bsky.social www.microbiologyresearch.org/content/jour... #MicroSky #Ancientbiotics
Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...
We are looking for a junior group leader in RNA biology to join us in Wรผrzburg at the @helmholtz-hiri.bsky.social !
A generous funding package, a great collaborative environment, and a beautiful city are all included :)
Deadline for application is Feb 15; more information below ๐
Our new paper on Insertion Sequences (IS) in #Klebsiella
- Lineages have vastly different IS loads and profiles
- An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution.
www.microbiologyresearch.org/content/jour...
๐ข We are hiring ๐ข 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology