Aaron Weimann 🇺🇦
@aaron_weimann
Researcher @Cambridge_Uni/@MRC_LMB working on infectious diseases, bacterial evolution, Pseudomonas aeruginosa, ML, AMR.
Check out Maciek's tweetorial for our new bacterial protein language model Bacformer, creating a unified representation of bacterial genomes with links to pre-print, code, tutorials and blog post: x.com/wiatrak_maciej…
💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.110… 🧵 1/n
Interested in MGEs? Check out our new short commentary paper 🧬 ⌚ about plasmid-dependent phages (PDPs): their history, the new wave of PDPs research, and their potential applications. Out in @NatureRevMicro👇
Rediscovering plasmid-dependent phages nature.com/articles/s4157… This Genome Watch highlights how renewed interest in phages targeting plasmid-carrying bacteria expands our knowledge of viral diversity, ecology, and evolution, key to developing safe biotherapeutics.
Josie Bryant (@Josie_M_B) and I have a 3yr joint postdoc project at Sanger & EBI (ESPOD) Topic: Developing new bioinformatic and modelling approaches for exciting new longitudinal microbiome datasets Project details: embl.org/editorhub/wp-c… To apply: ebi.ac.uk/research/postd…
Metagenomics postdoc fellowship available. We are looking for a talented individual who is willing to take on challenging datasets and develop new analytical approaches
Josie Bryant (@Josie_M_B) and I have a 3yr joint postdoc project at Sanger & EBI (ESPOD) Topic: Developing new bioinformatic and modelling approaches for exciting new longitudinal microbiome datasets Project details: embl.org/editorhub/wp-c… To apply: ebi.ac.uk/research/postd…
Interested on Bacterial Evolution? Check out our new Genome Watch 🧬 🔬👀 article about ✨Mutational Hotspots✨ out @NatureRevMicro @cazares_adr @cazares_dan nature.com/articles/s4157… rdcu.be/exiu6
Job alert: Join us for a postdoc in AI in genetics at @EMBL Heidelberg! Great collaboration with @Adrian Cortes @GSK, aiming to develop new tools to elucidate genetic effects using population-scale cohorts and single-cell readouts. Please share! embl.wd103.myworkdayjobs.com/de-DE/EMBL/det…
Exciting PhD studentship opportunity on understanding chemical permeability to advance antibiotic drug discovery @flotocambridge jobs.cam.ac.uk/job/50800/. Combines experimental approaches with in silico screening and generative AI.
If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc: sanger.wd103.myworkdayjobs.com/WellcomeSang... Incredibly exciting datasets on host-microbe interactions in the lung. Pls RT and reach out if you are interested
Tune into a Pseudomonas genomics webinar tomorrow at 11 UTC organised by @ESGEM_ESCMID to hear me present our paper on the evolution of Pseudomonas aeruginosa science.org/doi/10.1126/sc… and talks from Adesola Olalekan and Sara Cortes Lara. Register here: us06web.zoom.us/webinar/regist…
Incredibly excited to share that our manuscript was just published in @nature ! What a way to start the new year! 🎉 We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling
🚨New paper alert🚨 So happy to finally share this! now out @CellReports ✨ We explored the hierarchical structure that controls virulence in Pseudomonas🦠, finding a mutational hotspot that acts as a genetic switch for hypervirulence💀 and AMR💊 cell.com/cell-reports/f…
Now this is truly high throughput 🤯 “By tracking 140 million bacteria and generating over 20,000 in vitro time-kill curves, we can predict Mtb treatment outcomes in mice and human and link strain-specific survival (drug tolerance) in Mabs to clinical responses.” Congrats!!
💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.110… 🧵 1/n
Now published in bioinformatics, CELEBRIMBOR 'pangenomes from metagenomes' academic.oup.com/bioinformatics… I think reviewer comments helped make it better, so worth another look (at fig 1 particularly!)
Sam has then wrapped it all up in a nice snakemake pipeline CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs) which lets you go from MAGs to pangenome github.com/bacpop/CELEBRI…
Great pleasure to work with @shenwei356 on a new indexing and alignment scheme, called LexicMap: biorxiv.org/content/10.110… We have been working on uniformly reassembling, QC-ing and annotating all bacterial (+ now archaeal) data, & wanted to be able to do full alignment to it....
My PhD baby is finally in paper format (feat an annoying formatting glitch in Table 2). This has been a true labour of love. A story that started in 2019 and is no where near finished. @lizzy_darby @JessicaMABlair E. coli has a 7th RND pump. biorxiv.org/content/10.110…
We are excited to present our fantastic speaker lineup for the #SummerSchool for #AI in #Medicine! Join us and our world-leading experts from 9 to 13 September to start your AI journey as clinician or clinical student! Booking closes soon! Secure a spot: vanderschaar-lab.com/cambridge-ai-i…
“It is remarkable to see the speed with which these bacteria evolve and become epidemic and how they can specialize for a particular lung environment,” @aaron_weimann says of Pseudomonas aeruginosa. independent.co.uk/news/science/s…
It was great to discuss our paper with the amazing @zsaidso for the @ScienceMagazine podcast. Tune in from 17:50 science.org/content/podcas… to hear about how @LinkedIn Premium played a role in our discovery.
I'm in a Faculty of Medicine and a substantial number of people in this faculty don't understand why evolutionary biology is relevant to medicine. Papers like this are useful to make the case: science.org/doi/10.1126/sc…