lbarquist.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Presenting a new flexible web platform for sharing and integrating microbial omics data, including RNA-seq and transposon-insertion sequencing. Micromix: web infrastructure for visualizing and remixing microbial ‘omics data doi.org/10.1093/giga...

submitted 7 days ago • 0 comments

Roche SBX preprint out www.biorxiv.org/content/10.1...

submitted 2 days ago • 0 comments

New comment Call for prudent use of the term #hypervirulence in carbapenem-resistant #Klebsiella pneumoniae www.thelancet.com/journals/lan... #ClinMicro #IDSky #AMR #OpenAccess #OA

submitted 5 days ago • 0 comments

I spent some time cleaning up my repo demonstrating how to use the NCBI Datasets REST API to do automated and/or bulk retrieval of genomes, by accession or by taxonomy. It's not super well documented but it does all seem to work :). Enjoy!

submitted 3 days ago • 1 comment

Our paper describing the microGWAS pipeline was published yesterday in Microbial Genomics. Lots of fixes and additions to the code/documentation since the preprint, including a hard to reproduce bug that only showed up in a specific HPC 🥵 www.microbiologyresearch.org/content/jour...

submitted 14 days ago • 1 comment

If there's one thing you know about bacteria, it's that they're too small to see with the unaided eye, right? Wrong. Buried in the sediments around Caribbean mangroves is the largest known bacteria, Thiomargarita magnifica. It's the size of a human eyelash (~1 cm). (📷: Tomas Tyml)

submitted 5 days ago • 3 comments

Important work that changes the way we think about antibiotic resistance in vivo 🧪

submitted 5 days ago • 0 comments

I’m teaching a grad course for the first time (a bit terrifying 😅) and I’ve decided to write a short blog post after each lecture, that will highlight a key takeaway from it and reflect on what can be improved. First one ⬇️

submitted 5 days ago • 3 comments

Experimental evolution of evolvability | Science www.science.org/doi/10.1126/...

submitted 6 days ago • 0 comments

Brochado and Maier labs in Germany are looking for a PhD student to study horizontal gene transfer in bacteria. ENDAMR Marie Curie doctoral network (endamr.eu) - an amazing opportunity to work with top scientists in the field all around Europe! www.cmfi.uni-tuebingen.de/mariecuriephd

submitted 6 days ago • 0 comments

Exciting opportunity to do a PhD in Germany with two truly excellent PIs working at the cutting edge of gene regulation in gut pathogens and commensals!

submitted 9 days ago • 0 comments

Exciting opportunity to do a PhD in Germany with two truly excellent PIs working at the cutting edge of gene regulation in gut pathogens and commensals!

submitted 9 days ago • 0 comments

📣Fully funded PhD position available in our lab at @uniwuerzburg.bsky.social, in collaboration with Dr. Connolly at Newcastle University (@ruamicro.bsky.social). "Dissecting the RNA-centric landscape of microbiota-pathogen interactions in the gut”. 🦠 Apply here: www.uni-wuerzburg.de/karriere/sin...

submitted 12 days ago • 0 comments

TIL when you sort the codon wheel by the second base the quadrants align with the properties of the amino acids being coded for and also it looks like the mystic sigil of the coven of the four bases journals.asm.org/doi/pdf/10.1...

submitted 11 days ago • 2 comments

Just published: My (Janosch Hennig) view on the current capabilities of AF3 and similar for RNA and protein-RNA complex structure prediction plus a bit of forward looking: doi.org/10.1002/cbic...

submitted 13 days ago • 0 comments

New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!

submitted 18 days ago • 1 comment

My Departments vs Software Accuracy article is finally out -- with great support from the Editors, and some useful feedback from referees. doi.org/10.1093/bioa... #benchmarks #bioinformatics #genetics #software #compsci

submitted 22 days ago • 2 comments

And another funky sRNA in Caulobacter, from Fröhlich lab #microsky #rnasky #rnabiology 🦠 academic.oup.com/nar/article/...

submitted 21 days ago • 1 comment

Interested in collecting, sharing, and interacting with large collections of bacterial functional genomics data (RNA-seq, Tn-seq/TraDIS, etc.)? Check out our new web platform, Micromix, with case studies for Salmonella and Bacteroides! 🧫🧬🖥️🧪 Thread 1/n academic.oup.com/gigascience/...

submitted 22 days ago • 1 comment

The overview of AMR that you always wanted (someone else to write) - amazing! Truly brilliant paper with great figures! @lancetmicrobe.bsky.social www.thelancet.com/journals/lan...

submitted 21 days ago • 5 comments

Making LLMs run efficiently can feel scary, but scaling isn’t magic, it’s math! We wanted to demystify the “systems view” of LLMs and wrote a little textbook called “How To Scale Your Model” which we’re releasing today. 1/n

submitted 22 days ago • 3 comments

Interested in collecting, sharing, and interacting with large collections of bacterial functional genomics data (RNA-seq, Tn-seq/TraDIS, etc.)? Check out our new web platform, Micromix, with case studies for Salmonella and Bacteroides! 🧫🧬🖥️🧪 Thread 1/n academic.oup.com/gigascience/...

submitted 22 days ago • 1 comment

Most Shigella sonnei experimental work relies on a 70yr old lab strain that doesn’t reflect those circulating today - we are excited to share a (soon to be) publicly available set of genomes and isolates to fill that gap! An exciting part 2 featuring our favourite fish to follow very shortly… 🐟

submitted 22 days ago • 1 comment

Word on the street is that I am pretty good at helping people translate their domain expertise into productive Bayesian analyses, including designing models, implementing inferences, informing decisions, and summarizing results. I'm also available to hire, betanalpha.github.io/consulting/.

submitted 23 days ago • 1 comment

Don't forget to apply for the position as a Helmholtz Junior Research Group Leader at @helmholtz-hiri.bsky.social (HIRI) or @helmholtz-hioh.bsky.social (HIOH). ⏰ The application deadline on February 15 is coming up fast! 👉 More about the call: www.helmholtz-hzi.de/en/career/jo... @www.helmholtz.de

submitted 23 days ago • 0 comments

I'm very excited to share my first graduate research project! Check out our preprint which describes how data generated with directed evolution can be used to model the phenotypic effects of naturally-evolved sequence variants. (1/11) www.biorxiv.org/content/10.1...

submitted 27 days ago • 2 comments

#ResearchHighlight from Claire Chewapreecha @moru-mip.bsky.social Overcoming research challenges in resource-limited settings: perspectives from Thailand Invest in #LMIC talent for meaningful, lasting #impact Read more 👉 www.ndm.ac/tropmed.res-hi Full publication 👉 www.nature.com/articles/s41...

submitted 28 days ago • 0 comments

New preprint from the group just landed ‘Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut’ www.biorxiv.org/content/10.1... /1

submitted 30 days ago • 1 comment

This is an important problem. 👏

submitted 32 days ago • 0 comments

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

submitted 39 days ago • 2 comments

I'm excited to present my work at the IIMCB in Warsaw! If you're interested, you can join on Zoom: 🗓️23.01.2025 🕘09:15 AM CET 💻Zoom: bit.ly/3NxdIbY

submitted 36 days ago • 0 comments

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

submitted 36 days ago • 2 comments

This preprint makes a point that is valid for a lot of machine learning approaches. Organisms or genes are linked by evolutionary history; they are not independent. This results in correlation between learning and test sets, and often in over-optimistic evaluations of the methods' outcome.

submitted 39 days ago • 3 comments

Totally been sleeping on YDF, really feels like the proper successor to XGB. I mean, look at this classification report:

submitted 39 days ago • 5 comments

Very excited that my 1st first-author paper has just been published!! We present a novel mutant screening technique that can rapidly identify 100s of antibiotic resistance mutations, while evaluating how likely they are in different genetic backgrounds. www.nature.com/articles/s41...

submitted 39 days ago • 2 comments

Important!

submitted 39 days ago • 0 comments

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

submitted 39 days ago • 2 comments

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n www.biorxiv.org/content/10.1...

submitted 42 days ago • 2 comments

📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social

submitted 43 days ago • 2 comments

Happy to share our latest work published in @pnas.org In collaboration with @yjchao.bsky.social , we uncovered an RNase III-processed sRNA, ManS, that orchestrates sialic acid metabolism in Salmonella enterica during gut colonization. Link: doi.org/10.1073/pnas...

submitted 46 days ago • 3 comments