Weโve published a wee pilot study assessing the utility of metagenomics & full-length 16S sequencing for the detection of seasonal pathogens (and AMR) in our local urban recreational swimming hot-spot
Check it out if youโre into that stuff :)
www.microbiologyresearch.org/content/jour...
Can't wait to release a 10-year-old birthday version for SeqKit!
- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads
Thank you all, dear contributors and users!
I'll keep maintaining it.
github.com/shenwei356/s...
๐งต New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive โ by rewiring RNA turnover.
๐ www.biorxiv.org/content/10.6...
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics
๐Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
www.doi.org/10.1099/mgen.0.001644
๐ฅ๏ธ๐งฌ๐ป
#AcademicSky
#MicroSky
#IDSky
๐งช๐งซ๐ฆ
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...
๐๏ธโก If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
An ideal interviewee is someone whoโs spent a bit more time on formatting results than theyโd prefer ๐ The bioinformatics domain doesnโt matter much since Iโd like to gather diverse feedback
๐งฌ๐ฅ๏ธ Iโm building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools
Now looking for a few bioinformaticians for a brief usability feedback interview ๐ฉโ๐ป
DM me or respond here if interested ๐
Me getting back to sending nagging emails on January 6th when people return to work from the Christmas break
New preprint to close out the year! Led by Alana Papula and together with Daniel Fisher, we used single-cell genomes to infer the evolution of Prochlorococcusโone of the most abundant and genetically diverse bacteria on Earth. Check it out here: doi.org/10.64898/202...
Rapid and Consistent Genome Clustering for Navigating Bacterial Diversity with Millions of MAGs and Isolates www.biorxiv.org/content/10.6... #jcampubs
SIR of susceptible, infectious, and recovered compartments with individuals who take short "trips" to other locations away from home, plus diagram of four phylogenetic patterns of host-mediated infection (resident-to-resident, visitor-to-resident, resident-to-visitor, visitor-to-visitor).
New preprint modeling pathogen phylogeography, where infected hosts spread disease through short "trips" between locations. Very fun collaboration with the brilliant @albertchristian.bsky.social and Ammon Thompson.
www.medrxiv.org/content/10.6...
Collapsed phylogenetic tree of the Klebsiella pneumoniae Species Complex (top) and the presence of metabolic capabilities (bottom), leading to lineage-specific metabolic networks and traits
Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org ๐งช plos.io/4qdC2B2
Sharing a Shiny app I've been working on at
@leviwaldron1.bsky.social 's lab: BugSigDBEnrich. The app lets you compare a list of bacteria with published microbial signatures curated in bugsigdb.org.
shiny.sph.cuny.edu/BugSigDBEnri...
#rstats #microbiome #microbiomeresearch
A very cool app to compare a list of microbes with microbial signatures in BugSigDB and Bugphyzz ๐งซ #microbiome
Weโre excited to share our latest study that reshapes our understanding of Mycobacterium tuberculosis (Mtb) lipid composition, with major implications for drug discovery, immunity, and vaccine development.
www.nature.com/articles/s41...
A thread.
Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky
๐พ mlst 2.25.0 has been released!
Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases.
#bioinformatiocs #microbiology #genomics
github.com/tseemann/mls...
Antibiotic-resistant typhoid infections are a growing global health problem, made worse now by emerging carbapenem resistance.
tinyurl.com/4uy7f6y3 by Thirumoorthy et al.
๐งฌ #Bioinformatics AEGIS #PostdocJobs in metagenomic pipelines & HPC: Ancient Environmental Genomics at @ucph.bsky.social to reconstruct ecosystems and develop climate-resilient crops. ๐
Deadline: Jan 4, 2026.
Mikkel Winther Pedersen (mwpedersen@sund.ku.dk)
#AcademicJobs #aeDNA #ClimateChange
New preprint from the lab is out! ๐ฅณ
We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions.
www.biorxiv.org/content/10.6...
๐
Our recent paper in npj Antimicrobials and Resistance is a great example of scientific serendipity: after staring at thousands of bacterial growth curves over many studies, we started wondering whether the curve shapes themselves carry mechanistic information 1/9 ๐ฆ ๐งช
www.nature.com/articles/s44...
Reading the structured abstract alone should set off a half dozen statistical alarms in any scientists head.
The fact that this found its way into Science makes me wonder how we drive home those stats 101 lessons and make them intuitive.
www.science.org/doi/10.1126/...
This paper by Celentano et al. on scalable simulation under the birth death is one of my favourites for the year! It introduces some elegant thinning that has been sorely needed. Fantastic to pave the way forward for future simulation-heavy inference, including neural Bayes!
doi.org/10.1073/pnas...
I really love this model which brings real mechanistic insight to the barcode data which I had previously found interesting but mysterious!
elifesciences.org/reviewed-pre...
We just posted a new preprint describing an anti-MRSA phage targeting the terminal ฮฒ-GlcNAc on wall teichoic acid. The host becomes phage resistant, but methicillin susceptibility is the consequence in some pathways; cotreatment with methicillin is synergistic at achievable MICs. #phagesky #IDsky
#microsky #phagesky
The 3rd (? Lost track!) manuscript on a CRISPR/anti-CRISPR -based transposon tool to study gene essentiality in #phages
www.biorxiv.org/content/10.6...
We would be very happy to host a #bioinformatics #postdoc within this call!
If you have expertise in #gutmicrobiota, #metagenomics, #machinelearning and/or #multiomics approaches, please get in touch to discuss potential ๐งฌ& ๐ฅ๏ธ projects.
Please share!
@MicroSky
www.scilifelab.se/data-driven/...
๐ ๐๐ฆญ๐๐ง I have a PhD position available (4 years, start Mid-2026) at NRM Stockholm to work on the macrogenomics of sea warming.
Apply here:
recruit.visma.com/spa/public/a...
#PhD #MarineGenomics #ClimateChange #EvolutionaryBiology #PopGen #Bioinformatics #conservationgenomics
