It reminds me of the Three Body Problem (spoiler) where an intelligent particle interferes with the reproducibility of our physics, but in this case the saboteur is the supply chain itself
As a mostly comp biologist, I learned a lot re: antibody reproducibility issues from the Antibody Society's "Antibody Validation" series eps 01, 09, 10. Compelling argument that seq-verified recombinant Abs, not polyclonal or monoclonal Abs, are the future
www.antibodysociety.org/learningcent...
We thought a lot about how to deploy ππππππ·π·π°, and we are very proud of this implementation that integrates annotation+context+CoSearch+agent with FlashPPI on SeqHub!
I requested this feature yesterday - you are so fast! π
Definitely worth taking 10 min to check this out for your organism to see a prediction of what complexes/interacts
Proteinβprotein interactions (PPIs) are key to discovering and interpreting new biological functions.
Weβre excited to introduce ππππππ·π·π°: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.
New preprint! We propose "anergiobiosis" to describe microbial life at thermodynamic limits as a way of separating the physiological state from questions about aeonophilic extremophile specialization. ecoevorxiv.org/repository/v...
#Microbiology #Extremophiles #SubsurfaceMicrobiology #MicroSky
Upload your FASTA, CSV, or Genbank file. Generate annotations in seconds. Turn your data into a structured workspace.
SeqHub data tables make it easy to organize annotations, notes, links, and custom metadata as your analysis evolves.
Paul's great, and this is an important, arguably neglected, problem in microbiology!
Amazing! So, are we ready to go back to placing Eukaryota with morphological cladistics?
If you are interested in using AI to predict and test microbial (bacterial, archaeal) cultivation requirements, please reach out. We are ~waist deep in this already.
Co-convening "The art and science of microbial persuasion" at #ISME20 with Fengping Wang. Cultivation advances: methods, media, uncultured lineages. Coaxing reluctant microbes? Submit your abstract & join us in NZ!
isme.live.ws-django.co.uk/public/confe...
isme.live.ws-django.co.uk/public/confe...
Quantifying the oxygen preferences of bacterial communities using a metagenome-based approach www.biorxiv.org/content/10.6... #jcampubs
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)
The new genome browser tool.
𧬠#BacDive is also taking a long-awaited leap into the world of genomics with the debut of a genome browser ππ₯οΈ.
For the first time, BacDive now displays genomic information. The genome browser feature lists and visualizes #Bakta annotations of #INSDC genome assemblies.
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von KΓΌgelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
My fantastic department at CU Boulder is hiring a tenure-track Assistant Professor! This is a broad search spanning nearly all areas of biology. Applications are due Nov 13, 2025. Feel free to reach out to me with questions, and please share widely.
jobs.colorado.edu/jobs/JobDeta...
I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...
Phosphite oxidizers π€ Methanogens
In our new paper on βLithosyntrophyβ we show that phosphite oxidation drives methanogenesis through interspecies H2 transfer. Lithosyntrophy establishes a novel mechanistic link between the #phosphorus and carbon redox cycles
Woah, super cool! A class in how to piece apart metabolism in an enrichment culture, super interesting, and raises new questions of its own. Are you willing to speculate if there are any other lithotrophic metabolisms that involve syntrophy?
Yup the review I shared says this about terminal oxidases.
Perchlorate-reducing bacteria with Cld (super interesting, which I studied!) have so far always been facultative aerobes. Some obligate anaerobes without Cld can reduce perchlorate but ClO2 is removed chemically and no O2 is produced.
Well, GenomeSPOT uses amino acid frequency, so we think it reflects selection for aerobic or anaerobic metabolism. For gene-based, it depends. They can use O2-utilizing and O2-sensitive genes instead of just Cco, SOD, etc. One example: doi.org/10.1016/j.fr...
Yes! They use those enzymes to deplete (detoxify) oxygen, but have other enzymes that are sensitive to oxygen.
See: doi.org/10.1038/s415...
Possibly some genome annotations here: doi.org/10.1101/2023...
π₯ Excited to introduce Bacformer π¦ - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the βgrammarβ of how genes are arranged, interact and evolve.
Preprint π: biorxiv.org/content/10.1...
𧡠1/n
Our latest, lead by @ahoiching.bsky.social, uncovering physiological vulnerabilities and helping to explain growth rate limitation in SAR11.
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.biorxiv.org/content/10.1... #jcampubs
Very cool work. "The absence of cell cycle regulation genes may ... [predict] upper bounds on growth rates obtainable by these organisms" is a cool thought - we're all sick of not knowing *why* some taxa are harder to cultivate! Do you plan to expand on the prelim analysis?
The latest publication from our lab!
The famous "glomalin" from arbuscular mycorrhizal (AM) fungi is not a protein but a polysaccharide from AM fungi, so we renamed it "glomalose". Glomalin-related proteins are bacterial proteins stuck in this glomalose.
nph.onlinelibrary.wiley.com/doi/10.1111/...
Illustration showing a graduation ceremony, with speaker addressing graduates: βLet the example of my fluke success guide nearly all of you to crushing disappointmentβ.
Success in academia often has more to do with luck, patronage and the job market than βhard workβ.
Good academics acknowledge this.
I worked hard, but I was in the right place at the right time on occasion. Historians far more talented than I have fallen between the cracks.
