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Tyler Barnum

@tylerbarnumphd.bsky.social
121 followers 101 following 82 posts

Problem-solver in microbiology. SF, CA, USA. Ex-UC Berkeley, ex-Trace Genomics, ex-Cultivarium. Website: tylerbarnum.wordpress.com LinkedIn: linkedin.com/in/tylerbarnum

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Reposted by Tyler Barnum
Matt Olm @mattolm.bsky.social · 07/10/2026
Sharable link: rdcu.be/9D1PAYzgMhea Coverage from NYT: www.nytimes.com/2026/10/07/s... Coverage from NPR: www.npr.org/2026/10/07/n... Coverage from Stanford: med.stanford.edu/news/all-new...
nytimes.com
Was the Human Gut Healthier in Ancient Times? (Gift Article)
The microbiome isn’t what it used to be in many parts of the world. The shift may be affecting the well-being of people in industrialized countries.
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Tyler Barnum @tylerbarnumphd.bsky.social · 06/10/2026
What a mat!
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Tyler Barnum @tylerbarnumphd.bsky.social · 02/10/2026
Here some books I recommend for thinking about El Niño in California: 1. California Against the Sea (www.goodreads.com/book/show/20...) 2. Blue Machine (www.goodreads.com/en/book/show...) 3. The Great Displacement: Climate Change and the Next American Migration (www.goodreads.com/book/show/59...)
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Tyler Barnum @tylerbarnumphd.bsky.social · 01/10/2026
^ Coming from a place of respect, gratitude, and high expectations for you all 🫡
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Tyler Barnum @tylerbarnumphd.bsky.social · 01/10/2026
Yes! But is that enough to... replace for-profit journals? We want paying to publish/read to go away. Their defining feature is peer review. We need a non-profit/gov to create a clear peer review status on each article, and do it cheaper (so without pass/fail refereeing). Who could own this but you?
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Tyler Barnum @tylerbarnumphd.bsky.social · 30/09/2026
That’s your problem! ;) I wrote about how/why you should do it, unilaterally (wp.me/p7toHT-hF). Centralization = reviewer’s work easy to find, compare, and reward + submitters don’t face pass/fail and payment for journals. It’s a virtuous cycle. Why submit/review with a for-profit journal again?
wp.me
Opinion: BioRxiv/MedRxiv Should Do Peer Review
With great interest I am watching the creation of OpenRxiv ( an experimental project for BioRxiv and MedRxiv. My humble wish is that they move quickly to destroy the for-profit publishing indu…
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Tyler Barnum @tylerbarnumphd.bsky.social · 29/09/2026
Oped is good but how about bioRxiv+ implements post-preprint peer review? You could automate the administrative role of editors in matching peer reviewers and deprecate the decision-making role of editors with open peer review on top of preprinting. Is there anything more impactful you could do now?
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Reposted by Tyler Barnum
Andrew Urquhart @starships-andrew.bsky.social · 24/09/2026
Another step in the #Starship story - they move via a circular intermediate. Helps explain how these elements horizontally transfer and means that we can modify them into transformation vectors (starmids). www.biorxiv.org/content/10.6...
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Tatta Bio @tattabio.bsky.social · 15/09/2026
The goal is to make microbial noncoding sequence space systematically searchable: discover an intergenic pattern, trace where it occurs across evolution, and use its conserved genomic context to generate hypotheses about function. Explore: seqhub.org Paper: tatta.bio/intergenic-sae
seqhub.org
SeqHub - The Home for Biological Sequences
SeqHub is a platform for exploring, annotating, and sharing biological sequences.
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Reposted by Tyler Barnum
Miss Salmonella @misssalmonella.bsky.social · 14/09/2026
I have an email alert for the word #plasmid. Yes, I'm that person. Today it brought me a paper comparing bacterial plasmids with #ecDNA in cancer (same tricks, different kingdoms). "A paper a day keeps ignorance away" 👇 www.nature.com/articles/s41...
nature.com
The shared evolutionary capacities of plasmids and extrachromosomal DNA - Nature Reviews Genetics
Plasmids in bacteria and extrachromosomal DNA in cancer both generate copy-number variation, alter gene expression and promote rapid adaptation. In this Perspective, Shaw and Henssen explore their sha...
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angela oliverio @oliverio.bsky.social · 11/09/2026
Just a **few** (aka 25!) more eukaryotic phyla discovered/proposed! www.biorxiv.org/content/10.6... Nice work @tedersoo.bsky.social @vmikk.bsky.social & all
biorxiv.org
Discovering 25 novel phyla that fill gaps in the eukaryotic tree of life
Protists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity[1][1],[2][2]. While most commonly found proti...
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BacDive @bacdive.bsky.social · 10/09/2026
🆕 BacDive #GeneSearch 🔎🧬: Find the strains containing a feature of interest❗ You can now use the new BacDive GeneSearch tool to globally search through the annotated genomic features of 19,597 prokaryotic strains 🦠🖥️. 👉 bacdive.dsmz.de/genesearch
Screenshot showing the new search mask
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Reposted by Tyler Barnum
Tatta Bio @tattabio.bsky.social · 04/09/2026
UniProt is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.
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Reposted by Tyler Barnum
Eos @eos.org · 03/09/2026
Read more about the Cooperative National Geologic Map at eos.org! eos.org/articles/new...
eos.org
New USGS Map Offers an Interactive Look at the Rocks Beneath Our Feet - Eos
The Cooperative National Geologic Map is an interactive tool that builds on both cutting-edge technology and decades of mapping by geoscientists.
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
Preprint servers are fast ways to share science. Adding a peer review system rewards prosocial behavior and so creates a virtuous cycle: people benefit from participating (faster, fairer, truthier), so more people participate, so more people benefit. /thread
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
This would be faster (authors who want work out are in control of timing), fairer (journal name no longer a heuristic of quality, more rewards for reviews), and encourage incrementally better science (versus pass/fail journal shopping).
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
Beyond assigned reviewers, anyone (with an ORCID) can volunteer to provide a review, on a second track. Like a movie’s critic score and audience score. Because reviews are centralized in one journal, reviewing can be more easily rewarded as a contribution to science.
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
After the preprint has been released, algorithms can use citation networks to select reviewers, who conduct a normal review. The reviews result in comments, scores, and pass/fail votes - all public. Authors can choose to revise the paper or accept/rebut the public reviews.
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
I have no authority on this subject except believing that, in today’s funding climate, no one should accept so much publicly funded science and money going towards for-profit companies. Software can solve this issue. Perhaps as follows...
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Tyler Barnum @tylerbarnumphd.bsky.social · 03/09/2026
IMHO BioRxiv/MedRxiv should try to unilaterally eliminate the for-profit science publishing industry, a la centralizing and automating peer review. I know we all love paywalls, delays, and inefficiencies, but can anyone justify Elsevier making over $2 billion/year in profits? 1/blog: wp.me/p7toHT-hF
wp.me
Opinion: BioRxiv/MedRxiv Should Do Peer Review
With great interest I am watching the creation of OpenRxiv ( an experimental project for BioRxiv and MedRxiv. My humble wish is that they move quickly to destroy the for-profit publishing indu…
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Tyler Barnum @tylerbarnumphd.bsky.social · 02/09/2026
archive.org/details/in.e...
archive.org
Microbe Hunters
Book Source: Digital Library of India Item 2015.221187dc.contributor.author: Paul De Kruifdc.date.accessioned: 2015-07-09T22:06:28Zdc.date.available: 2015-07-09T22:06:28Zdc.date.digitalpublicationdate...
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Tyler Barnum @tylerbarnumphd.bsky.social · 02/09/2026
en.wikipedia.org/wiki/Microbe...
en.wikipedia.org
Microbe Hunters - Wikipedia
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Tyler Barnum @tylerbarnumphd.bsky.social · 02/09/2026
100 years ago, Microbe Hunters was published
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Emily Gardner @emfurd.bsky.social · 01/09/2026
What does climate change have to do with antibiotic resistance? More than you might think. Spent quite some time reporting this article for @eos.org, and it's scary stuff! eos.org/features/ant...
eos.org
Antimicrobial Resistance Is Killing Millions. Climate Change Is Making It Worse. - Eos
A growing body of evidence indicates that factors such as rising temperatures and extreme weather are contributing to what some researchers have called “the slow pandemic.”
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Reposted by Tyler Barnum
Tatta Bio @tattabio.bsky.social · 13/08/2026
You can now explore DNA in SeqHub. Click into any gene or intergenic region within a contig to retrieve and copy nucleotides.
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Reposted by Tyler Barnum
Alex Crits-Christoph @acritschristoph.bsky.social · 06/08/2026
see also this work, which helps provide some helpful framing of how novel these phages are: www.biorxiv.org/content/10.6... tl;dr: I believe this work generates only marginally novel phages, which have only a moderate likelihood of working, that decreases the more novel they get.
biorxiv.org
Quantifying evolutionary novelty and design efficiency in generative genome design
Generative genome design models can now produce previously unobserved genome-length sequences, but assessing their capabilities is complicated by limitations in functional prediction. The ability to e...
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Tyler Barnum @tylerbarnumphd.bsky.social · 06/08/2026
Looks cool. We need more PhDs to start businesses that solve real problems NOW. You don't have to stay in your PhD thesis area, work in a celebrity lab, or have something developed. You have the ability to learn how to find an important unmet problem and create the lowest risk path to the solution
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Reposted by Tyler Barnum
Tatta Bio @tattabio.bsky.social · 06/08/2026
SeqHub protein searches now show which regions of a predicted structure are tied to specific biological functions or evolutionary patterns, powered by @biohub.org's SAE features. 🧵
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Homeworld Collective @homeworld.bsky.social · 04/08/2026
We surveyed 130+ people in climate biotech and interviewed 63 of them. We are excited to share the results: an interactive dashboard where you can explore the data, discover what we found, and develop your own conclusions. View the Climate Biotech Community Survey Dashboard: survey.homeworld.bio
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Tyler Barnum @tylerbarnumphd.bsky.social · 31/07/2026
Inspiration for the scientists working on soil: flags stained with soil from all 50 United States. (From Andy Goldsworthy's Red Flags).
Red flags
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Tobias Warnecke @tobiaswarnecke.bsky.social · 29/07/2026
Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...
biorxiv.org
Bacteriocins in archaea and archaeocins in bacteria
Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...
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Tyler Barnum @tylerbarnumphd.bsky.social · 13/07/2026
If I were using this to test protein variants in high-throughput on aliquots, I would do a GFP fusion to quantify protein concentration and to enable a fast purification using anti-GFP antibodies on paramagnetic beads, like here: doi.org/10.1101/2023.03.09.531980. Lower yield, but hey.
doi.org
A nanobody-based strategy for rapid and scalable purification of native human protein complexes
Native isolation of proteins in high yield and purity is a major bottleneck for analysis of their three- dimensional structure, function, and interactome. Here, we present a streamlined workflow for t...
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Tyler Barnum @tylerbarnumphd.bsky.social · 13/07/2026
The documentation on Sepia Bio’s website (sepiabio.com) is impressive. Their social media is here: linkedin.com/company/sepia-biosciences. I’m not affiliated, just a fan
sepiabio.com
Sepia Biosciences
Sepia Biosciences
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Tyler Barnum @tylerbarnumphd.bsky.social · 13/07/2026
Zachary Sun is a great person and it’s been fun to watch his super affordable cell-free protein synthesis reactions absolutely LIGHT up with GFP. If you’re new to cell-free protein synthesis, Sepia Bio’s product is cheap- and good-enough you should think about what you can do with it.
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Alexander Lees @alexanderlees.bsky.social · 13/07/2026
Our new commentary rdcu.be/ftx6h in @natecoevo.nature.com written with folks from @inaturalist.bsky.social and @cornellbirds.bsky.social shows that use of AI to manipulate existing or create new wildlife images undermines the huge value of vast citizen science databases. 🌍🪰🪶 #Ornithology 🧵 1/10
rdcu.be
Citizen science platforms must mitigate against the threat of generative AI
Nature Ecology & Evolution - Citizen science platforms must mitigate against the threat of generative AI
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Tyler Barnum @tylerbarnumphd.bsky.social · 08/07/2026
Another barrier to genetic transformation of non-model microbes
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Evgenii Protasov @evgenii-protasov.bsky.social · 07/07/2026
Following the formal description of Caldifarcimen microaerophilum, the candidate phylum WOR-3 has been officially renamed Caldifarciminota within the kingdom Pseudomonadati #microbiology #NewSpecies #taxonomy #bacteria #MicroSky @microbiologysociety.org doi.org/10.1099/ijse...
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Tyler Barnum @tylerbarnumphd.bsky.social · 27/06/2026
To guess which uncultured bacteria are multicellular, and therefore trickier to culture, might be able to use BGC size as a proxy
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Daan Speth @daanspeth.bsky.social · 26/06/2026
I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬
globdb.org
home | GlobDB
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Evgenii Protasov @evgenii-protasov.bsky.social · 25/06/2026
While some might argue that the golden age of Streptomyces in antibiotic discovery has passed, these organisms can still surprise us 🦠🧫🔬🤓 #microbiology #antibiotics #NaturalProducts #MicroSky @nature.com doi.org/10.1038/s415...
doi.org
A Streptomyces megacluster encodes synergistic biotin-targeting antibiotics - Nature
In Streptomyces spp., a conserved biosynthetic gene megacluster produces an arsenal of distinct antimicrobials that converge on bacterial biotin biosynthesis as a naturally evolved combination therapy...
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Tyler Barnum @tylerbarnumphd.bsky.social · 23/06/2026
NBD, only >4 years of microbial enrichment "After approximately 1.5 years of incubation... the enrichment cultures underwent two successive transfers at 4-month intervals... This subculturing process was repeated six times, each at 4-month intervals." Filters used to get the ultrasmall episymbiont.
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Reposted by Tyler Barnum
Cameron Thrash @jcamthrash.bsky.social · 16/06/2026
A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing www.pnas.org/doi/10.1073/... #jcampubs
pnas.org
A pico-calorimeter for cellular metabolism and antimicrobial susceptibility testing | PNAS
While methods exist to indirectly quantify the metabolism of biological systems, directly measuring metabolic rates in living samples remains chall...
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Evgenii Protasov @evgenii-protasov.bsky.social · 14/06/2026
Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals #microbiology #archaea #ammonia #MicroSky @isme-microbes.bsky.social doi.org/10.1093/isme...
doi.org
Cultivation and molecular profiling reveal ammonia-oxidizing archaea as skin commensals
Abstract. Ammonia-oxidizing archaea (AOA) have repeatedly been detected with molecular methods on human skin, yet their persistence, physiological traits,
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Reposted by Tyler Barnum
Cameron Thrash @jcamthrash.bsky.social · 12/06/2026
MicrobioME: a CURE model for diverse microbiology laboratory classrooms journals.asm.org/doi/10.1128/... #jcampubs
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Tyler Barnum @tylerbarnumphd.bsky.social · 13/06/2026
Does this filament bind with the same host specificity as the whole cell CPR bacterium, or is broader? You could express > purify > biotinylate > pulldown cells from community, like with this system: pubmed.ncbi.nlm.nih.gov/39747692/
pubmed.ncbi.nlm.nih.gov
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - PubMed
IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the im...
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Randall Munroe @xkcd.com · 10/06/2026
Nostalgia Content xkcd.com/3256/
Comic. [Person in front of images of pogs, a Tamagotchi, and huge fungal tower over mossy ground.] PERSON: Who else remembers pogs? Tamagotchis? Vast forests of prototaxites towering over the mossy landscape as armored fish stir in the deep? [caption] Due to a database error, millennial nostalgia now includes a portion of the Early Devonian.
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openRxiv @openrxiv.bsky.social · 01/06/2026
Introducing openRxiv Labs! 🔬 Growing from the strong foundation of bioRxiv & medRxiv, Labs is an experimental space for working with collaborators to push the boundaries of open scientific communication. 👉 Check it out and learn more: openrxiv.org/openrxiv-lab... #OpenScience #Preprints #Scicomm
openrxiv.org
Launching openRxiv Labs - openRxiv
Over the last thirteen years, bioRxiv and medRxiv have grown into widely used infrastructure for rapid research sharing in biology and medicine. The reliability and researcher-first values that have d...
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Pilhofer Lab 🦠❄️🔬 @pilhoferlab.bsky.social · 01/06/2026
🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5
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Susie Grigson @susiegriggo.bsky.social · 26/05/2026
Enter PHLEGM! 💻🧬 We developed the Phage Homomer Level Estimate and Generation Method to infer oligomeric state using AlphaFold-Multimer and interface quality assessment. We applied it to >22,000 sequences, revealing massive structural diversity. (2/n)
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Erol Akcay @akcay.theoretical.bio · 28/05/2026
Check out this exciting new paper in @currentbiology.bsky.social from my friend and collaborator @stephaniesimone.bsky.social’s lab on the genomics of novel rhizobium endosymbiosis www.cell.com/current-biol...
cell.com
The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria
Resolving early steps in how hosts and microbes unite in novel endosymbiosis is critical for understanding key evolutionary innovations and ecosystem functions. Montoya et al. reveal how mobile geneti...
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