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Titus Brown

@titus.idyll.org
3.8K followers 614 following 1.1K posts

I am not a deep man, but I have many shallows. ctbrown@ucdavis.edu, ivory.idyll.org/blog.

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Reposted by Titus Brown
Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Chrystal Starbird @drstarbird.bsky.social · 02/10/2026
We are excited to share research, but I want to take some time to share a little about myself. I LOVE science, but I also spend a lot of time advocating for more inclusive science. This work is promoted by my own obstacles in pursuing science which I talk about here: www.cell.com/cell/fulltex...
cell.com
Transforming myself and academia for good
Dr. Chrystal Starbird is the winner of the first Rising Black Scientist Award for a post-graduate scholar. For this award, we asked emerging Black scientists to tell us about the experiences that spar...
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Titus Brown @titus.idyll.org · 02/10/2026
Hello this is my colleague Jeff.
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Jake Grumbach @jakemgrumbach.bsky.social · 30/09/2026
Enjoyed Corey Robin's essay "On Nikole Hannah-Jones" coreyrobin675129.substack.com/p/on-nikole-...
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Jason Stajich @hyphaltip.bsky.social · 29/09/2026
... and another from Cassie Ettinger and summer student Jennifer Arroyo on comparative genomic analysis of seagrass doi.org/10.1016/j.aq... and conservation of some of the genes involved in symbioses between plants and AMF (Fungi).
sciencedirect.com
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GGBN @ggbnoutreach.bsky.social · 28/09/2026
Congrats to the NEON Biorepository at Arizona State University for receiving funding from NSF to co-lead a project aimed at creating a national resource for sequencing and analysing the DNA of important species! news.asu.edu/20260924-env...
news.asu.edu
Decoding important wildlife DNA | ASU News
There is a wealth of knowledge to be found in the DNA of our nation’s spectacular wildlife. A team of researchers co-led by Arizona State University will create a national resource to sequence and ana...
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Titus Brown @titus.idyll.org · 29/09/2026
oh that first solution is nice :). thank you!
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Titus Brown @titus.idyll.org · 29/09/2026
I can't get the search terms right... how, on Mac OS X, do you click the checkboxes in a Word document? I've been right clicking, going to Properties, and changing the default state to "Checked". But, seriously... there's a way, right??
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Titus Brown @titus.idyll.org · 26/09/2026
Yes. (From www.reddit.com/media?url=ht...)
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Titus Brown @titus.idyll.org · 25/09/2026
yes, that's what I do. But it requires more maintenance and is less secure, was my thinking. No?
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Titus Brown @titus.idyll.org · 25/09/2026
A colleague is looking for a NodeJS-specific hosting service for a relatively low-compute-need academic Web site. Are there good ones that are less flexible than a full VPS/specialized for NodeJS, or realistically does everyone just spin up a VPS and install stuff? Curious. Thank you!
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Titus Brown @titus.idyll.org · 24/09/2026
Strongly recommend. I collaborate with several people in this department and they are all wonderful peeps.
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Tiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 24/09/2026
Please repost/share We're hiring! UC Davis Plant Pathology seeks a tenure-track Assistant Professor in plant health & microbiomes. recruit.ucdavis.edu/JPF07904 My department is full of great colleagues, and we look forward to recruiting our new colleague!
recruit.ucdavis.edu
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
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Rebecca Solnit @rebeccasolnit.bsky.social · 23/09/2026
What gets you booted from Substack? Andrew Tate still seems to have a newsletter there while charged with: 10 counts of rape, 3 of trafficking for sexual exploitation, 3 of assault occasioning actual bodily harm, & making/distributing indecent images of a child. possessing extreme pornography.
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Titus Brown @titus.idyll.org · 23/09/2026
Assistant Professor of Food Microbiology position here at UC Davis (tenure track) - apply by Dec 1, 2026!
recruit.ucdavis.edu
Assistant Professor of Food Microbiology
University of California, Davis is hiring. Apply now!
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Richard Lenski @relenski.bsky.social · 23/09/2026
Here's a link to @chrisadami.bsky.social 's book, which I highly recommend: press.princeton.edu/books/paperb...
press.princeton.edu
The Evolution of Biological Information
Why information is the unifying principle that allows us to understand the evolution of complexity in nature
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Ethan White @ethanwhite.weecology.org · 22/09/2026
Interested in airborne monitoring using computer vision? We (@weecology) just released annotated data with bounding boxes and species IDs for over 50,000 individual birds of 6 widely distributed species from our drone work in the Everglades. doi.org/10.1002/ecy....
doi.org
EverWatch airborne bird imagery dataset for detection and classification of Everglades wading birds
Large-scale monitoring of populations and communities using airborne remote sensing is increasingly central to a broad range of research, management, and decision-making efforts. Performing this work....
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Titus Brown @titus.idyll.org · 22/09/2026
they confirmed it was next Thursday. Whew!
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Titus Brown @titus.idyll.org · 22/09/2026
Colleague just e-mailed asking if I was ready to lecture on Thursday. I'm supposed to lecture on Thursday in a week, per the schedule he sent me a few months back. Now soft-panicking that the schedule changed and he didn't tell me 😆
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Titus Brown @titus.idyll.org · 21/09/2026
Focusing in on a new env metatranscriptome analysis project this week, and our collaborators sent us a whole bunch of papers by @nekton4plankton.bsky.social (former pd w/me) as well as others by colleagues here at UC Davis. Kinda funny, I guess I've been in this field for a while, eh?!
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Iris van Rooij 💭 @irisvanrooij.bsky.social · 19/09/2026
It's GENUINELY like this: You cannot "solve" intractability with heuristics. Trust me. I devoted 20 years to this, and really, if you squeeze out intractability in one spot it'll pop up in another. It may look different on the surface, but in essence you're still facing the same epistemic problem.
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Daniel Knowles @dlknowles.bsky.social · 19/09/2026
I really hate the framing of these stories as "an AI agent broke out and hacked something." No, an inadequate sandbox meant that a powerful and unpredictable computer program was set loose on the open internet by the company that designed it. The agency isn't with the "AI agent", it's with the firm
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Quinn Slobodian @quinnslobodian.com · 17/09/2026
“The human becomes the bottleneck.” - former Palantir employee giftarticle.ft.com/giftarticle/...
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Dr. Rebecca Calisi-Rodríguez @rebeccacalisi.bsky.social · 16/09/2026
We spend a lot of time asking whether our animals make us happy. Maybe we should ask whether we make them happy, too. Turns out, the two may be more connected than we thought.
kcra.com
UC Davis study shows how mini horses and donkeys can ease teen anxiety
A UC Davis professor's study examines how interactions with mini horses and donkeys can reduce anxiety and sadness in teens while also considering the animals' responses.
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Titus Brown @titus.idyll.org · 15/09/2026
Congrats Carlos! Looking forward to your qual!! 😂
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Global Voices @globalvoices.org · 15/09/2026
"I used to think that the fundamental role of journalism was to produce information. Today, however, I believe there is another responsibility that is just as important: Transforming complex information into information that people can actually use."
globalvoices.org
The people behind the numbers: Bringing the reality of Turkish prisons to light
“[W]hen we can see the human stories behind that statistic, we can begin to talk about human rights violations and solutions.”
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Nur Shahir, PhD (Hire me!) @gigiomics.bsky.social · 15/09/2026
Same session but now Better Python Notebooks with Marimo from @tshafer.com (I think this is the right Tom Shafer 🙏🏿) #positconf #positconf26
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Nur Shahir, PhD (Hire me!) @gigiomics.bsky.social · 15/09/2026
Now attending Quarto Notebook and Literate Programming in Positron with Jonathan McPherson #positconf26 #positconf
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Titus Brown @titus.idyll.org · 14/09/2026
Well this title certainly caught my attention: "Invasion Pythons in the Florida Everglades: History, Ecology, Impact, and Control" How cool! (Talk here at UCD in late Oct.)
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Titus Brown @titus.idyll.org · 14/09/2026
looks like samtools depth doesn't report secondary alignments so I'm good there!
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Titus Brown @titus.idyll.org · 14/09/2026
thank you sir!
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Titus Brown @titus.idyll.org · 14/09/2026
Microbial #bioinformatics tweeps (@acritschristoph.bsky.social and others) if I want to critically evaluate how well metagenome ONT is mapping to specific genomes, what are the big technical gotchas I should be checking for? thx! Using minimap2 currently.
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Kate Elliott @kateelliottsff.bsky.social · 12/09/2026
I am not first and will be far from the last to say this: I have purchased so many books because I saw them recommended or publicized here on bsky. I cannot urge you all enough to KEEP TALKING ABOUT BOOKS. I know it's easier to talk up someone else's book, but this also means you, the shy author.
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Diversify Microbiology @diversifymicro.bsky.social · 11/09/2026
UNC Greensboro Department of Biology is hiring for three positions this year including one in microbiology! spartantalent.uncg.edu/postings/35918
spartantalent.uncg.edu
Assistant Professor Microbiology
The Department of Biology at UNC Greensboro (UNCG) seeks an individual with a strong record of accomplishment in microbiology broadly defined for a tenure-track faculty position at the rank of Assista...
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Titus Brown @titus.idyll.org · 11/09/2026
Got a spam e-mail trying to sell me bioinformatics processing services. I wish I were enough of an arsehole to respond "google me" but anyway I am just posting to see I really hate the incessant cold e-mails I get from sundry biotech firms.
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Titus Brown @titus.idyll.org · 11/09/2026
For me there was a really noticeable upswing at exactly 24 hours. Good luck!!!
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Neil Turkewitz @neilturkewitz.bsky.social · 11/09/2026
“There’s another element where you’re so privileged that you can’t imagine other things harming you. Like if you’re not worried about police brutality, or floods, or warfare—things that can actually kill you—then you can obsess over the machine-god.” @timnitgebru.blacksky.app
links.wired.com
We’re all gonna die—just maybe not from AI
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 11/09/2026
And lest you think I am blaming teachers, I am not. They are trying their best in the circumstances they find themselves in, which includes chronic underfunding of CA K-12 public schools bsky.app/profile/scho...
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 11/09/2026
“Q: Did the decision to drop the SAT lead to declines in student preparedness at UC? A: While preparedness seems to have declined in recent years, this has been a nationwide phenomenon, and as such cannot be attributed to UC’s admissions policies…
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Nature @nature.com · 11/09/2026
The most successful early-career researchers often rely on a network of mentors who each have different roles — from advising on research and grants to making professional introductions and providing emotional support go.nature.com/46U5PXy
go.nature.com
Successful early-career scientists rely on network of mentors
Large networks are particularly beneficial to researchers in under-represented groups.
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Richard Lenski @relenski.bsky.social · 10/09/2026
A nice timeline of the #LTEE in the #MSU Spartan #Science magazine: spartanscience.natsci.msu.edu/evolution-in...
spartanscience.natsci.msu.edu
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Niema Moshiri @niema.net · 09/09/2026
Not an example of Jupyter Notebooks -> Jupyter Book, but here's a Jupyter Book I maintain that uses GitHub Actions to auto-generate the website and a PDF niema.net/How-to-Teach...
niema.net
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Titus Brown @titus.idyll.org · 09/09/2026
Thinking of doing supp material for a paper as a jupyter book site. Basically I have a lot of Jupyter Notebooks to share and want to do so in a structured way. Any good examples of this (i.e. pubs) out there?
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Titus Brown @titus.idyll.org · 08/09/2026
thanks all - that is an obvious thing that I should have tried. I feel dumb. But happy to have the info. I will try on some more. Thank you!! cc @cgberger.bsky.social
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Titus Brown @titus.idyll.org · 08/09/2026
Right, I've found the center - but I'm hoping to narrow it down further :). Thanks!
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Titus Brown @titus.idyll.org · 08/09/2026
interesting! when I do that for PRJNA668104, I do not see submitter ID in the filter list!
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Titus Brown @titus.idyll.org · 08/09/2026
it's not visible in any of the Web portal displayy stuff, nor do I see anything in the XML.
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Titus Brown @titus.idyll.org · 08/09/2026
OK #bioinformatics peeps, I'm looking at NCBI Sequence Read Archive submissions without papers, and trying to figure out who submitted them. Is there any way to find submitter info??
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Alliance of Genome Resources @alliancegenome.bsky.social · 08/09/2026
This month's Alliance webinar "PAVI: From genome to alignment", presented by Paulo Nuin, will be Thurs. Sept 17 at noon ET. To get the Zoom link, please register tinyurl.com/4f9ycybt by Weds. Sept. 1 (before 11pm ET). Join us to hear about this upcoming new Alliance tool!
tinyurl.com
Alliance Of Genome Resources Event Registration
Webinar recordings are posted at https://www.youtube.com/@AllianceOfGenomeResources A schedule of future events is on the Alliance Events Calendar https://www.alliancegenome.org/event-calendar
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