Titus Brown
@titus.idyll.org
I am not a deep man, but I have many shallows. [email protected], http://ivory.idyll.org/blog/.
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December 15, 2025 at 7:42 PM
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Reposted by Titus Brown
Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
December 15, 2025 at 3:19 PM
Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
Reposted by Titus Brown
While Amazon is investing billions of dollars to expand AI, independent bookstores are hosting community events, personally recommending books to readers, and providing a space that is safe and welcoming during a time when we need them most.
Never underestimate the power of a local bookstore.
Never underestimate the power of a local bookstore.
December 15, 2025 at 4:11 PM
While Amazon is investing billions of dollars to expand AI, independent bookstores are hosting community events, personally recommending books to readers, and providing a space that is safe and welcoming during a time when we need them most.
Never underestimate the power of a local bookstore.
Never underestimate the power of a local bookstore.
Reposted by Titus Brown
it's actually kinda funny in a way to get to the finish line of curing cancer and having the government go eh you know what. never mind
A tiny trial in New York has shown that personalized mRNA vaccines can provoke massive, lasting immune responses against pancreatic cancer, even as sweeping federal cuts now threaten the fragile labs required to produce them.
theintellectualistofficial.substack.com/p/a-breakthr...
theintellectualistofficial.substack.com/p/a-breakthr...
December 13, 2025 at 2:50 AM
it's actually kinda funny in a way to get to the finish line of curing cancer and having the government go eh you know what. never mind
Reposted by Titus Brown
Yay! Preorder through bookshop.org like I did, or wherever you like to order books.
In her upcoming book, The Edge of Space-Time, 2022 award winner @chanda.blacksky.app embraces cosmic wonder and draws on poetry and pop culture to take readers on a mind-altering journey to the boundaries of the universe. 🌌
Available for preorder: www.penguinrandomhouse.com/books/746817... #scicomm
Available for preorder: www.penguinrandomhouse.com/books/746817... #scicomm
The Edge of Space-Time by Chanda Prescod-Weinstein: 9780593701683 | PenguinRandomHouse.com: Books
A fresh, charming, socially conscious tour of the mysteries of space-time, from the award-winning author of The Disordered Cosmos In her highly acclaimed debut, distinguished cosmologist and particle...
www.penguinrandomhouse.com
December 12, 2025 at 11:19 PM
Yay! Preorder through bookshop.org like I did, or wherever you like to order books.
Reposted by Titus Brown
We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
December 11, 2025 at 4:16 PM
We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Reposted by Titus Brown
🫵🏻 Are you a data visualization specialist who wants to make a difference in the current US political environment? @americansunlight.org needs you!
December 12, 2025 at 3:05 PM
🫵🏻 Are you a data visualization specialist who wants to make a difference in the current US political environment? @americansunlight.org needs you!
Reposted by Titus Brown
This is what systematic racism looks like.
ICE detain U.S. citizen for looking Somali—use illegal chokehold to tackle him to ground.
Man repeatedly begs agents to look at his digital passport ID—they refuse.
Drove him 7 miles away before releasing him alone into Minnesota snow storm—told him to "walk home" in freezing weather advisory.
Man repeatedly begs agents to look at his digital passport ID—they refuse.
Drove him 7 miles away before releasing him alone into Minnesota snow storm—told him to "walk home" in freezing weather advisory.
December 10, 2025 at 8:22 PM
This is what systematic racism looks like.
That feeling when you google a term because you want to figure out how to calculate it right (the way the scientific community does) and ...the top & only code hit is your own code. Does not inspire confidence that this is the community way 😭.
(spacegraphcats.github.io/spacegraphca...)
(spacegraphcats.github.io/spacegraphca...)
Calculating taxonomic purity of spacegraphcats outputs - spacegraphcats documentation
spacegraphcats.github.io
December 9, 2025 at 1:42 PM
That feeling when you google a term because you want to figure out how to calculate it right (the way the scientific community does) and ...the top & only code hit is your own code. Does not inspire confidence that this is the community way 😭.
(spacegraphcats.github.io/spacegraphca...)
(spacegraphcats.github.io/spacegraphca...)
Reposted by Titus Brown
What really seems to happen is not just too much coverage, but too much population diversity in the dataset without a clear dominant genotype, leading to a very complex assembly graph that can't be resolved from short read alone (just look at this tangled mess 😮)
December 9, 2025 at 3:25 AM
What really seems to happen is not just too much coverage, but too much population diversity in the dataset without a clear dominant genotype, leading to a very complex assembly graph that can't be resolved from short read alone (just look at this tangled mess 😮)
Reposted by Titus Brown
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
doi.org
December 9, 2025 at 3:25 AM
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
Reposted by Titus Brown
Spotify is garbage on every count: Its treatment of artists, its ICE advertising, the CEO's investment in military AI, its leading role in the commodification and AI slopification of music, its terrible audio quality—you name it.
So I quit, and put together a complete guide to getting off Spotify:
So I quit, and put together a complete guide to getting off Spotify:
How to quit Spotify
This Black Friday, here's a guide to finding the best Spotify alternative
www.bloodinthemachine.com
December 8, 2025 at 5:00 PM
Come for the compelling science, stay for the gorgeous pictures of assembly graphs.
(COI: I'm a co-author ;)
(COI: I'm a co-author ;)
100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
academic.oup.com
December 8, 2025 at 5:32 PM
Come for the compelling science, stay for the gorgeous pictures of assembly graphs.
(COI: I'm a co-author ;)
(COI: I'm a co-author ;)
Reposted by Titus Brown
100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
academic.oup.com
December 8, 2025 at 4:25 PM
100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...
Reposted by Titus Brown
Here's Rep. Ann Wagner (R-Mo.) raging about Missouri's elections being "decided in California" in response to an article about Missourians protesting a gerrymandering petition in California -- except the article is about the town of California in Missouri.
December 8, 2025 at 4:14 PM
Here's Rep. Ann Wagner (R-Mo.) raging about Missouri's elections being "decided in California" in response to an article about Missourians protesting a gerrymandering petition in California -- except the article is about the town of California in Missouri.
Reposted by Titus Brown
This is why I’m cautiously optimistic — in the long run.
December 7, 2025 at 1:56 PM
This is why I’m cautiously optimistic — in the long run.
Reposted by Titus Brown
A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...
Redirecting
doi.org
December 6, 2025 at 5:02 PM
A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...
Reposted by Titus Brown
"Google's 'free' search comes with the cost of your time wading through ads, your attention sold to advertisers, and results that prioritize revenue over relevance. Kagi flips that model."
www.makeuseof.com/i-switched-d...
www.makeuseof.com/i-switched-d...
I switched my browser’s default search from Google to this niche engine—and I’m sticking with it
Paying for search sounds off, but Google's decline made it worth every penny.
www.makeuseof.com
December 6, 2025 at 4:48 PM
"Google's 'free' search comes with the cost of your time wading through ads, your attention sold to advertisers, and results that prioritize revenue over relevance. Kagi flips that model."
www.makeuseof.com/i-switched-d...
www.makeuseof.com/i-switched-d...
Reposted by Titus Brown
microsoft promised to "empower every user" and google to "revolutionise knowledge and technological innovation" but in reality what they have given us is an invasive surveillance dystopian nightmare hard to escape
www.forbes.com/sites/zakdof...
www.forbes.com/sites/zakdof...
Microsoft Teams Starts Telling Your Boss Where You Are—Now Just 8 Weeks Away
Microsoft confirms start date for new Teams update — no more hiding places.
www.forbes.com
December 6, 2025 at 10:55 AM
microsoft promised to "empower every user" and google to "revolutionise knowledge and technological innovation" but in reality what they have given us is an invasive surveillance dystopian nightmare hard to escape
www.forbes.com/sites/zakdof...
www.forbes.com/sites/zakdof...
Reposted by Titus Brown
It's good—very good, and very important—that district courts keep issuing these 100-page rulings upholding the law. It must be incredibly dispiriting to see them overturned in a two-page, lawless, unsigned order, but please, keep them coming. They expose SCOTUS' corruption like nothing else.
December 5, 2025 at 12:41 AM
It's good—very good, and very important—that district courts keep issuing these 100-page rulings upholding the law. It must be incredibly dispiriting to see them overturned in a two-page, lawless, unsigned order, but please, keep them coming. They expose SCOTUS' corruption like nothing else.
Reposted by Titus Brown
ICE raided a James Beard award winning restaurant & because the chef/owner was prepared, left emptyhanded:
December 5, 2025 at 3:24 PM
ICE raided a James Beard award winning restaurant & because the chef/owner was prepared, left emptyhanded:
Reposted by Titus Brown
1/ Why I sometimes ignore Nature Methods papers when picking bioinformatics tools.
A practical guide to choosing tools that actually work.
A practical guide to choosing tools that actually work.
December 5, 2025 at 2:15 PM
1/ Why I sometimes ignore Nature Methods papers when picking bioinformatics tools.
A practical guide to choosing tools that actually work.
A practical guide to choosing tools that actually work.
Reposted by Titus Brown
My department at California State University Northridge is hiring! We're looking for a new colleague studying microbiology or molecular/cellular biology. I'm not on the search committee, but happy to answer questions about the department and campus, and life in LA
buff.ly/Pc1KOaC
buff.ly/Pc1KOaC
Career Opportunities
Applicant Log-In
careers.pageuppeople.com
December 4, 2025 at 7:19 PM
My department at California State University Northridge is hiring! We're looking for a new colleague studying microbiology or molecular/cellular biology. I'm not on the search committee, but happy to answer questions about the department and campus, and life in LA
buff.ly/Pc1KOaC
buff.ly/Pc1KOaC
Reposted by Titus Brown
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Phage–bacteria dynamics: The tragedy of the commons at hyperspeed
A recent study found that apparently stable coexistence between a clinically important
pathogen, Pseudomonas aeruginosa, and its integrated prophages can break down, setting
off an evolutionary cycle ...
www.cell.com
December 4, 2025 at 8:56 PM
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Perhaps my best birthday gift this year will be a zoom call with @ethanwhite.weecology.org to talk about collaboration ideas. Excited!!
December 4, 2025 at 2:39 PM
Perhaps my best birthday gift this year will be a zoom call with @ethanwhite.weecology.org to talk about collaboration ideas. Excited!!