www.pnas.org/doi/10.1073/...
If you ever need lto be convinced by how bad the "Contributed by" track is at @pnas.org ...
Only author: David Lipman, handling editor: David Lipman. Only integrity-free person not embarrassed by such a paper: David Lipman.
Even uses "I did" in the abstract. Shameful.
Host read removal sounds simple. It's not. 🧫
Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2.
#metagenomics
on.soundcloud.com/gEm7QyaTauvd...
Why not give links to cdc's site for foodborne outbreaks
If you work in genomics and haven't thought about vibe coding yet — episode 150 is your wake-up call. #microbinfie #genomicx
🤯 y'all... I have been on the edge of my seat waiting to show you this episode. Not only is it the 150th episode of #microbinfie but we show you some pretty outrageous vibe coding. 🫨
Let us know what you think with #microbinfie #genomicx
pca.st/episode/3784...
We just uploaded the 150th episode of the #microbinfie podcast, scheduled for Thursday, where we blow your mind with vibe coding. I can't believe we have actually made it this far.
🍻 To the next 150 episodes 🥂
@happykhan.mstdn.science.ap.brid.gy @andrewjpage.bsky.social
Huge blind spot on #riskyornot! @benchapmanncsu.bsky.social @bugcounter.bsky.social
Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.
Do iiiit
2) make a group project and make it very independent
Running CDC is not a part time job or an afterthought and the agency needs stable leadership @medpagetoday.com @gfriedman.bsky.social @altcdc.altgov.info
BRIG v1.0.0 Released — BLAST Ring Image Generator
This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1.
BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]
🪧New patch for Kalamari, a database of reference genome assemblies, backed by subject matter experts!
🧫New bacterial respiratory pathogens
🥔Precompiled Mash database
conda install kalamari
🦑 github.com/lskatz/Kalam...
I used it to create a microbial bioinformatics G-Funk 90's rap snippet 😆
gemini.google.com/share/1df0e1...
Day 1 in a new lab:
“You’ll be working on this organism now.”
Me: cool cool cool
(has never heard of it)
I wrote the checklist I use to survive that situation:
👉 self-onboarding a new pathogen
lskatz.github.io/posts/2026/0...
Just added a measles genome (subtype D8) to Kalamari.
Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes.
Measles is relevant again. Infrastructure matters. 🦑
More than a week after his death, I’m still reflecting on the life and legacy of Bill Foege—the Babe Ruth of public health—whose work with others saved the lives of literally hundreds of millions of people. His accomplishments are in a league of their own.
Happy Groundhog Day to all those who enjoy orderly shutdowns
I remember that you tried to buy Doorman from Marvel
@planetmoney.bsky.social have you seen Wonder Man yet?
(1/2) MMWR: Measles Outbreak Linked to Air Travel — Colorado, 2025
An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to:
• 9 secondary & 1 tertiary case in Colorado
• 7 more cases in other states
• 4 hospitalizations, mostly unvaxxed
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
Screenshot of an X.com post by The Associated Press (@AP) stating that dozens of immigrant families protested for better treatment behind fences at a Texas detention facility, where a 5-year-old Ecuadorian boy and his father were sent after being detained in Minnesota. Below is a video thumbnail showing a crowd gathered outdoors along a fenced walkway; many people wear bright blue or red outerwear, and some hold signs.
After being held in two of them as a boy, I fought for decades urging America to never again build concentration camps and put human beings in them. It breaks my heart to watch this happen twice now in my own lifetime.
> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely.
And if you love podcasts:
open.spotify.com/episode/0wrp...
Just a couple shots protect you from having to bury your child.
THIS ISN’T HARD. VACCINATE!
Happy anniversary of Jesus's bris to those who celebrate
Happy new years for those who celebrate
