I've been using #ClaudeCode for #research #informatics—cohort building, debugging pipelines, genomics in #AllofUs. Before any of that was useful, I had to set things up right. The setup isn't complicated, but it matters. Here's how I do it: 1/
Bennett Waxse
@bwaxse.bsky.social
Med-Peds ID Fellow Doing EHR Informatics Research | Driven by data, music, bicycle | Thoughts & typo-planting skill my own
What I've been reading: a natural experiment to estimate the herpes #zoster vaccine's effect on dementia--did you know that the effect was predominantly observed in females? pmc.ncbi.nlm.nih.gov/articles/PMC... 1/
A natural experiment on the effect of herpes zoster vaccination on dementia
Neurotropic herpesviruses may be implicated in the development of dementia1–5. Moreover, vaccines may have important off-target immunological effects6–9. Here we aim to determine the effect of live-attenuated herpes zoster vaccination on the ...
pmc.ncbi.nlm.nih.gov
There's something mesmerizing about watching an infant discover their smile. The way it floods the cheeks, squints the eyes, shakes down into the chest. They draw their gaze away--almost like it's too much--before turning back to do it all again. 1/
The death of any child is tragic. We always think it will not be my child, they are healthy. Severe influenza can be unpredictable & deadly. Getting vaccinated considerably reduces dz severity and deaths. Please make sure you are vaccinated & your children are too. people.com/alabama-boy-...
Boy, 11, Dies After Severe Case of the Flu: ‘Jace Never Even Got to Open His Christmas Gifts’
Jace Watkins, 11, of Alabama died on Dec. 27 after being hospitalized due to complications from the flu.
people.com
What I’m reading: a super cool real-time RWE EHR study by Truveta that assessed vaccination behavior during the recent Texas measles outbreak. jamanetwork.com/journals/jam... 1/
Early MMR Vaccine Adoption During the 2025 Texas Measles Outbreak
This cross-sectional study examines early vaccination rates for measles in Texas following updated 2025 guidance from the US Centers for Disease Control and Prevention.
jamanetwork.com
What I'm Reading: Curiosity, a 1B-parameter model built on Epic Cosmos. It's genuinely interesting: zero-shot outputs rivaled supervised baselines across 78 real-world tasks, and the scaling laws (α=0.52) mirror NLP. Cool to see how information scales across domains. arxiv.org/abs/2508.12104 1/
This link will take you to a page that’s not on LinkedIn
lnkd.in
🧵How do you study 8 respiratory viruses across 265K (now 369K) patients across the US? We built computable phenotypes using #AllofUs EHR data - out now in Scientific Reports! 📊 Spoiler: performance varies wildly by pathogen 🔗 nature.com/articles/s41598-025-02183-9 #IDSky #EpiSky
Computable phenotypes to identify respiratory viral infections in the All of Us research program - Scientific Reports
Scientific Reports - Computable phenotypes to identify respiratory viral infections in the All of Us research program
nature.com
Good people trying to do good work because they believe in the promise of science. This is a dark, difficulty day for the NIH. www.nature.com/articles/d41...
‘One of the darkest days’: NIH purges agency leadership amid mass layoffs
In shock move, four institute directors at the US biomedical agency are removed from their posts.
nature.com
THREAD The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X. By quite a lot. Release the Kraken... #AcademicSky #HigherEd #Altmetrics 1/11
14 pages of terminated NIH grants--everyone should read through the list. The sweep is VERY broad, including "The Impact of the Herpes Zoster Vaccine on Herpes Zoster Ophthalmicus" & "Mitochondrial-based Determinants of Sex Differences in Acute Kidney Injury"🧪 1/n taggs.hhs.gov/Content/Data...
taggs.hhs.gov
“It is a strength of the scientific enterprise that we have diverse ideas, identities, and approaches to communication...just as leaders deserve some leeway to decide when to speak out most effectively, they should support their constituencies by not trying to squelch or steer more strident voices.”
Come together, right now
The chaos, conflicting information, firings, and hurtful rhetoric of the Trump administration’s approach to science over the past month are causing anxiety, grief, and concern for the scientific commu...
science.org
🧵Censor, purge, defund - how Trump is following the authoritarian playbook on science & universities. This isn't chaos - it's deliberate & well-established methods. I've mapped 40 actions into 3 categories covering attacks on science, attacks on universities and international collaboration. 1/16
A lot of people who got the measles as children died or suffered lifelong disabilities as a result. The measles vaccine was a godsend to worldwide public health, and it’s an absolute scandal that this lethally ignorant dolt has any power over public health.
Aaron Rupar@atrupar.com · last yr.RFK Jr: "It used to be that everybody got measles. And the measles gave you lifetime protection against measles infection. The vaccine doesn't do that ... it used to be that very young kids were protected by breast milk. Women who get vaccinated do not provide that level of immunity."
Are we surprised? No. Horrifying? Yep. Dark Age 2.0. NIH to terminate or limit grants related to vaccine hesitancy and uptake wapo.st/3Dw7WG0
NIH to terminate or limit grants related to vaccine hesitancy and uptake
The order covers more than 40 awards to researchers around the country seeking to understand why vaccine acceptance has declined.
wapo.st
Disrupted “treatment and diagnosis during the Covid pandemic resulted in doctors seeing “more complicated” forms of TB, Ditiu said, including some with holes in their lungs. It was a pattern she expected to see repeated, particularly among the poor and vulnerable.” Chillingly bad US policy on this
Madhu Pai, MD, PhD@madhupai.bsky.social · last yr.2 deaths from measles w/ most “cases across [TX, NM] in people < 18 and people who are unvaccinated or have an unknown vaccination status.” This IS unusual #vaccinate #VaccinesSavesLives #IDSky #EpiSky apnews.com/article/measles-texas-new-mexico-deaths-mmr-vaccine-a1295c78fade561479da65d72d8a5774
West Texas reports nearly 200 measles cases. New Mexico is up to 30
Health officials say West Texas now has almost 200 measles cases and New Mexico's case number has tripled to 30. The case counts were updated on Friday.
apnews.com
Great work, @standupforscience.bsky.social! It was so great to be in community with believers in the transformative power of science. #IDSky #ScienceSavesLives #SciencePowersEconomies
Incredible turnout at the @standupforscience.bsky.social rally today! Science isn't political—it's what cures cancer, defeats pandemics, and reveals our universe's secrets. When politicians silence scientists, people die. Period. Share widely. Let science work!
This dork is reporting for duty! But you don’t have to be a dork to fear for what will happen if we gut universities, cancel grants, shutter graduate programs, and set back a generation of science. #IDSky #EpiSky #StandUpForScience
Colette Delawalla, PhD@cdelawalla.bsky.social · last yr.Get in Dorks, we are going protesting. STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS. More information to come.
Starting your own members-only journal without peer review surely isn’t the answer either.
Mallory Harris, PhD@malar0ne.bsky.social · last yr.From your soon-to-be NIH Director: "Control over grant funding...and an amoral willingness to marginalize dissident scientists will buy a lot of silence." Indeed.
Stellar list of back-up resources if pubmed becomes unreliable
Hilda Bastian@hildabast.bsky.social · last yr.Hate that it has come to this, but it's time to consider PubMed vulnerable to enshittification. My latest post @plos.org discusses the lines we need to fight to hold – and alternatives we can rely on internationally: absolutelymaybe.plos.org/2025/02/14/w... #medlibs
#VaccinePreventableCancer The HPV vaccine is one of my favorite scientific successes of recent history. #IDSky
Kevin Ault @kevinault.bsky.social · last yr.The #HPV vaccine has decreased high grade cervical dysplasia in the USA by 80 % in the youngest age group. Reported in today's MMWR. #MedSky + #ObGynSky. www.cdc.gov/mmwr/volumes...
