BW ID Fellow

Infectious Diseases Clinical Fellowship Program The NIAID Infectious Diseases Fellowship Program provides training for internal medicine and pediatric residents interested in academic careers.

12/ As an ID fellow doing EHR research, this represents my path toward independence - using informatics to understand host-pathogen interactions.
Huge thanks to Josh Denny lab at NHGRI, #AllofUs Research Program, and www.niaid.nih.gov/about/infect... for making this possible! 🙏
#MedSky #IDSky

11/ For the #IDSky #EpiSky #AcademicSky community:
What other episodic infectious diseases need computable phenotypes? UTIs? Pneumonia subtypes? C. diff?

I'm building expertise in ID EHR methods - reach out for collaborations! Always happy to help with phenotyping approaches in and out of ID.

10/ What's next from our NHGRI lab:
🧬 GWAS to identify genetic risk factors for severe respiratory infections
📈 Clinical determinants of hospitalization across viruses
💊 Diagnostic stewardship for multiplex respiratory panels

Phenotypes are just the beginning! #IDSky

9/ Important caveats (transparency matters):

Low sensitivity = can't estimate true prevalence
#AllofUs demographics ≠ general US population
Oversamples severe disease, misses mild infections

Remember: Always validate your phenotypes

But, methods likely applicable to any US EHR dataset

8/ Want to use these phenotypes or create your own EHR methods? Let's collaborate! 🤝
✨ Code available in #AllofUs Community Workspace
🧬 Perfect for GWAS, health disparities, clinical outcomes research
📊 Framework adaptable to other episodic infectious diseases

DM me - my passion is EHR phenotyping

levels of care by virus and by phenotype composition. more intense bars are higher level of care (e.g., hospitalization)

7/ Unexpected finding: Our phenotype oversamples severe disease 🏥
Non-flu/non-COVID viruses showed high hospitalization rates vs. known epidemiology. Why?

Limited outpatient testing
No specific treatments = less testing motivation
Diagnostic value mainly in hospital settings

test percent positivity for All of Us (gray) and CDC (blue) cohorts by virus, over time

virus type proportions for those with available data

6/ Our phenotypes matched CDC surveillance beautifully 🎯
✅ Expected seasonal patterns
✅ Geographic distribution aligned with national data
✅ Virus type proportions matched NREVSS/GISRS
Mean absolute error: <6% for all viruses vs CDC positivity rates

hCOV PPV and episode counts during the COVID pandemic.

5/ Plot twist: COVID disrupted everything 😷
Common coronavirus ICD codes spiked during the pandemic (clinicians coding concern for COVID) despite no positive tests. Excluding hCoV codes after Feb 2020 corrected counts and PPV.

Lesson: Always validate phenotypes across time periods!

specificity, PPV, and sensitivity by virus and phenotype composition.

4/ Performance varied dramatically by virus:
High ICD sensitivity: Influenza (67%), RSV (55%)
Moderate: COVID-19, adenovirus, hMPV (33-45%)
Low: Rhinovirus (9%), parainfluenza (8%)
But, PPV was consistently high (90-97%) for non-flu/non-COVID viruses 📈

Schematic for computable phenotype and heatmap of detected cohorts.

3/ Our approach combines 3 data types within 90-day episodes:
🔹 Virus-specific ICD codes (e.g., J12.1 for RSV pneumonia)
🔹 Laboratory results (PCR, antigen, culture)
🔹 Antiviral prescriptions (flu/COVID only)
This integration > any single component alone, with varying breakdowns by virus.

2/ Why does this matter? 🤔
Respiratory infections are the most common human diseases, but research typically focuses on influenza, RSV, and COVID-19. Meanwhile, rhinovirus, hMPV, PIV, and common coronaviruses cause comparable illness but remain understudied.
#EHRphenotyping could unlock this. #IDSky

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

🧵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

#VaccinesSaveLives

‘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.

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...

Butterflies on a blue sky

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...

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...

“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.”

🧵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.

What an important conversation. Thanks for putting it out there!

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.

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

The data shouts for itself.

(Yes, data is plural, but it didn’t sound as good to me.)

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

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.

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

DC! So lovely seeing all of the activity across the world for #standupforscience2025.

CDC plans to study autism, vaccines Move comes despite strong evidence finding no link between them. By LENA H. SUN and LAUREN WEBER • The Washington Post

I got your waste, fraud, and abuse right here

‘It would be seen as political’: why the Royal Society is torn over Elon Musk Many fellows feel the billionaire has breached its code of conduct, but others say scientific neutrality is at stake

Thanks for sharing.

Looks like some others might need it as well:

www.theguardian.com/science/2025...

I’m into that distinction. Tell us more.

Man holding a sign protesting the dismantling of American science

Great work, @standupforscience.bsky.social!

It was so great to be in community with believers in the transformative power of science.

#IDSky #ScienceSavesLives #SciencePowersEconomies

Photo of the Lincoln memorial from the stand up for science rally

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!​​​​​​​​​​​​​​​​