BW ID Fellow
@bw-id.bsky.social
Med-Peds ID Fellow Doing EHR Informatics Research | Driven by data, music, bicycle | Thoughts & typos: both my own
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
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
June 2, 2025 at 12:12 PM
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
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
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
✅ 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
June 2, 2025 at 12:10 PM
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
✅ 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
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!
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!
June 2, 2025 at 12:08 PM
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!
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!
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 📈
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 📈
June 2, 2025 at 12:06 PM
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 📈
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 📈
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.
🔹 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.
June 2, 2025 at 12:04 PM
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.
🔹 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.
DC! So lovely seeing all of the activity across the world for #standupforscience2025.
March 9, 2025 at 1:59 AM
DC! So lovely seeing all of the activity across the world for #standupforscience2025.
Great work, @standupforscience.bsky.social!
It was so great to be in community with believers in the transformative power of science.
#IDSky #ScienceSavesLives #SciencePowersEconomies
It was so great to be in community with believers in the transformative power of science.
#IDSky #ScienceSavesLives #SciencePowersEconomies
March 7, 2025 at 10:32 PM
Great work, @standupforscience.bsky.social!
It was so great to be in community with believers in the transformative power of science.
#IDSky #ScienceSavesLives #SciencePowersEconomies
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!
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!
March 7, 2025 at 6:35 PM
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!
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!
Vaccine Information Statements (VISs) pulled from the CDC’s website. #IDSky #EpiSky
Still available on Immunize.org
Still available on Immunize.org
February 1, 2025 at 2:32 PM
Vaccine Information Statements (VISs) pulled from the CDC’s website. #IDSky #EpiSky
Still available on Immunize.org
Still available on Immunize.org
The ID march of shorter treatment is ok continues, this time for bacteremia (not including S. aureus).
FYI, E. coli, Klebsiella, Enterococcus, and CoNS made up > 70% of organisms.
By pathogen breakdown of risk difference emphasizes applicability of these results for GN bacteremia.
FYI, E. coli, Klebsiella, Enterococcus, and CoNS made up > 70% of organisms.
By pathogen breakdown of risk difference emphasizes applicability of these results for GN bacteremia.
November 20, 2024 at 8:31 PM
The ID march of shorter treatment is ok continues, this time for bacteremia (not including S. aureus).
FYI, E. coli, Klebsiella, Enterococcus, and CoNS made up > 70% of organisms.
By pathogen breakdown of risk difference emphasizes applicability of these results for GN bacteremia.
FYI, E. coli, Klebsiella, Enterococcus, and CoNS made up > 70% of organisms.
By pathogen breakdown of risk difference emphasizes applicability of these results for GN bacteremia.
Great #AMIA2024 presentation by Azza Shoaibi, emphasizing the challenging state of EHR phenotyping in research. Looking at alzheimer's, depression and pulmonary hypertension, studies rarely reported full phenotype details, and incidence rate (IR) calculated between 7 databases varied dramatically.
November 12, 2024 at 11:59 PM
Great #AMIA2024 presentation by Azza Shoaibi, emphasizing the challenging state of EHR phenotyping in research. Looking at alzheimer's, depression and pulmonary hypertension, studies rarely reported full phenotype details, and incidence rate (IR) calculated between 7 databases varied dramatically.
Critical work done by Sarah El-Azab presented at #AMIA2024: Race and ethnicity concepts (including disaggregated data) had reduced standard equivalents, leading to increased data silences in populations historically underrepresented in biomedical science.
November 11, 2024 at 9:18 PM
Critical work done by Sarah El-Azab presented at #AMIA2024: Race and ethnicity concepts (including disaggregated data) had reduced standard equivalents, leading to increased data silences in populations historically underrepresented in biomedical science.
Any #IDSky folks at #AMIA2024? I'm excited to present how we phenotype respiratory viral infections using the NIH All of Us Research Program this Wednesday morning (S107). Can't wait to connect and learn with fellow informaticians! #DataScience #ID #Informatics #AllofUs
November 11, 2024 at 3:49 AM
Any #IDSky folks at #AMIA2024? I'm excited to present how we phenotype respiratory viral infections using the NIH All of Us Research Program this Wednesday morning (S107). Can't wait to connect and learn with fellow informaticians! #DataScience #ID #Informatics #AllofUs