John Belmont
@jwbelmon.bsky.social
#MD, #PhD | #Pediatrics | #Medical #Genetics | #Human #Genetics | #Cardiovascular | #Congenital | #Genome #Sequencing | #HealthEcon | #Causal #Inference
belmontgenetics.org
belmontgenetics.org
Pinned
John Belmont
@jwbelmon.bsky.social
· Aug 19
The Causal Pivot: A structural approach to genetic heterogeneity and variant discovery in complex diseases
We present the Causal Pivot (CP) as a structural causal model (SCM) for analyzing genetic heterogeneity in complex diseases. The CP leverages an estab…
www.sciencedirect.com
Causal Pivot is an idea that comes from differential diagnosis in medical practice www.sciencedirect.com/science/arti... Chad Shaw and I drew DAGs for molecular diagnosis and gene discovery. He saw an opportunity to exploit collider bias in an interesting way.
Reposted by John Belmont
It’s not clear that Prasad’s new ‘standards’ for vaccine clinical trials could be approved by an IRB
FDA official proposes ‘impossible’ standards for vaccine testing that could curtail access to immunizations | CIDRAP www.cidrap.umn.edu/childhood-va...
FDA official proposes ‘impossible’ standards for vaccine testing that could curtail access to immunizations
www.cidrap.umn.edu
December 2, 2025 at 12:29 AM
It’s not clear that Prasad’s new ‘standards’ for vaccine clinical trials could be approved by an IRB
Reposted by John Belmont
Texas Tech University System Chancellor Brandon Creighton on Monday imposed restrictions on how faculty discuss race, sex, gender identity and sexual orientation in classrooms and introduced a new course content approval process.
Texas Tech System restricts race and gender teaching
Tech, now the second Texas public university system to add similar teaching restrictions, had earlier directed faculty to follow state and federal guidance recognizing only two sexes.
www.texastribune.org
December 2, 2025 at 12:20 AM
Texas Tech University System Chancellor Brandon Creighton on Monday imposed restrictions on how faculty discuss race, sex, gender identity and sexual orientation in classrooms and introduced a new course content approval process.
Prasad has no training or clinical experience in Pediatrics. He has no relevant expertise in Immunology.
If there were 10 deaths among the millions of children who received COVID vaccines, one should consider them rare, severe, complex phenotypes ...
If there were 10 deaths among the millions of children who received COVID vaccines, one should consider them rare, severe, complex phenotypes ...
NEW: The F.D.A. announced in an internal memo that 10 children died "because of" the Covid shot. Other experts want to see proof.
“This is a profound revelation,” Dr. Prasad's memo said. “For the first time, the U.S. F.D.A. will acknowledge that Covid-19 vaccines have killed American children.”
“This is a profound revelation,” Dr. Prasad's memo said. “For the first time, the U.S. F.D.A. will acknowledge that Covid-19 vaccines have killed American children.”
F.D.A. Attributes 10 Children’s Deaths to Covid Vaccines
www.nytimes.com
December 1, 2025 at 4:31 AM
Prasad has no training or clinical experience in Pediatrics. He has no relevant expertise in Immunology.
If there were 10 deaths among the millions of children who received COVID vaccines, one should consider them rare, severe, complex phenotypes ...
If there were 10 deaths among the millions of children who received COVID vaccines, one should consider them rare, severe, complex phenotypes ...
Reposted by John Belmont
A gentle summary of the last twenty-odd years of Pearl-style causal inference with DAGs, perhaps most helpful if you're just arriving from old-school philosophy of causation.
I like this genre. And if you do too, I can also recommend Weinberger et al.'s forthcoming piece in BJPS
1/2
I like this genre. And if you do too, I can also recommend Weinberger et al.'s forthcoming piece in BJPS
1/2
New paper out in Synthese—a metaphysical theory of causation designed to explain statistical causal inference. Basically a summary of a 100,000-word book (Causation: Science, Statistics and Metaphysics) that'll go into production with CUP soon. Watch this space link.springer.com/article/10.1...
Causal inference and the metaphysics of causation - Synthese
The techniques of causal inference are widely used throughout the non-experimental sciences to derive causal conclusions from probabilistic premises. This poses a philosophical question. What in the n...
link.springer.com
November 30, 2025 at 5:37 PM
A gentle summary of the last twenty-odd years of Pearl-style causal inference with DAGs, perhaps most helpful if you're just arriving from old-school philosophy of causation.
I like this genre. And if you do too, I can also recommend Weinberger et al.'s forthcoming piece in BJPS
1/2
I like this genre. And if you do too, I can also recommend Weinberger et al.'s forthcoming piece in BJPS
1/2
Raccoon
Bobcat
Coyote
Coral Snake
Copperhead
Bobcat
Coyote
Coral Snake
Copperhead
Introduce yourself with 5 animals you've seen in the wild:
- Coatimundi
- Coyote
- Black Bear
- Brown Bear
- Alligator
- Coatimundi
- Coyote
- Black Bear
- Brown Bear
- Alligator
Introduce yourself with 5 animals you've seen in the wild:
Caribou
Ravens
Seals
Kea
Turkeys
Caribou
Ravens
Seals
Kea
Turkeys
November 28, 2025 at 11:22 PM
Raccoon
Bobcat
Coyote
Coral Snake
Copperhead
Bobcat
Coyote
Coral Snake
Copperhead
The leaf cutter ants caught red fucking handed stealing my winter kale. 🌱
November 28, 2025 at 11:12 PM
The leaf cutter ants caught red fucking handed stealing my winter kale. 🌱
Reposted by John Belmont
Reposted by John Belmont
Our paper on rare genetic variants and cardiometabolic, ancestry-adjusted polygenic risk scores (PRS) in a familial hypercholesterolemia (FH) cohort from Mexico is now published! link.springer.com/article/10.1...
Analysis of a deeply-phenotyped familial hypercholesterolemia cohort from Mexico shows a role for both rare and common alleles across known dyslipidemia genes and reveals structural variation in a nov...
Familial hypercholesterolemia (FH) is a genetic disorder driven in part by mutations in three genes that encode components of the cholesterol pathway: LDLR, APOB, and PCSK9. However, the majority of F...
link.springer.com
November 26, 2025 at 7:42 PM
Our paper on rare genetic variants and cardiometabolic, ancestry-adjusted polygenic risk scores (PRS) in a familial hypercholesterolemia (FH) cohort from Mexico is now published! link.springer.com/article/10.1...
Reposted by John Belmont
"It may be uncomfortable to conclude that a widely used study design has been producing spurious results. But the evidence is in, and telling uncomfortable truths is a part of doing science."
Problems with twin studies.
theinfinitesimal.substack.com/p/the-missin...
Problems with twin studies.
theinfinitesimal.substack.com/p/the-missin...
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 22, 2025 at 2:03 PM
"It may be uncomfortable to conclude that a widely used study design has been producing spurious results. But the evidence is in, and telling uncomfortable truths is a part of doing science."
Problems with twin studies.
theinfinitesimal.substack.com/p/the-missin...
Problems with twin studies.
theinfinitesimal.substack.com/p/the-missin...
Reposted by John Belmont
Kingston Flemings has scored in double-digits in all four games for the second-ranked Cougars this season. bit.ly/3LTc2vK
November 21, 2025 at 4:10 AM
Kingston Flemings has scored in double-digits in all four games for the second-ranked Cougars this season. bit.ly/3LTc2vK
Fucking idiot
For years Robert F. Kennedy Jr. has been pushing the notion that germ theory is overrated. Now other HHS officials are picking up that argument. Katherine J. Wu reports:
To Survive the Next Pandemic, Walk More, the NIH Says
The agency is picking up Robert F. Kennedy Jr.’s argument that a healthy immune system can keep even pandemic germs at bay.
bit.ly
November 20, 2025 at 7:47 AM
Fucking idiot
Reposted by John Belmont
A bobcat!
November 19, 2025 at 11:13 PM
A bobcat!
Reposted by John Belmont
Estimation and mapping of the missing heritability of human phenotypes www.nature.com/articles/s41... 🧬🖥️🧪
November 13, 2025 at 9:29 AM
Estimation and mapping of the missing heritability of human phenotypes www.nature.com/articles/s41... 🧬🖥️🧪
Reposted by John Belmont
The work of Sue Welfare, contemporary UK printmaker #ReframingWomenPrintmaker
November 13, 2025 at 8:36 AM
The work of Sue Welfare, contemporary UK printmaker #ReframingWomenPrintmaker
Reposted by John Belmont
6/ We also have some good news on the vaccine front. Ahead of the next ACIP meeting, the independent Vaccine Integrity Project (VIP) is reviewing evidence on Hep B. VIP is an independent group of scientists formed in response to waning trust in RFK Jr.’s ACIP.
November 11, 2025 at 7:25 PM
6/ We also have some good news on the vaccine front. Ahead of the next ACIP meeting, the independent Vaccine Integrity Project (VIP) is reviewing evidence on Hep B. VIP is an independent group of scientists formed in response to waning trust in RFK Jr.’s ACIP.
Reposted by John Belmont
2/ First up, the American Academy of Pediatrics (AAP) is standing up for science. The AAP is suing HHS Sec. RFK Jr., arguing that his vaccine advisory panel (ACIP) should be dissolved. The lawsuit also seeks to overturn the panel’s recent decisions.
November 11, 2025 at 7:25 PM
2/ First up, the American Academy of Pediatrics (AAP) is standing up for science. The AAP is suing HHS Sec. RFK Jr., arguing that his vaccine advisory panel (ACIP) should be dissolved. The lawsuit also seeks to overturn the panel’s recent decisions.
Reposted by John Belmont
We need more institutions like the American Academy of Pediatrics to stand up and fight for science and medicine.
Pediatricians are the best of us in the house of medicine, our backbone fighting to defend all of us and doing it with sunshine and rainbows and silly flashlights on their stethoscopes.
Pediatricians are the best of us in the house of medicine, our backbone fighting to defend all of us and doing it with sunshine and rainbows and silly flashlights on their stethoscopes.
2/ First up, the American Academy of Pediatrics (AAP) is standing up for science. The AAP is suing HHS Sec. RFK Jr., arguing that his vaccine advisory panel (ACIP) should be dissolved. The lawsuit also seeks to overturn the panel’s recent decisions.
November 12, 2025 at 7:11 PM
We need more institutions like the American Academy of Pediatrics to stand up and fight for science and medicine.
Pediatricians are the best of us in the house of medicine, our backbone fighting to defend all of us and doing it with sunshine and rainbows and silly flashlights on their stethoscopes.
Pediatricians are the best of us in the house of medicine, our backbone fighting to defend all of us and doing it with sunshine and rainbows and silly flashlights on their stethoscopes.
Reposted by John Belmont
The Matthew Effect is alive and well in academia - always makes me wary of programs aimed at identifying rising stars in an already highly talented pool...
elifesciences.org/reviewed-pre...
elifesciences.org/reviewed-pre...
elifesciences.org
November 12, 2025 at 7:03 PM
The Matthew Effect is alive and well in academia - always makes me wary of programs aimed at identifying rising stars in an already highly talented pool...
elifesciences.org/reviewed-pre...
elifesciences.org/reviewed-pre...
Reposted by John Belmont
Stay tuned here for upcoming updates to pgsc_calc (github.com/PGScatalog/p...), our tool for reproducible PGS calculation. Our next version aims to increase the scalability to WGS data in cloud trusted research environments (e.g. All of Us).
GitHub - PGScatalog/pgsc_calc: The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation - PGScatalog/pgsc_calc
github.com
November 11, 2025 at 5:43 PM
Stay tuned here for upcoming updates to pgsc_calc (github.com/PGScatalog/p...), our tool for reproducible PGS calculation. Our next version aims to increase the scalability to WGS data in cloud trusted research environments (e.g. All of Us).
Reposted by John Belmont
{report} #rstats package version 0.6.2 is now on CRAN!
MANY bug fixes in this version! Including corrected duplicated text outputs and dramatic speed increases for brmsfit models (which used to refit the model entirely every time).
easystats.github.io/report/
With the @easystats.github.io team
MANY bug fixes in this version! Including corrected duplicated text outputs and dramatic speed increases for brmsfit models (which used to refit the model entirely every time).
easystats.github.io/report/
With the @easystats.github.io team
Automated Reporting of Results and Statistical Models
The aim of the report package is to bridge the gap between R’s output and the formatted results contained in your manuscript. This package converts statistical models and data frames into textual repo...
easystats.github.io
November 8, 2025 at 11:07 PM
{report} #rstats package version 0.6.2 is now on CRAN!
MANY bug fixes in this version! Including corrected duplicated text outputs and dramatic speed increases for brmsfit models (which used to refit the model entirely every time).
easystats.github.io/report/
With the @easystats.github.io team
MANY bug fixes in this version! Including corrected duplicated text outputs and dramatic speed increases for brmsfit models (which used to refit the model entirely every time).
easystats.github.io/report/
With the @easystats.github.io team
Reposted by John Belmont
Reposted by John Belmont
In its first year tidyplots.org has become the go-to data viz for many life science researchers, got 620+ stars on Github, ~30K CRAN downloads, and 11 citations. Thank you for using, sharing, citing, and feedback! There is more to come 🤩
#rstats #dataviz #phd
#rstats #dataviz #phd
November 8, 2025 at 9:24 AM
In its first year tidyplots.org has become the go-to data viz for many life science researchers, got 620+ stars on Github, ~30K CRAN downloads, and 11 citations. Thank you for using, sharing, citing, and feedback! There is more to come 🤩
#rstats #dataviz #phd
#rstats #dataviz #phd
Reposted by John Belmont
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - Nature Communications
The authors give a method for learning causal gene networks using Perturb-seq data. In K562 cells, they find a network with small-world and scale-free properties. Analysis shows a relationship between...
nature.com
November 3, 2025 at 7:09 PM
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Reposted by John Belmont
The ceramics of Acoma artist Barbara Cerno, who was born in Acoma Pueblo in 1959 #WomensArt
November 6, 2025 at 5:02 AM
The ceramics of Acoma artist Barbara Cerno, who was born in Acoma Pueblo in 1959 #WomensArt