Shai Carmi
@shaicarmi.bsky.social
Associate professor at the Hebrew University of Jerusalem.
Statistical, population, and medical genetics; preimplantation genetic testing. Views my own.
http://scarmilab.org
Statistical, population, and medical genetics; preimplantation genetic testing. Views my own.
http://scarmilab.org
Pinned
Shai Carmi
@shaicarmi.bsky.social
· Nov 10
Slack
join.slack.com
Given several new followers here, I'm posting the link to our Slack group "genetic genealogy science".
We post and discuss manuscripts on phasing/imputation, IBD, recombination, demographic inference, ancient DNA, ancestry/admixture, etc.
All are welcome.
join.slack.com/t/geneticgen...
We post and discuss manuscripts on phasing/imputation, IBD, recombination, demographic inference, ancient DNA, ancestry/admixture, etc.
All are welcome.
join.slack.com/t/geneticgen...
Reposted by Shai Carmi
The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup!
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
November 19, 2025 at 1:41 PM
The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup!
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.
Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
Reposted by Shai Carmi
This comment made me wonder: what kinds of cases or research goals/questions would geneticists generally consider scientifically useful/interesting/valid when it comes to looking at the genomes of long-dead famous people?
November 17, 2025 at 10:01 AM
This comment made me wonder: what kinds of cases or research goals/questions would geneticists generally consider scientifically useful/interesting/valid when it comes to looking at the genomes of long-dead famous people?
More details emerge on this affair.
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
November 14, 2025 at 9:13 AM
More details emerge on this affair.
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
1. A paper has been submitted to a "high profile" journal. I think no editor in their right mind should take it, but I have no hope.
2. Details on the psychiatric PRS analysis were reported by the investigator.
edition.cnn.com/2025/11/13/s...
One of my core principles is to defend the freedom of sequencing the DNA of everyone for every purpose.
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
Hitler had genetic sexual disorder, new DNA analysis reveals
Findings also debunked myth that Nazi dictator had Jewish ancestry
www.independent.co.uk
November 13, 2025 at 6:27 AM
One of my core principles is to defend the freedom of sequencing the DNA of everyone for every purpose.
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
This should not mean it is always a good (or responsible) idea.
And at least post a preprint before going on TV (reminding me of the Columbus fiasco).
www.independent.co.uk/news/science...
Reposted by Shai Carmi
Straight onto the reading list: Forensic genetics in the omics era www.nature.com/articles/s41...
Forensic genetics in the omics era - Nature Reviews Genetics
Recent advances in forensic genetics have improved the range, precision and reliability of forensic information obtainable from biological trace material. The author reviews how non-targeted and ...
www.nature.com
November 9, 2025 at 5:12 PM
Straight onto the reading list: Forensic genetics in the omics era www.nature.com/articles/s41...
Reposted by Shai Carmi
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes
Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...
www.biorxiv.org
November 7, 2025 at 2:33 PM
Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Effects of polygenic risk score communication on health outcomes: systematic review and meta-analysis
Abstract Objective. The purpose of this systematic review and meta-analysis is to summarize evidence from all RCTs to-date on the efficacy of polygenic risk score (PRS) communication in changing healt...
www.medrxiv.org
November 7, 2025 at 8:33 AM
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Multi-lineage natural gene therapy mediated by embryonic triploid mosaicism in the context of Fanconi anaemia
Fanconi anemia is a rare inherited bone marrow failure syndrome caused by inactivation of genes in the Fanconi anemia/BRCA DNA repair pathway. We report a patient with X-linked Fanconi anemia, and aty...
www.medrxiv.org
November 5, 2025 at 8:04 AM
Interesting story in this preprint.
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
A male infant was diagnosed with Fanconi anemia due to an X-linked frameshift mutation.
Three years later, his hematopoiesis became normal (without intervention). How?
www.medrxiv.org/content/10.1...
Reposted by Shai Carmi
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
November 4, 2025 at 2:05 PM
Excited to help host the 54th European Mathematical Genetics Meeting in Davos, Switzerland, next spring!
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Speakers include @timfrayling.bsky.social, @marylynritchie.bsky.social, Dr. Joelle Mbatchou and Dr. Eleonora Porcu
Travel grants available - register here: emgm2026.sciencesconf.org?lang=en
Reposted by Shai Carmi
New from FinnGen!! 🚀🚀🚀
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
October 24, 2025 at 12:09 AM
New from FinnGen!! 🚀🚀🚀
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!!
All results are open for browsing & download:
👉 labvalues.finngen.fi.
🧬🧬🧬
Have fun!! 🏄🏄♀️🏄♂️
Reposted by Shai Carmi
Online now!
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
Ploidy abnormalities affect over 1% of human embryos. Haploidy typically results from
absent sperm DNA, while triploidy mainly arises from maternal meiosis II errors. Triploidy
also shows a linear mat...
www.cell.com
October 20, 2025 at 5:32 PM
Online now!
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
📄Maternal age and genome-wide failure of meiotic recombination are associated with triploid conceptions in humans
🧑🤝🧑 @shaicarmi.bsky.social @eva-hoffmann.bsky.social & co
Reposted by Shai Carmi
FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1
October 14, 2025 at 5:34 PM
FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1
Hebrew University graduate wins Economics Nobel prize.
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
October 13, 2025 at 12:36 PM
Hebrew University graduate wins Economics Nobel prize.
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
Not bad for one day :)
www.nobelprize.org/prizes/econo...
www.nobelprize.org/events/nobel...
Celebrating the release of the hostages in my neighborhood and all over Israel.
After two years, we can breathe again.
Let's hope this day follows with peace and prosperity to the whole region.
After two years, we can breathe again.
Let's hope this day follows with peace and prosperity to the whole region.
October 13, 2025 at 11:12 AM
Celebrating the release of the hostages in my neighborhood and all over Israel.
After two years, we can breathe again.
Let's hope this day follows with peace and prosperity to the whole region.
After two years, we can breathe again.
Let's hope this day follows with peace and prosperity to the whole region.
Big day ahead, can't sleep :)
* Hostages return from Gaza after two years
* War ends
* Trump in Jerusalem
* Hostages return from Gaza after two years
* War ends
* Trump in Jerusalem
October 13, 2025 at 2:29 AM
Big day ahead, can't sleep :)
* Hostages return from Gaza after two years
* War ends
* Trump in Jerusalem
* Hostages return from Gaza after two years
* War ends
* Trump in Jerusalem
Reposted by Shai Carmi
Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...
Inference of complex demographic history using composite likelihood based on whole-genome genealogies
Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...
www.biorxiv.org
October 8, 2025 at 2:48 PM
Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...
What will be achieved first: in-vitro gametogenesis, or peace in the Middle East?
October 4, 2025 at 7:02 AM
What will be achieved first: in-vitro gametogenesis, or peace in the Middle East?
Reposted by Shai Carmi
Please repost: we are recruiting a postdoc for a project in my lab on genes and environment in autism
We are proud to be one of the 13 projects funded by the NIH Autism Data Science Initiative. Our project: "Elucidating the Interplay of Genes and Environment in Autism Using Genomic and Exposure Data from Large Populations" 🧵https://www.nytimes.com/2025/09/26/health/autism-research-trump-kennedy.html
Despite False Claims, Trump Funnels Millions Into Credible Autism Research
www.nytimes.com
October 2, 2025 at 1:25 AM
Please repost: we are recruiting a postdoc for a project in my lab on genes and environment in autism
There is a lot of hype around this new paper. It's a great advance, but it will never result in the birth of a healthy baby. The reason is that in this method, chrs that end up in the egg are a random sample of the 46 somatic chrs,
1/2
www.bbc.com/news/article...
1/2
www.bbc.com/news/article...
Human skin DNA fertilised to make embryo for first time
US scientists testing the technique say it could help people overcome infertility and potentially allow same-sex couples to have a genetically related child.
www.bbc.com
October 1, 2025 at 4:41 PM
There is a lot of hype around this new paper. It's a great advance, but it will never result in the birth of a healthy baby. The reason is that in this method, chrs that end up in the egg are a random sample of the 46 somatic chrs,
1/2
www.bbc.com/news/article...
1/2
www.bbc.com/news/article...
Hi hive mind - would appreciate feedback on the following.
I have ~3k whole-genomes, each called individually with GATK. I have 3k GVCFs.
I don't have enough resources for joint calling.
Should I use bcftools to merge into a multi-sample VCF? Or joint call in batches (say, 100) and then merge?
I have ~3k whole-genomes, each called individually with GATK. I have 3k GVCFs.
I don't have enough resources for joint calling.
Should I use bcftools to merge into a multi-sample VCF? Or joint call in batches (say, 100) and then merge?
October 1, 2025 at 10:21 AM
Hi hive mind - would appreciate feedback on the following.
I have ~3k whole-genomes, each called individually with GATK. I have 3k GVCFs.
I don't have enough resources for joint calling.
Should I use bcftools to merge into a multi-sample VCF? Or joint call in batches (say, 100) and then merge?
I have ~3k whole-genomes, each called individually with GATK. I have 3k GVCFs.
I don't have enough resources for joint calling.
Should I use bcftools to merge into a multi-sample VCF? Or joint call in batches (say, 100) and then merge?
Reposted by Shai Carmi
The final thesis chapter is published OA at
@ajhgnews.bsky.social!
In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review.
www.sciencedirect.com/science/arti...
@ajhgnews.bsky.social!
In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review.
www.sciencedirect.com/science/arti...
Multiple-testing corrections in selection scans using identity-by-descent segments
Failing to correct for multiple testing in selection scans can lead to false discoveries of recent genetic adaptations. The scanning statistics in sel…
www.sciencedirect.com
September 26, 2025 at 4:29 PM
The final thesis chapter is published OA at
@ajhgnews.bsky.social!
In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review.
www.sciencedirect.com/science/arti...
@ajhgnews.bsky.social!
In short, we determine a valid significance level for a "selection" scan and apply it to 3 ancestry groups in 2 biobanks. 🧵 for updates from the helpful peer review.
www.sciencedirect.com/science/arti...
Reposted by Shai Carmi
🚨 New preprint out!
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
September 26, 2025 at 5:10 PM
🚨 New preprint out!
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation.
This reveals intensified assortment in recent generations.
www.biorxiv.org/content/10.1...
Reposted by Shai Carmi
Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity https://www.biorxiv.org/content/10.1101/2025.09.23.678138v1
September 24, 2025 at 8:33 AM
Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity https://www.biorxiv.org/content/10.1101/2025.09.23.678138v1
Reposted by Shai Carmi
To analyze millions of genetic variants, we need tools that are fast and memory efficient. Some of the most efficient tools have problems with numerical instability on dense sets of snps. Bercovich et al. figured out how to overcome a common source of instability: www.biorxiv.org/content/10.1...
LD Matrix Approximations for Scalable Analysis of High-dimensional Genetic Data
Linkage disequilibrium (LD) matrices are an essential part of many statistical genetics methods. However, their high dimensionality makes their computation and storage impractical for large genomic da...
www.biorxiv.org
September 22, 2025 at 6:38 PM
To analyze millions of genetic variants, we need tools that are fast and memory efficient. Some of the most efficient tools have problems with numerical instability on dense sets of snps. Bercovich et al. figured out how to overcome a common source of instability: www.biorxiv.org/content/10.1...