Reposted by Shai CarmiEvan Irving-Pease @evanirvingpease.bsky.social · 06/10/2026New #aDNA paper! 💀🧬 Ancient DNA from colonial Montréal challenges narratives of a French–Indigenous “admixed founding population”—narratives that continue to shape false-Indigeneity debates today. Our study of Notre-Dame Cemetery finds exclusively French European ancestry. doi.org/10.1073/pnas...doi.orgAncient DNA challenges to admixture narratives: Insights from Notre-Dame Cemetery (1683–1796) in Colonial Montreal, Canada | PNASHistorical narratives of early colonization in Quebec frequently portray French–Indigenous relations as cooperative and characterized by admixture;... 052
Shai Carmi @shaicarmi.bsky.social · 03/10/2026Thank you ❤️ My own vote will definitely support a new government! 010
Reposted by Shai CarmiPol Solé Navais @polsolenavais.bsky.social · 02/10/2026📣📣📣 We are hiring a PhD student in reproductive genetics! The candidate will join our computational efforts to map the genetics behind pregnancy loss from both the fetal and maternal sides, working with a large pregnancy loss cohort and a new sequencing effort that we are launching. #PhD 1/3web103.reachmee.comDoctoral student in Medical Science - reproductive genetics and bioinformaticsDoctoral position in Medical Science Project title: The role of aneuploidies and fetal and maternal genetics 135
Shai Carmi @shaicarmi.bsky.social · 02/10/2026It is now October 2026. Since June 2025 (16 months), my kids have had only 7 months of normal school schedule. Since 2019 we have not had a single normal year. I am running on fumes. 120
Shai Carmi @shaicarmi.bsky.social · 24/09/2026To be fair it's a terrible journal and it's been a mistake submitting there. But the current publication model makes zero sense. The current value of journals is negative. It's a burden on society. 011
Shai Carmi @shaicarmi.bsky.social · 23/09/2026Just received from a journal an entirely AI-generated peer review. I knew the day would come. Academia is doomed. 152
Shai Carmi @shaicarmi.bsky.social · 22/09/2026Given the recent decline of social media for high quality science discussions, I have recently moved most of my activity into this Slack group, dedicated to population genetics and genetic genealogy. Everyone is welcome to join: join.slack.com/t/geneticgen...join.slack.comJoin Genetic genealogy science on SlackSlack is a new way to communicate with your team. It’s faster, better organized, and more secure than email. 0167
Shai Carmi @shaicarmi.bsky.social · 20/09/2026Academic Age Acceleration: Your age minus your h-index (Mine's positive unfortunately) 031
Shai Carmi @shaicarmi.bsky.social · 20/09/2026Indeed well powered. It seems solid, except that I didn't see any validation of the genotyping. Extremely rare variants are very difficult to genotype using an array (e.g. www.bmj.com/content/372/...). And unclear how/if it was imputed in chips not including it. 010
Shai Carmi @shaicarmi.bsky.social · 18/09/2026Well, 23andMe and Harvard researchers just published a candidate SNP study in Science... 120
Reposted by Shai Carmialex ioannidis @alexgioannidis.bsky.social · 17/09/2026Fst is a key genetic differentiation metric, but it emphasizes common variants over rare. In IEEE ICASSP out now lab member Margarita Geleta introduces Fq, which can be tuned across the allele freq spectrum. Fst & Shannon differentiation fall out of it as special cases. arxiv.org/abs/2511.03063 1124
Reposted by Shai CarmibioRxiv Genomics @biorxiv-genomic.bsky.social · 15/09/2026Estimating de novo mutation rates using parent-offspring pairs www.biorxiv.org/content/10.64898/20… 062
Shai Carmi @shaicarmi.bsky.social · 13/09/2026Paradoxically, the more fluent the writing, the more carefully I have to read to identify the nonsense. What a waste of our collective time. 020
Reposted by Shai CarmibioRxiv Genomics @biorxiv-genomic.bsky.social · 12/09/2026Sparse Linear Algebra Accelerates Genotype Representation Graph Computation at Biobank Scale www.biorxiv.org/content/10.64898/20… 097
Shai Carmi @shaicarmi.bsky.social · 11/09/2026One unrelated but amazing thing about this article is the reference to a "preprint published in August". Finally! Yes a preprint *is* a publication! 021
Reposted by Shai CarmiRémy Furrer @remyfurrer.bsky.social · 10/09/2026What are IVF doctors’ views on polygenic embryo screening (PES/PGT-P), and what criteria shape their decisions? New survey results from 152 clinicians. @gimjournal.bsky.social @shaicarmi.bsky.social @toddlencz.bsky.social www.gimjournal.org/article/S109...gimjournal.orgDecision-making criteria in polygenic embryo screening: A survey of reproductive medicine physiciansPolygenic embryo screening (PES) examines embryos for their genetic likelihood of developing complex conditions and traits. The commercialization of PES places reproductive endocrinologists and infert... 001
Reposted by Shai CarmiRémy Furrer @remyfurrer.bsky.social · 03/09/2026Link to letter: www.economist.com/letters/2026... Link to study: jamanetwork.com/journals/jam...economist.comThe opposition of scientific research on animals | Sep 5th 2026 EditionAlso this week, humanitarian aid, polygenic embryo selection, Dolly Parton, relaxing holidays, Lake Ontario 012
Reposted by Shai Carmialex ioannidis @alexgioannidis.bsky.social · 01/09/2026Gnomix is published! www.nature.com/articles/s41... Still the most accurate & fastest local ancestry inference (LAI) method, bests Flare and others (RecombMix & Orchestra) released since our preprint. Easy to use, github.com/AI-sandbox/g... Use it with our toolkit, snputils.orgnature.comScalable high resolution ancestry deconvolution for genomic data - Nature CommunicationsThe authors present Gnomix, a local ancestry framework that delivers leading accuracy across diverse admixed datasets on both whole-genome and array data with high efficiency, together with Gnofix, it... 22614
Reposted by Shai CarmiErkin Alaçamlı @masterolojist.bsky.social · 20/08/2026Our new preprint is out: www.biorxiv.org/content/10.6... (1/n)biorxiv.org 162
Reposted by Shai CarmiShai Carmi @shaicarmi.bsky.social · 12/08/2026New preprint! Investigative genetic genealogy has revolutionized forensic identification, with hundreds of cases solved to date. But for any given new case, how likely is genetic genealogy to succeed? We used a whole-country genealogy to find out! 1/10 www.biorxiv.org/content/10.6...biorxiv.orgForensic investigative genetic genealogy match rate estimated from a nation-wide population registerForensic investigative genetic genealogy (FIGG) is a revolutionary method in forensic genetics, whereby genetic relatives of an unknown target person are detected in direct-to-consumer genomic databas... 1124
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Great work by Harel Ismach, a student in my group, who has led the data analysis. Thanks to collaborators @gilig.bsky.social and @debbiekennett.bsky.social. The register data was made available by Israel's Central Bureau of Statistics. 031
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Nevertheless, our results are important because they apply to genealogical data *already accessible* to law enforcement in many countries, without relying on commercial providers. Our results should inform regulators and practitioners of FIGG, as well as quantify biobank privacy risks. 10/10 121
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Key limitations: * Finding a match does not guarantee identification * Many relatives missed because of the limited time depth of the register * Data errors (clerical, adoption, non-paternity, gamete donation, relationship misclassification, MZ twins) * Generalizability to other countries 9/10 121
Shai Carmi @shaicarmi.bsky.social · 12/08/2026What is the probability of having *two* (or more) relatives in the database? This is important, as it is often the intersection of the family trees of multiple matches that leads to identification. The match rate naturally decreases, although not as much for the very large databases. 8/10 111
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Unexpectedly, the match rate barely increases beyond 5th-degree (2nd cousins). This is probably because the common ancestors of third cousins usually lived before the country's foundation. Implication: whenever relatives are found in the database, they are usually not too distant. 7/10 111
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Results: The match rate is the proportion of people with at least one relative (a "match") in the database. For a database covering 1% of the country, the match rate is ~25%. For a database covering 10% of the country, the rate is 68%. 6/10 131
Shai Carmi @shaicarmi.bsky.social · 12/08/2026FIGG simulation: We designated a random subset of the population as the "database". For each person in the database, we used the register to track all of their relatives up to 7th degree (eg, 3rd cousins). This gave us the list of people who would have one or more relatives in the database. 5/10 111
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Data: We used the entire Israeli national population register, documenting all parent-child relationships in all present and past citizens. After QC, the dataset covered 12.5 million people, among them 10.4 million alive. Summary stats look reasonable. 4/10 131
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Our research question: Given a genomic database covering x% of the population of a country, what is the probability that a target person has one or more relatives in the database? Particularly, we focus on relatives from whom the target can be traced using available genealogical data. 3/10 111
Shai Carmi @shaicarmi.bsky.social · 12/08/2026In forensic investigative genetic genealogy (FIGG), law enforcement people upload the DNA of an unknown person (a criminal or unidentified remains) to a consumer genomics database (eg FTDNA), find relatives, and intersect their family trees until reaching an identification. 2/10 121
Shai Carmi @shaicarmi.bsky.social · 12/08/2026New preprint! Investigative genetic genealogy has revolutionized forensic identification, with hundreds of cases solved to date. But for any given new case, how likely is genetic genealogy to succeed? We used a whole-country genealogy to find out! 1/10 www.biorxiv.org/content/10.6...biorxiv.orgForensic investigative genetic genealogy match rate estimated from a nation-wide population registerForensic investigative genetic genealogy (FIGG) is a revolutionary method in forensic genetics, whereby genetic relatives of an unknown target person are detected in direct-to-consumer genomic databas... 1124
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Great work by Harel Ismach, a student in my group, who has led the data analysis. Thanks to collaborators @gilig.bsky.social and @debbiekennett.bsky.social. The register data was made available by Israel's Central Bureau of Statistics. 000
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Nevertheless, our results are important because they apply to genealogical data *already accessible* to law enforcement in many countries, without relying on commercial providers. Our results should inform regulators and practitioners of FIGG, as well as quantify biobank privacy risks. 10/10 110
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Key limitations: * Finding a match does not guarantee identification * Many relatives missed because of the limited time depth of the register * Data errors (clerical, adoption, non-paternity, gamete donation, relationship misclassification, MZ twins) * Generalizability to other countries 9/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026What is the probability to have *two* (or more) relatives in the database? This is important, as it is often the intersection of the family trees of multiple matches that leads to identification. The match rate naturally decreases, although not as much for the very large databases. 8/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Unexpectedly, the match rate barely increases beyond 5th-degree (2nd cousins). This is probably because the common ancestors of third cousins usually lived before the country's foundation. Implication: whenever relatives are found in the database, they are usually not too distant. 7/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Results: The match rate is the proportion of people with at least one relative (a "match") in the database. For a database covering 1% of the population, the match rate is ~25%. For a database covering 10% of the pop, the rate is 68%. 6/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026FIGG simulation: We designated a random subset of the population as the "database". For each person in the database, we used the register to track all of their relatives up to 7th degree (eg, 3rd cousins). This gave us the list of people who would have one or more relatives in the database. 5/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Data: We used the entire Israeli national population register, documenting all parent-child relationships in all present and past citizens. After QC, the dataset covered 12.5 million people, among them 10.4 million alive. Summary stats look reasonable. 4/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026Our research question: Given a genomic database covering x% of the population of a country, what is the probability that a target person has one or more relatives in the database? Particularly, we focus on relatives from whom the target can be traced using available genealogical data. 3/10 100
Shai Carmi @shaicarmi.bsky.social · 12/08/2026In forensic investigative genetic genealogy (FIGG), law enforcement people upload the DNA of an unknown person (a criminal or unidentified remains) to a consumer genomics database (eg FTDNA), find relatives, and intersect their family trees until reaching an identification. 2/10 100
Shai Carmi @shaicarmi.bsky.social · 10/08/2026It reminds me of when I TA'd physics to biology undergrads and the very first exercise I taught was to estimate the weight of all oceans. 030
Reposted by Shai CarmiMike Inouye @mikeinouye.bsky.social · 02/08/2026If you're looking to do a postdoc or a PhD, check out our exemplar publications and feel free to get in touch: www.inouyelab.org/home/publica...inouyelab.orgInouye Lab - PublicationsGoogle Scholar Inouye Lab authors * denotes equal contribution 013
Reposted by Shai Carmialex ioannidis @alexgioannidis.bsky.social · 30/07/2026Just got our @genomeresearch.bsky.social article by Margarita Geleta. 📬 I love hard copies...still here's a link genome.cshlp.org/content/36/2... Rita's article was a tour de force of genomic uses for the autoencoder architecture: compression, dim reduction, ancestry, synthetic genomes. 1113
Reposted by Shai CarmiSini Nagpal @nagpalsini.bsky.social · 24/07/2026Excited to share our work on "Pervasive interactions between exposures and polygenic risk can inform more effective clinical and behavioral interventions" @genomestake.bsky.social @natgenet.nature.com - www.nature.com/articles/s41... 131
Reposted by Shai CarmiNicola Pirastu @npirastu.bsky.social · 25/07/2026We’re looking for a Statistical Geneticist to join our team at @humantechnopole.bsky.social. The role offers the opportunity to work across a wide range of projects, supporting research groups throughout Human Technopole while developing and implementing new statistical methods tinyurl.com/44uyt8u2tinyurl.comStatistical GeneticistStatistical Geneticist 046
Reposted by Shai Carmiloic-yengo.bsky.social @loic-yengo.bsky.social · 21/07/2026Come and join our dream team! We’re recruiting a PhD candidate with a strong background in statistics, machine learning and (human) genetics to work at the interface of biological sequence foundational models and scores polygenic score methods. 2108
Reposted by Shai CarmiPadraig Dixon @padraigdixon.bsky.social · 16/07/2026New preprint: genetic variation and healthcare spending Across ~1.43M people, we identify hundreds of cost-associated variants, strong HLA signals, and higher costs among carriers of rare pathogenic variants in genes including BRCA1/2 and APC. www.medrxiv.org/content/10.6...medrxiv.orgQuantifying the contribution of genetic variation to healthcare expenditure across diverse healthcare systemsHealthcare systems must balance rising costs with the delivery of effective care, yet the factors underlying large inter-individual differences in healthcare expenditure remain incompletely understood... 013