Charikleia Karageorgiou (Clio)
@evobioclio.bsky.social
Postdoc at @UBuffalo | Gokcumen Lab
Evolution, structural variants and population genetics.
PhD from @uab.cat | Inversion polymorphism.
https://biolevol.github.io/
Evolution, structural variants and population genetics.
PhD from @uab.cat | Inversion polymorphism.
https://biolevol.github.io/
Pinned
Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation
Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, seq...
www.science.org
The typeset version of our article, "Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation", is now online. This thread will provide an overview of how gene duplications have shaped modern variation in the amylase locus.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Charikleia Karageorgiou (Clio)
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
November 25, 2025 at 8:27 PM
The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)
Reposted by Charikleia Karageorgiou (Clio)
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
DNA mutagenesis driven by transcription factor competition with mismatch repair
Competition between transcription factors and mismatch repair machinery drives localized
hypermutation at regulatory elements, with implications for cancer and genome evolution.
www.cell.com
October 2, 2025 at 11:37 PM
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
Reposted by Charikleia Karageorgiou (Clio)
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 7:22 PM
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
Reposted by Charikleia Karageorgiou (Clio)
Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...
November 23, 2025 at 9:49 PM
Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...
Reposted by Charikleia Karageorgiou (Clio)
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Charikleia Karageorgiou (Clio)
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Charikleia Karageorgiou (Clio)
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 Charikleia Karageorgiou (Clio)
Next paper published in the @hpgg-pivot.bsky.social special issue on popgen methods and software!
Coll Macià & Skov "Best practices and pitfalls in using hmmix for reference-free detection of introgressed sequences"
doi.org/10.47248/hpg...
Submission for contributions still open to 15 January!
Coll Macià & Skov "Best practices and pitfalls in using hmmix for reference-free detection of introgressed sequences"
doi.org/10.47248/hpg...
Submission for contributions still open to 15 January!
Best practices and pitfalls in using <monospace>hmmix</monospace> for reference-free detection of introgressed sequences
Best practices and pitfalls in using <monospace>hmmix</monospace> for reference-free detection of introgressed sequences
doi.org
November 19, 2025 at 11:18 AM
Next paper published in the @hpgg-pivot.bsky.social special issue on popgen methods and software!
Coll Macià & Skov "Best practices and pitfalls in using hmmix for reference-free detection of introgressed sequences"
doi.org/10.47248/hpg...
Submission for contributions still open to 15 January!
Coll Macià & Skov "Best practices and pitfalls in using hmmix for reference-free detection of introgressed sequences"
doi.org/10.47248/hpg...
Submission for contributions still open to 15 January!
Reposted by Charikleia Karageorgiou (Clio)
Paper out now: A curated dataset of the great ape genome diversity!
rdcu.be/eQLCi
rdcu.be/eQLCi
A curated dataset of great ape genome diversity
Scientific Data - A curated dataset of great ape genome diversity
rdcu.be
November 19, 2025 at 2:27 PM
Paper out now: A curated dataset of the great ape genome diversity!
rdcu.be/eQLCi
rdcu.be/eQLCi
Reposted by Charikleia Karageorgiou (Clio)
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...
High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation
The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...
doi.org
November 18, 2025 at 12:15 AM
Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...
Reposted by Charikleia Karageorgiou (Clio)
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
November 15, 2025 at 5:23 PM
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
Reposted by Charikleia Karageorgiou (Clio)
Amazing to have a byline with @cbo.bsky.social - read our take on Watson’s ultimate legacy in the Boston Globe. Will be in Sunday’s print edition.
"What James Watson got wrong about DNA"
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
What James Watson got wrong about DNA - The Boston Globe
The science he helped pioneer consistently undermines his view that genes determine everything about us.
www.bostonglobe.com
November 14, 2025 at 5:48 PM
Amazing to have a byline with @cbo.bsky.social - read our take on Watson’s ultimate legacy in the Boston Globe. Will be in Sunday’s print edition.
Reposted by Charikleia Karageorgiou (Clio)
Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals
go.nature.com/47UiBWa
go.nature.com/47UiBWa
An ancient recombination desert is a speciation supergene in placental mammals - Nature
Deep learning methods identified a large and evolutionarily conserved X-linked low recombination region in placental mammals that serves as both a barrier to gene flow in hybridizing lineages and an accurate phylogenomic marker.
go.nature.com
November 14, 2025 at 2:03 PM
Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals
go.nature.com/47UiBWa
go.nature.com/47UiBWa
Reposted by Charikleia Karageorgiou (Clio)
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
November 14, 2025 at 5:05 PM
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
Reposted by Charikleia Karageorgiou (Clio)
"Homologous recombination counteracts mismatch repair to promote fertility and genetic diversity"
by Ting-Fang Wang (@tingfangwang.bsky.social) & Ji-Long Liao (廖吉隆)
"We postulate that counter-actions of MMR and HR contribute to the post-zygotic isolation..."
authors.elsevier.com/sd/article/S...
by Ting-Fang Wang (@tingfangwang.bsky.social) & Ji-Long Liao (廖吉隆)
"We postulate that counter-actions of MMR and HR contribute to the post-zygotic isolation..."
authors.elsevier.com/sd/article/S...
November 14, 2025 at 2:25 PM
"Homologous recombination counteracts mismatch repair to promote fertility and genetic diversity"
by Ting-Fang Wang (@tingfangwang.bsky.social) & Ji-Long Liao (廖吉隆)
"We postulate that counter-actions of MMR and HR contribute to the post-zygotic isolation..."
authors.elsevier.com/sd/article/S...
by Ting-Fang Wang (@tingfangwang.bsky.social) & Ji-Long Liao (廖吉隆)
"We postulate that counter-actions of MMR and HR contribute to the post-zygotic isolation..."
authors.elsevier.com/sd/article/S...
Reposted by Charikleia Karageorgiou (Clio)
Happy to share Jialin's first publication. She did a great job exploring the transition to land in animals. Co-supervised by the great Jordi Paps and me and in collaboration with Davide Pisani and @phil-donoghue.bsky.social
Nature research paper: Convergent genome evolution shaped the emergence of terrestrial animals
go.nature.com/4i0i61w
go.nature.com/4i0i61w
Convergent genome evolution shaped the emergence of terrestrial animals - Nature
Comparisons of 154 genomes from 21 animal phyla and outgroups have been used to reconstruct ancestral adaptation to life on land across 11 distinct terrestrialization events, revealing strong evidence for convergent genomic evolution across the animal kingdom and recurring periods of terrestrial colonization.
go.nature.com
November 13, 2025 at 3:18 PM
Happy to share Jialin's first publication. She did a great job exploring the transition to land in animals. Co-supervised by the great Jordi Paps and me and in collaboration with Davide Pisani and @phil-donoghue.bsky.social
Reposted by Charikleia Karageorgiou (Clio)
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:34 PM
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Reposted by Charikleia Karageorgiou (Clio)
Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections:
sites.google.com/berkeley.edu...
sites.google.com/berkeley.edu...
October 23, 2025 at 1:20 PM
Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections:
sites.google.com/berkeley.edu...
sites.google.com/berkeley.edu...
Reposted by Charikleia Karageorgiou (Clio)
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
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...
Reposted by Charikleia Karageorgiou (Clio)
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Charikleia Karageorgiou (Clio)
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Charikleia Karageorgiou (Clio)
Super cool new use of single gamete (single molecule!) genome sequencing - catching de novo mobile element insertions! www.biorxiv.org/content/10.1...
Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm
Mobile element insertions (MEIs) are a significant source of human genetic variation, yet the rates and properties of de novo MEIs are poorly characterized due to technical limitations in sequencing t...
www.biorxiv.org
November 5, 2025 at 4:42 PM
Super cool new use of single gamete (single molecule!) genome sequencing - catching de novo mobile element insertions! www.biorxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
Generating long deletions across the genome with pooled paired prime editing screens
Engineered deletions are a powerful probe for studying genome architecture, function, and regulation. Yet, the lack of effective methods to create them in large numbers and at multi-kilobase scale has...
biorxiv.org
November 5, 2025 at 2:17 PM
New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome.
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇
🔗 biorxiv.org/content/10.1...
A short thread (by Juliane Weller)👇