Charikleia Karageorgiou (Clio)
@evobioclio.bsky.social
Postdoc at @UBuffalo | Gokcumen Lab
Evolution, structural variants and population genetics.
PhD from @UABBarcelona | Inversion polymorphism.
https://biolevol.github.io/
Evolution, structural variants and population genetics.
PhD from @UABBarcelona | 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)
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)👇
Reposted by Charikleia Karageorgiou (Clio)
New preprint from another part of my PhD! 📝👇
Some mutations arise after fertilisation 🧬, so early they can appear in both a parent’s body and their germ cells.
By analysing family trio genomes 👪, we built one of the largest catalogues of these “hidden” inherited variants yet.
tinyurl.com/mvns2ytv
Some mutations arise after fertilisation 🧬, so early they can appear in both a parent’s body and their germ cells.
By analysing family trio genomes 👪, we built one of the largest catalogues of these “hidden” inherited variants yet.
tinyurl.com/mvns2ytv
Landscape of parental postzygotic mutations in >11,000 rare disease trios
Postzygotic mutations (PZMs) arising post-fertilisation, prior to primordial germ cell specification, may be subsequently inherited by both somatic and germ cells, causing somatic mosaicism in the par...
tinyurl.com
October 28, 2025 at 11:04 AM
New preprint from another part of my PhD! 📝👇
Some mutations arise after fertilisation 🧬, so early they can appear in both a parent’s body and their germ cells.
By analysing family trio genomes 👪, we built one of the largest catalogues of these “hidden” inherited variants yet.
tinyurl.com/mvns2ytv
Some mutations arise after fertilisation 🧬, so early they can appear in both a parent’s body and their germ cells.
By analysing family trio genomes 👪, we built one of the largest catalogues of these “hidden” inherited variants yet.
tinyurl.com/mvns2ytv
Reposted by Charikleia Karageorgiou (Clio)
The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.
October 28, 2025 at 9:31 PM
The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.
Reposted by Charikleia Karageorgiou (Clio)
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 25, 2025 at 4:46 AM
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Reposted by Charikleia Karageorgiou (Clio)
The new Flex-sweep v2 is ready! We welcome feedback from users to further improve user experience and address compatibility issues that often occur given the many moving parts. Flex-sweep v2 now implements DANN from the Siepel lab. journals.plos.org/plosgenetics...
Postdoc J. M. Moreno is very close to release Flex-sweep v2 to make users' life easier. v2 is entirely recoded, faster and uses much less RAM. Robustness is up thanks to adding Siepel's lab domain adaptive step.
Available soon at pypi.org/project/flex...
flexsweep.readthedocs.io/en/latest/
Available soon at pypi.org/project/flex...
flexsweep.readthedocs.io/en/latest/
October 21, 2025 at 3:38 PM
The new Flex-sweep v2 is ready! We welcome feedback from users to further improve user experience and address compatibility issues that often occur given the many moving parts. Flex-sweep v2 now implements DANN from the Siepel lab. journals.plos.org/plosgenetics...
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
www.biorxiv.org
October 22, 2025 at 11:15 PM
Reposted by Charikleia Karageorgiou (Clio)
Hot off the press! Our latest work on the evolution of facultative symbiosis in stony corals, focusing on a remarkable Mediterranean species: Oculina patagonica.
🪸 🌊
#evobio #corals #coralbiology
www.nature.com/articles/s41...
🪸 🌊
#evobio #corals #coralbiology
www.nature.com/articles/s41...
October 15, 2025 at 8:29 PM
Hot off the press! Our latest work on the evolution of facultative symbiosis in stony corals, focusing on a remarkable Mediterranean species: Oculina patagonica.
🪸 🌊
#evobio #corals #coralbiology
www.nature.com/articles/s41...
🪸 🌊
#evobio #corals #coralbiology
www.nature.com/articles/s41...
Reposted by Charikleia Karageorgiou (Clio)
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
October 15, 2025 at 3:53 PM
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by Charikleia Karageorgiou (Clio)
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
October 14, 2025 at 8:34 PM
When transposons jump, genomes diverge - even in cultured cells.
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
I am happy to share our new preprint: a chromosome-scale genome assembly for Drosophila OSC cells, one of the key model systems in the piRNA field, especially for nuclear piRNA biology. 🧬🧵 (1/12)
Reposted by Charikleia Karageorgiou (Clio)
This suggest that telomere maintenance in sperm is more robust than in oocytes and impacts the inherited telomeres. Full paper is below. Curious to know what you think as this is a new area for us!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Long-read sequencing reveals telomere inheritance patterns from human trios
Telomeres are essential for maintaining genomic integrity and are associated with cellular aging and disease, yet the factors influencing their inheritance across generations remain poorly understood....
www.biorxiv.org
October 9, 2025 at 5:33 AM
This suggest that telomere maintenance in sperm is more robust than in oocytes and impacts the inherited telomeres. Full paper is below. Curious to know what you think as this is a new area for us!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
Our preprint, "Read mismapping from segmental duplications drives spurious trans associations," is out!
We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them!
Link: www.biorxiv.org/content/10.1...
We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them!
Link: www.biorxiv.org/content/10.1...
Read mismapping from segmental duplications drives spurious trans associations
Heritable variation in gene regulation shapes both disease risk and evolution. Trans -acting quantitative trait loci ( trans -QTLs) are the primary source of this variation within species, yet they re...
www.biorxiv.org
October 10, 2025 at 6:01 PM
Our preprint, "Read mismapping from segmental duplications drives spurious trans associations," is out!
We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them!
Link: www.biorxiv.org/content/10.1...
We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them!
Link: www.biorxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
Reposted by Charikleia Karageorgiou (Clio)
Excited to be presenting part of my thesis at VESS! I’ll be discussing work from my recent pre-print on gene dosage response curves. Drop by if you’ve been curious but haven’t had a chance to read it yet!
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
October 10, 2025 at 4:50 PM
Excited to be presenting part of my thesis at VESS! I’ll be discussing work from my recent pre-print on gene dosage response curves. Drop by if you’ve been curious but haven’t had a chance to read it yet!
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
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...
Reposted by Charikleia Karageorgiou (Clio)
New preprint out with Brenna Henn, led by two fantastic grad students in our labs! www.biorxiv.org/content/10.1...
Recovering the pre-colonial population structure of Khoe-San descendant populations
San populations from Botswana and Namibia retain exceptional linguistic, cultural and genetic diversity, but few Khoisan-speaking groups remain south of the Kalahari Desert. However, historically, far...
www.biorxiv.org
October 8, 2025 at 4:23 PM
New preprint out with Brenna Henn, led by two fantastic grad students in our labs! www.biorxiv.org/content/10.1...
Reposted by Charikleia Karageorgiou (Clio)
Now published! Our paper on:
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
Sperm sequencing reveals extensive positive selection in the male germline - Nature
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
www.nature.com
October 8, 2025 at 3:51 PM
Now published! Our paper on:
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
(1) Accurate sequencing of sperm at scale
(2) Positive selection of spermatogenesis driver mutations across the exome
(3) Offspring disease risks from male reproductive aging
[1/n]
www.nature.com/articles/s41...
