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)
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:30 AM
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
Reposted by Charikleia Karageorgiou (Clio)
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
tinyurl.com
January 5, 2026 at 7:27 PM
I'm just delighted to announce our new preprint on genome-scale perturb-seq in CD4+ T cells. We learned both general lessons about the power of perturb-seq, and specific lessons about T cell biology.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Led by amazing postdocs Emma Dann and Ronghui Zhu, with my wonderful collaborator Alex Marson.
Reposted by Charikleia Karageorgiou (Clio)
Thawornwattana, Rannala & @zihengyang.bsky.social use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors.
🔗 doi.org/10.1093/molbev/msaf327
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf327
#evobio #molbio #compbio
On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection
Abstract. The multispecies coalescent (MSC) model provides a framework for detecting gene flow using genomic data, including between sister species. Howeve
doi.org
January 5, 2026 at 3:21 PM
Thawornwattana, Rannala & @zihengyang.bsky.social use simulation to study the false positive rate of a Bayesian test of gene flow under the MSC with multiple influencing factors.
🔗 doi.org/10.1093/molbev/msaf327
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msaf327
#evobio #molbio #compbio
Reposted by Charikleia Karageorgiou (Clio)
Reposted by Charikleia Karageorgiou (Clio)
Somatic and germline mutational processes across the tree of life https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1
December 30, 2025 at 2:32 PM
Somatic and germline mutational processes across the tree of life https://www.biorxiv.org/content/10.64898/2025.12.28.691837v1
Reposted by Charikleia Karageorgiou (Clio)
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado
In avocado and certain wild relatives in Lauraceae, pollination occurs via a synchronized rhythm of floral sex timing between two hermaphroditic flowering types. A-type plants present female-phase flo...
www.biorxiv.org
December 29, 2025 at 7:13 PM
Did you know there are 2 types of avocado varieties? A-types switch from female to male, B-types male to female, within a single day. This reciprocal sex alternation promotes cross-pollination and has a simple genetic basis. Read more in this recent preprint from the final chapter of my PhD thesis 🥑
Reposted by Charikleia Karageorgiou (Clio)
I launched my lab at UMass Amherst this fall. We study the mechanisms of meiotic homolog pairing using advanced live‑cell and super‑resolution imaging. Currently in budding yeast, with plans to expand to other eukaryotes. #Chromosome #Meiosis #Mitosis
www.umass.edu/biology/abou...
www.umass.edu/biology/abou...
November 13, 2025 at 12:13 PM
I launched my lab at UMass Amherst this fall. We study the mechanisms of meiotic homolog pairing using advanced live‑cell and super‑resolution imaging. Currently in budding yeast, with plans to expand to other eukaryotes. #Chromosome #Meiosis #Mitosis
www.umass.edu/biology/abou...
www.umass.edu/biology/abou...
Reposted by Charikleia Karageorgiou (Clio)
Excited about our new preprint showing bidirectional adaptive introgression between invasive and native crop pests over ecological timescales www.biorxiv.org/content/10.6...
The collision of two genomes threatens global food security
Human activity alters selection pressures and species' ranges, creating opportunities for hybridisation through secondary contact. Ancient hybridization has enabled adaptive radiation, but its role in...
www.biorxiv.org
December 26, 2025 at 11:21 AM
Excited about our new preprint showing bidirectional adaptive introgression between invasive and native crop pests over ecological timescales www.biorxiv.org/content/10.6...
Reposted by Charikleia Karageorgiou (Clio)
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system https://www.biorxiv.org/content/10.64898/2025.12.22.696042v1
December 25, 2025 at 7:32 PM
Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system https://www.biorxiv.org/content/10.64898/2025.12.22.696042v1
Reposted by Charikleia Karageorgiou (Clio)
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
December 25, 2025 at 12:31 AM
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
Reposted by Charikleia Karageorgiou (Clio)
🎯Excited to share our new collaborative paper in Mol Ecol - Beautifully lead by @marta-fb.bsky.social & @coreykirkland.bsky.social - Exploring the fascinating evolutionary story of the waterbuck, shaped by climate and unique chromosome changes
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...
Chromosome‐Level Genomics and Historical Museum Collections Reveal New Insights Into the Population Structure and Chromosome Evolution of Waterbuck
Advances in sequencing and chromosome-scale assembly have brought non-model animals into focus, deepening our understanding of genome and chromosome evolution. Here, we present the waterbuck (Kobus e...
onlinelibrary.wiley.com
December 24, 2025 at 11:04 AM
🎯Excited to share our new collaborative paper in Mol Ecol - Beautifully lead by @marta-fb.bsky.social & @coreykirkland.bsky.social - Exploring the fascinating evolutionary story of the waterbuck, shaped by climate and unique chromosome changes
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Charikleia Karageorgiou (Clio)
Origin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1
December 24, 2025 at 2:32 AM
Origin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1
Reposted by Charikleia Karageorgiou (Clio)
So excited to finally share my recent work on sex differences in crossing over using mice from diverse genetic backgrounds!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Chromosome length is not the sole determinant of sexually dimorphic crossover rates during mammalian meiosis: Insights from genetically diverse mouse strains
Meiotic recombination generates crossovers (COs), reciprocal exchanges between homologous chromosomes critical for accurate chromosome segregation. Inappropriate CO frequency and distribution drive an...
www.biorxiv.org
December 23, 2025 at 3:02 AM
So excited to finally share my recent work on sex differences in crossing over using mice from diverse genetic backgrounds!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Charikleia Karageorgiou (Clio)
Now accepted in Genetics!
academic.oup.com/genetics/adv...
We ask why and when rescaling of forward simulations in population genetics is not accurate. There are some interesting results for people performing simulations with selection.
academic.oup.com/genetics/adv...
We ask why and when rescaling of forward simulations in population genetics is not accurate. There are some interesting results for people performing simulations with selection.
Effects of rescaling forward-in-time population genetic simulations
Abstract. Forward-in-time population genetic simulations enable modelling of a wide array of complex evolutionary scenarios. Simulating small genomic regio
academic.oup.com
December 22, 2025 at 3:25 PM
Now accepted in Genetics!
academic.oup.com/genetics/adv...
We ask why and when rescaling of forward simulations in population genetics is not accurate. There are some interesting results for people performing simulations with selection.
academic.oup.com/genetics/adv...
We ask why and when rescaling of forward simulations in population genetics is not accurate. There are some interesting results for people performing simulations with selection.
Reposted by Charikleia Karageorgiou (Clio)
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
www.biorxiv.org
December 22, 2025 at 3:09 PM
Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
Reposted by Charikleia Karageorgiou (Clio)
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
December 21, 2025 at 3:10 AM
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
Reposted by Charikleia Karageorgiou (Clio)
Hi all!
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
CAD-C reveals centromere pairing and near-perfect alignment of sister chromatids
Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)-derived methods have revoluti...
www.biorxiv.org
December 20, 2025 at 4:43 PM
Hi all!
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids.
www.biorxiv.org/content/10.6...
#3DGenome #chromatin #Cohesin #centromere
Reposted by Charikleia Karageorgiou (Clio)
Population genetics analysis in a phylogenetic framework shows convergent evolution in the genomes of five brood-parasitic species, including selection on genes involved in spermatogenesis, sperm function and nervous system development 🧪 www.nature.com/articles/s41...
Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism - Nature Ecology & Evolution
Population genetics analysis in a phylogenetic framework shows convergent evolution in the genomes of five brood-parasitic species, including selection on genes involved in spermatogenesis, sperm func...
www.nature.com
December 19, 2025 at 9:33 AM
Population genetics analysis in a phylogenetic framework shows convergent evolution in the genomes of five brood-parasitic species, including selection on genes involved in spermatogenesis, sperm function and nervous system development 🧪 www.nature.com/articles/s41...
Reposted by Charikleia Karageorgiou (Clio)
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:53 PM
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Charikleia Karageorgiou (Clio)
"The 3D genome during germline development and meiosis"
by Yuka Kitamura & Satoshi Namekawa
"Distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis..."
FREE till Feb 4 at
authors.elsevier.com/a/1mHYpcQbJF...
by Yuka Kitamura & Satoshi Namekawa
"Distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis..."
FREE till Feb 4 at
authors.elsevier.com/a/1mHYpcQbJF...
December 17, 2025 at 1:45 PM
"The 3D genome during germline development and meiosis"
by Yuka Kitamura & Satoshi Namekawa
"Distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis..."
FREE till Feb 4 at
authors.elsevier.com/a/1mHYpcQbJF...
by Yuka Kitamura & Satoshi Namekawa
"Distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis..."
FREE till Feb 4 at
authors.elsevier.com/a/1mHYpcQbJF...
Reposted by Charikleia Karageorgiou (Clio)
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
December 16, 2025 at 4:06 PM
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
Reposted by Charikleia Karageorgiou (Clio)
Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance www.biorxiv.org/content/10.6...
Determining the driving factors shaping genetic architecture of complex traits in recently admixed populations
Understanding the genetic architecture of complex traits in admixed populations remains challenging due to heterogeneous genetic backgrounds and demographic histories. Mischaracterizing admixture can ...
www.biorxiv.org
December 16, 2025 at 1:47 PM
Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance www.biorxiv.org/content/10.6...
Reposted by Charikleia Karageorgiou (Clio)
New preprint from our lab: ‘Retroviral insertions contributed to the divergence of human and chimpanzee brains’. Very proud of this piece which took almost a decade to finish.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Retroviral insertions contributed to the divergence of human and chimpanzee brains
Over the past 5 to 7 million years, humans and chimpanzees have diverged in brain size, structural complexity, and cognitive abilities despite high conservation of protein-coding genes. Notably, the e...
www.biorxiv.org
December 14, 2025 at 8:16 PM
New preprint from our lab: ‘Retroviral insertions contributed to the divergence of human and chimpanzee brains’. Very proud of this piece which took almost a decade to finish.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...