Maddy Comerford
@maddycomerford.bsky.social
phd grad interested in human evolutionary genetics and archaic introgression @ SVIMR
Pinned
Using sequence-to-function models to interpret archaic hominin introgression https://www.biorxiv.org/content/10.64898/2026.08.31.748430v1
Very pleased to be sharing this one! Understanding the consequences of Denisovan introgression remains challenging given the poor representation of global introgression in functional genomics resources. We wanted to know if, and how, AlphaGenome could help us navigate that gap 🧭 ⬇️
Reposted by Maddy Comerford
New online! Genomic insights into natural selection in recent human history
Genomic insights into natural selection in recent human history
Nature Reviews Genetics, Published online: 11 September 2026; doi:10.1038/s41576-026-01010-9Advances in genome-wide selection scans and ancient DNA have greatly expanded our ability to study human evolution. This Review discusses the conceptual and statistical challenges in identifying and interpreting selection signals, and how recent approaches are reshaping our understanding of human evolution over the past 10,000 years.
dlvr.it
September 11, 2026 at 10:38 AM
New online! Genomic insights into natural selection in recent human history
Reposted by Maddy Comerford
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the ...
www.science.org
September 11, 2026 at 5:11 PM
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Maddy Comerford
An abandoned quarry in southwestern China has given scientists an unprecedented glimpse into the lives and abilities of the mysterious ancient humans called Denisovans
go.nature.com/46NsuVp
go.nature.com/46NsuVp
Who were the Denisovans? Rich trove of fossils and tools paints new picture
Objects found in a cave in southwestern China suggest that these enigmatic ancient humans were accomplished hunters.
go.nature.com
September 9, 2026 at 4:07 PM
An abandoned quarry in southwestern China has given scientists an unprecedented glimpse into the lives and abilities of the mysterious ancient humans called Denisovans
go.nature.com/46NsuVp
go.nature.com/46NsuVp
Reposted by Maddy Comerford
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415...
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Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...
doi.org
September 9, 2026 at 5:46 PM
We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415...
(1/n)
(1/n)
Reposted by Maddy Comerford
AI model AlphaGenome forecasts the consequences of altering every single DNA letter in the human genome
go.nature.com/4xQ7ZDK
go.nature.com/4xQ7ZDK
DeepMind’s new genome ‘atlas’ charts effects of all 9 billion human gene mutations
AI model AlphaGenome forecasts the consequences of altering every single DNA letter in the human genome.
go.nature.com
September 8, 2026 at 2:31 PM
AI model AlphaGenome forecasts the consequences of altering every single DNA letter in the human genome
go.nature.com/4xQ7ZDK
go.nature.com/4xQ7ZDK
Reposted by Maddy Comerford
Since they are not on Bluesky, here sharing the fantastic new paper by the Archaeo- and Paleogenetics group here in Tübingen on the settlement history of western Remote Oceania.🧬
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Ancient genomes reveal distinct human dispersals and social stratification in the settlement history of western Remote Oceania
The peopling of Remote Oceania involved some of humanity’s greatest expansions into
the open ocean. Ancient DNA spanning the last 3,000 years from the Solomon Islands,
Vanuatu, Fiji, and Tonga reveals...
www.cell.com
September 7, 2026 at 7:58 AM
Since they are not on Bluesky, here sharing the fantastic new paper by the Archaeo- and Paleogenetics group here in Tübingen on the settlement history of western Remote Oceania.🧬
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Maddy Comerford
Our paper on archaic introgression in imputed ancient genomes is out.
Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable.
doi.org/10.1038/s414...
Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable.
doi.org/10.1038/s414...
Archaic ancestry inference in imputed ancient human genomes - Nature Communications
Genotype imputation enables accurate detection of Neanderthal and Denisovan ancestry in low-coverage ancient genomes and allows the identification of introgressed haplotypes as well as candidate genes...
doi.org
September 4, 2026 at 3:13 PM
Our paper on archaic introgression in imputed ancient genomes is out.
Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable.
doi.org/10.1038/s414...
Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable.
doi.org/10.1038/s414...
Reposted by Maddy Comerford
cool
Using sequence-to-function models to interpret archaic hominin introgression https://www.biorxiv.org/content/10.64898/2026.08.31.748430v1
September 2, 2026 at 4:21 AM
cool
Very pleased to be sharing this one! Understanding the consequences of Denisovan introgression remains challenging given the poor representation of global introgression in functional genomics resources. We wanted to know if, and how, AlphaGenome could help us navigate that gap 🧭 ⬇️
Using sequence-to-function models to interpret archaic hominin introgression https://www.biorxiv.org/content/10.64898/2026.08.31.748430v1
September 3, 2026 at 5:56 AM
Very pleased to be sharing this one! Understanding the consequences of Denisovan introgression remains challenging given the poor representation of global introgression in functional genomics resources. We wanted to know if, and how, AlphaGenome could help us navigate that gap 🧭 ⬇️
Reposted by Maddy Comerford
Here's something a bit different that we've been noodling around with! Nearly 10y ago we established a panel of cell lines from Papuan donors, which let us check predictions from AlphaGenome against experimental data. If you've followed the field you'll know that expression prediction is very tough
Using sequence-to-function models to interpret archaic hominin introgression https://www.biorxiv.org/content/10.64898/2026.08.31.748430v1
September 3, 2026 at 2:54 AM
Here's something a bit different that we've been noodling around with! Nearly 10y ago we established a panel of cell lines from Papuan donors, which let us check predictions from AlphaGenome against experimental data. If you've followed the field you'll know that expression prediction is very tough
Reposted by Maddy Comerford
Ancient parchments, covered in ancient disease DNA! Researchers led by @ucddublin.bsky.social's @gingerhowley.bsky.social recover the genes of a deadly animal pathogen from medieval manuscripts. @science.org
Ancient sheep virus found hiding in medieval parchment
Newly recovered sheeppox sequences reveal when and how the virus emerged
www.science.org
September 2, 2026 at 8:06 PM
Ancient parchments, covered in ancient disease DNA! Researchers led by @ucddublin.bsky.social's @gingerhowley.bsky.social recover the genes of a deadly animal pathogen from medieval manuscripts. @science.org
Reposted by Maddy Comerford
This is what a Jurassic forest may have sounded like.
By combining exquisitely preserved fossil wings with experiments on living insects, computer simulations, and machine learning, scientists have re-created what they say is a partial Middle Jurassic soundscape. scim.ag/4cirWKy
By combining exquisitely preserved fossil wings with experiments on living insects, computer simulations, and machine learning, scientists have re-created what they say is a partial Middle Jurassic soundscape. scim.ag/4cirWKy
August 31, 2026 at 6:50 PM
This is what a Jurassic forest may have sounded like.
By combining exquisitely preserved fossil wings with experiments on living insects, computer simulations, and machine learning, scientists have re-created what they say is a partial Middle Jurassic soundscape. scim.ag/4cirWKy
By combining exquisitely preserved fossil wings with experiments on living insects, computer simulations, and machine learning, scientists have re-created what they say is a partial Middle Jurassic soundscape. scim.ag/4cirWKy
Reposted by Maddy Comerford
I'm very excited to share the preprint of the central project of my postdoc, titled "Sequence-to-function deep learning decodes human cis-regulatory evolution" available today on BioRxiv.
Preprint: www.biorxiv.org/content/10.6...
Preprint: www.biorxiv.org/content/10.6...
August 28, 2026 at 5:05 PM
I'm very excited to share the preprint of the central project of my postdoc, titled "Sequence-to-function deep learning decodes human cis-regulatory evolution" available today on BioRxiv.
Preprint: www.biorxiv.org/content/10.6...
Preprint: www.biorxiv.org/content/10.6...
Reposted by Maddy Comerford
Agwamba et al. identify the western Iberian Peninsula as the primary source of American populations of house mice; divergence dates are consistent with post-15th-century European maritime expansion and settlement in the Americas
🔗 academic.oup.com/gbe/article/...
#societyjournal #evolution #genome
🔗 academic.oup.com/gbe/article/...
#societyjournal #evolution #genome
August 19, 2026 at 10:01 AM
Agwamba et al. identify the western Iberian Peninsula as the primary source of American populations of house mice; divergence dates are consistent with post-15th-century European maritime expansion and settlement in the Americas
🔗 academic.oup.com/gbe/article/...
#societyjournal #evolution #genome
🔗 academic.oup.com/gbe/article/...
#societyjournal #evolution #genome
Reposted by Maddy Comerford
A new international study, led by Associate Professor Irene Gallego Romero, has revealed gaps in how human diversity is represented and reported in some of the world’s largest public genomics databases.
Find out more: www.svi.edu.au/news-events/...
Find out more: www.svi.edu.au/news-events/...
August 21, 2026 at 12:22 AM
A new international study, led by Associate Professor Irene Gallego Romero, has revealed gaps in how human diversity is represented and reported in some of the world’s largest public genomics databases.
Find out more: www.svi.edu.au/news-events/...
Find out more: www.svi.edu.au/news-events/...
Reposted by Maddy Comerford
maybe this is my new lab photo?
August 18, 2026 at 9:23 AM
maybe this is my new lab photo?
Reposted by Maddy Comerford
Don't let the title mislead you - we parsed through 700,000 SRA record so you don't have to! We looked at who's doing research, where, who they're including, and how they're describing them.
In brief: knowledge generation is concentrated in HICs, and heavily features people who live in said HICs.
In brief: knowledge generation is concentrated in HICs, and heavily features people who live in said HICs.
Old lady in first author paper shocker! 🧪🧬🖥️
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
Reporting and representation of population descriptors in public RNA-seq databases
By combining repository metadata, genotype-inferred ancestry, and manual curation
of publications, Gallego Romero et al. demonstrate that public RNA-seq datasets are
dominated by samples from high-inc...
www.cell.com
August 14, 2026 at 6:34 AM
Don't let the title mislead you - we parsed through 700,000 SRA record so you don't have to! We looked at who's doing research, where, who they're including, and how they're describing them.
In brief: knowledge generation is concentrated in HICs, and heavily features people who live in said HICs.
In brief: knowledge generation is concentrated in HICs, and heavily features people who live in said HICs.
Reposted by Maddy Comerford
New preprint out! The Punan of Borneo offer rare windows into what happens molecularly when a hunter-gatherers transitions to a settled lifestyle, and the answer is: a lot and fast. Deep gratitude to the communities for their trust & participation. Feedback welcome 🙏
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers
The transition from hunter-gatherer to agricultural lifestyles is one of the landmarks in the history of human societies, but its phenotypic and immediate molecular consequences remain poorly understo...
www.biorxiv.org
August 14, 2026 at 2:15 AM
New preprint out! The Punan of Borneo offer rare windows into what happens molecularly when a hunter-gatherers transitions to a settled lifestyle, and the answer is: a lot and fast. Deep gratitude to the communities for their trust & participation. Feedback welcome 🙏
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Maddy Comerford
Old lady in first author paper shocker! 🧪🧬🖥️
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
Reporting and representation of population descriptors in public RNA-seq databases
By combining repository metadata, genotype-inferred ancestry, and manual curation
of publications, Gallego Romero et al. demonstrate that public RNA-seq datasets are
dominated by samples from high-inc...
www.cell.com
August 14, 2026 at 12:14 AM
Old lady in first author paper shocker! 🧪🧬🖥️
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
(ok but seriously I worked very hard on this and I am proud of it. Taught myself some neat new tricks while doing it, too!)
www.cell.com/cell-genomic...
Reposted by Maddy Comerford
We have a new preprint out :D
www.biorxiv.org/content/10.6...
Did Denisovans inherit their AMBN gene from Homo erectus?
We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social
~Summary below~
www.biorxiv.org/content/10.6...
Did Denisovans inherit their AMBN gene from Homo erectus?
We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social
~Summary below~
August 13, 2026 at 12:20 PM
We have a new preprint out :D
www.biorxiv.org/content/10.6...
Did Denisovans inherit their AMBN gene from Homo erectus?
We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social
~Summary below~
www.biorxiv.org/content/10.6...
Did Denisovans inherit their AMBN gene from Homo erectus?
We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social
~Summary below~
Reposted by Maddy Comerford
Denisovan leg bones from Taiwan reveal large body size https://www.biorxiv.org/content/10.64898/2026.08.07.743438v1
August 8, 2026 at 10:00 AM
Denisovan leg bones from Taiwan reveal large body size https://www.biorxiv.org/content/10.64898/2026.08.07.743438v1
Reposted by Maddy Comerford
Must-know numbers in human genetics --
As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties.
jkpritchard.substack.com/p/on-fermi-p...
As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties.
jkpritchard.substack.com/p/on-fermi-p...
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
jkpritchard.substack.com
August 9, 2026 at 6:13 PM
Must-know numbers in human genetics --
As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties.
jkpritchard.substack.com/p/on-fermi-p...
As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties.
jkpritchard.substack.com/p/on-fermi-p...
Reposted by Maddy Comerford
Some of the last surviving Neanderthals of northwestern Europe may have lived in large, well-connected groups, separate from other Neanderthals and early humans, according to research in Nature. go.nature.com/4ahgsWF 🧬🏺🧪
June 24, 2026 at 10:15 PM
Some of the last surviving Neanderthals of northwestern Europe may have lived in large, well-connected groups, separate from other Neanderthals and early humans, according to research in Nature. go.nature.com/4ahgsWF 🧬🏺🧪
Reposted by Maddy Comerford
The 12 souls aboard will drift for a long 8 months, mostly without seeing the Sun, through one of the most inhospitable and least explored regions on Earth. Fun story by Richard Stone for @science.org
A dozen people will spend 8 months trapped in Arctic ice—for science
Battling darkness and cold, researchers on a drifting laboratory will probe the biology of the Arctic Ocean
www.science.org
June 24, 2026 at 11:40 AM
The 12 souls aboard will drift for a long 8 months, mostly without seeing the Sun, through one of the most inhospitable and least explored regions on Earth. Fun story by Richard Stone for @science.org
Reposted by Maddy Comerford
So happy and proud to see this paper out in @natcomms.nature.com today! We show that traces of human DNA can persist on cave walls for thousands of years.
Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team!
www.nature.com/articles/s41...
Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team!
www.nature.com/articles/s41...
Investigating ancient human DNA preservation on cave walls and in rock art - Nature Communications
Ancient DNA can be preserved on materials from archaeological floor deposits such as bones, sediments and artifacts. Here, the authors investigate whether Palaeolithic wall art can preserve human DNA ...
www.nature.com
June 23, 2026 at 6:58 PM
So happy and proud to see this paper out in @natcomms.nature.com today! We show that traces of human DNA can persist on cave walls for thousands of years.
Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team!
www.nature.com/articles/s41...
Absolutely fantastic work by the wonderful Alba Bossoms Mesa at @mpi-eva-leipzig.bsky.social and a great team!
www.nature.com/articles/s41...