Latest from Shendure & Qiu labs (@cxqiu.bsky.social)
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
April 10, 2026 at 12:40 AM
Latest from Shendure & Qiu labs (@cxqiu.bsky.social)
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
)! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
(1/3) 🌍 EBP’s Zoonomia Project (zoonomiaproject.org) is transforming how we understand both biodiversity and human health!
#Zoonomia #Science Article 2023:
www.science.org/doi/10.1126/...
www.sciencenews.org/article/find...
#ComparativeGenomics #ZoonomiaProject #Evolution #Conservation
#Zoonomia #Science Article 2023:
www.science.org/doi/10.1126/...
www.sciencenews.org/article/find...
#ComparativeGenomics #ZoonomiaProject #Evolution #Conservation
June 12, 2025 at 5:58 PM
(1/3) 🌍 EBP’s Zoonomia Project (zoonomiaproject.org) is transforming how we understand both biodiversity and human health!
#Zoonomia #Science Article 2023:
www.science.org/doi/10.1126/...
www.sciencenews.org/article/find...
#ComparativeGenomics #ZoonomiaProject #Evolution #Conservation
#Zoonomia #Science Article 2023:
www.science.org/doi/10.1126/...
www.sciencenews.org/article/find...
#ComparativeGenomics #ZoonomiaProject #Evolution #Conservation
Died This Day: Erasmus Darwin (Dec 12, 1731 – April 18, 1802). Grandfather of Charles Darwin, he was a philosopher/naturalist who formulated one of the first theories of evolution in his ‘Zoonomia’ (1794-1796). In it he discussed how life evolved from a single common ancestor
April 18, 2025 at 1:54 PM
Died This Day: Erasmus Darwin (Dec 12, 1731 – April 18, 1802). Grandfather of Charles Darwin, he was a philosopher/naturalist who formulated one of the first theories of evolution in his ‘Zoonomia’ (1794-1796). In it he discussed how life evolved from a single common ancestor
Really enjoyed the inspiring talk given by @elinork.bsky.social for the first inaugural Janet Thornton lecture! Demonstrates the exciting future ahead for #comparativegenomics led by the #zoonomia consortium @earlhaminst.bsky.social
November 25, 2024 at 3:54 PM
Really enjoyed the inspiring talk given by @elinork.bsky.social for the first inaugural Janet Thornton lecture! Demonstrates the exciting future ahead for #comparativegenomics led by the #zoonomia consortium @earlhaminst.bsky.social
They sequenced Balto's DNA. I live for this shit
July 21, 2026 at 12:15 PM
They sequenced Balto's DNA. I live for this shit
Leveraging the conserved enhancer code and the large number of available mammalian genomes (Zoonomia consortium, doi.org/10.1038/s41586-020-2876-6), we inferred CRE accessibility across 240 mammals and reconstructed the evolutionary histories of human CREs.
March 16, 2025 at 10:31 AM
Leveraging the conserved enhancer code and the large number of available mammalian genomes (Zoonomia consortium, doi.org/10.1038/s41586-020-2876-6), we inferred CRE accessibility across 240 mammals and reconstructed the evolutionary histories of human CREs.
Huge thanks to the teams whose work inspired Gencube:
🔹 GenArk team (e.g., @genomebrowser.bsky.social )
🔹 Ensembl Beta ( @ensembl.bsky.social )
🔹 Zoonomia Consortium ( @elinork.bsky.social & @KltLab)
Your contributions to scalable infrastructure and comparative genomics were truly foundational. 🙏
🔹 GenArk team (e.g., @genomebrowser.bsky.social )
🔹 Ensembl Beta ( @ensembl.bsky.social )
🔹 Zoonomia Consortium ( @elinork.bsky.social & @KltLab)
Your contributions to scalable infrastructure and comparative genomics were truly foundational. 🙏
April 30, 2025 at 5:12 PM
Huge thanks to the teams whose work inspired Gencube:
🔹 GenArk team (e.g., @genomebrowser.bsky.social )
🔹 Ensembl Beta ( @ensembl.bsky.social )
🔹 Zoonomia Consortium ( @elinork.bsky.social & @KltLab)
Your contributions to scalable infrastructure and comparative genomics were truly foundational. 🙏
🔹 GenArk team (e.g., @genomebrowser.bsky.social )
🔹 Ensembl Beta ( @ensembl.bsky.social )
🔹 Zoonomia Consortium ( @elinork.bsky.social & @KltLab)
Your contributions to scalable infrastructure and comparative genomics were truly foundational. 🙏
Huge team effort led by CX Qiu, Riza Daza, and Ian Welsh. Jay Shendure supervised the project. Key contributions from Rupali Patwardhan, @niklaskemp.bsky.social & @steinaerts.bsky.social (CREsted), built on our mouse timelapse with @coletrapnell.bsky.social. Grateful to the whole team and Zoonomia.
April 9, 2026 at 9:02 PM
Huge team effort led by CX Qiu, Riza Daza, and Ian Welsh. Jay Shendure supervised the project. Key contributions from Rupali Patwardhan, @niklaskemp.bsky.social & @steinaerts.bsky.social (CREsted), built on our mouse timelapse with @coletrapnell.bsky.social. Grateful to the whole team and Zoonomia.
Brian Aldiss' "Billion Year Spree: The True History of Science Fiction" (1973) begins with a 50-page chapter on Mary Shelley, how it was inspired by Erasmus Darwin's "Zoonomia", how she also wrote the first post-apocalyptic book ("The Last Man"), and a short story anticipating Dr Jekyll and Mr Hyde.
September 21, 2024 at 9:49 AM
Brian Aldiss' "Billion Year Spree: The True History of Science Fiction" (1973) begins with a 50-page chapter on Mary Shelley, how it was inspired by Erasmus Darwin's "Zoonomia", how she also wrote the first post-apocalyptic book ("The Last Man"), and a short story anticipating Dr Jekyll and Mr Hyde.
Leaving Boston for ☀️ San Diego #PAG31 starting off w AMAZING Comparative Mammalian Genomics workshop FRIDAY at 10:30AM!!! Gene loss! Cattle GWAS! Bats! Viruses! Primary fibroblast cultures! Zoonomia! AND HIBERNATING BEARS (Warning: as cochair w @elliecat.bsky.social I’m slightly biased)
January 11, 2024 at 10:27 PM
Leaving Boston for ☀️ San Diego #PAG31 starting off w AMAZING Comparative Mammalian Genomics workshop FRIDAY at 10:30AM!!! Gene loss! Cattle GWAS! Bats! Viruses! Primary fibroblast cultures! Zoonomia! AND HIBERNATING BEARS (Warning: as cochair w @elliecat.bsky.social I’m slightly biased)
Honey badger is one of the species sequenced as part of the Zoonomia project, in an effort to better understand evolutionary constraint, and novel evolutionary genetics. www.science.org/doi/10.1126/... #2026MMM
March 27, 2026 at 12:07 AM
Honey badger is one of the species sequenced as part of the Zoonomia project, in an effort to better understand evolutionary constraint, and novel evolutionary genetics. www.science.org/doi/10.1126/... #2026MMM
We applied STEAM to all 241 Zoonomia genomes: 32 × 241 = 7,712 genome-wide enhancer tracks. HumMus for human + mouse. BabaGanoush for the full spread!
April 9, 2026 at 9:02 PM
We applied STEAM to all 241 Zoonomia genomes: 32 × 241 = 7,712 genome-wide enhancer tracks. HumMus for human + mouse. BabaGanoush for the full spread!
Meet the Malayan tapir, the herbivore with a taste for variety! From fruits and leaves to bark and grasses, this gentle giant loves to graze in Southeast Asia’s jungles. Its genome was sequenced by both Zoonomia Project and Vertebrate Genome Project, unveiling the secrets of this unique creature.
December 18, 2024 at 9:51 PM
Meet the Malayan tapir, the herbivore with a taste for variety! From fruits and leaves to bark and grasses, this gentle giant loves to graze in Southeast Asia’s jungles. Its genome was sequenced by both Zoonomia Project and Vertebrate Genome Project, unveiling the secrets of this unique creature.
The library also has a first edition of Darwin’s Origin of Species. But while this wasn’t on display they did have a copy of his grandfather Erasmus Darwin’s Zoonomia on display.
It was great to see John Stevens Henslow get a mention too. He was influential in Charles Darwin’s career.
It was great to see John Stevens Henslow get a mention too. He was influential in Charles Darwin’s career.
June 1, 2026 at 3:56 PM
The library also has a first edition of Darwin’s Origin of Species. But while this wasn’t on display they did have a copy of his grandfather Erasmus Darwin’s Zoonomia on display.
It was great to see John Stevens Henslow get a mention too. He was influential in Charles Darwin’s career.
It was great to see John Stevens Henslow get a mention too. He was influential in Charles Darwin’s career.
2023: Findings from the Zoonomia Project are published, in which the genomes of 240 mammals are collected and compared; they reveal that 10.7% of the human genome is identical across almost all species
April 27, 2026 at 2:37 PM
2023: Findings from the Zoonomia Project are published, in which the genomes of 240 mammals are collected and compared; they reveal that 10.7% of the human genome is identical across almost all species
"heavily conditioning on the outcome of survival" and reproduction, aka natural selection 🙂
Protein coding sequences are highly conserved across species (and many non-coding sequences are too), e.g. www.science.org/doi/10.1126/...
Protein coding sequences are highly conserved across species (and many non-coding sequences are too), e.g. www.science.org/doi/10.1126/...
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...
www.science.org
June 29, 2025 at 4:11 PM
"heavily conditioning on the outcome of survival" and reproduction, aka natural selection 🙂
Protein coding sequences are highly conserved across species (and many non-coding sequences are too), e.g. www.science.org/doi/10.1126/...
Protein coding sequences are highly conserved across species (and many non-coding sequences are too), e.g. www.science.org/doi/10.1126/...
Enter STEAM: we augment training with syntenic enhancer orthologs from up to 241 Zoonomia genomes — a ~200× expansion in sequence diversity, preserving cell-class labels. Orthologous enhancers are nature's data augmentation: divergent sequences, shared function.
April 9, 2026 at 9:02 PM
Enter STEAM: we augment training with syntenic enhancer orthologs from up to 241 Zoonomia genomes — a ~200× expansion in sequence diversity, preserving cell-class labels. Orthologous enhancers are nature's data augmentation: divergent sequences, shared function.
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
![OCR Ortholog Open Chromatin Status Prediction Framework Overview. a We trained a convolutional neural network (CNN) for predicting brain open chromatin using sequences underlying brain open chromatin region (OCR) orthologs in a small number of species and used the CNN to predict brain OCR ortholog open chromatin status across the species in the Zoonomia Consortium. Specifically, we used the sequences underlying the orthologs for which we have brain open chromatin data to train a CNN for predicting open chromatin. Then, we used the CNN to predict the probability of brain open chromatin for all brain OCR orthologs; predictions are illustrated on the right. Animals for which we do not have open chromatin data are in dark gray instead of black to indicate that their brain open chromatin is imputed. While we cannot evaluate the accuracy of most of our predictions, obtaining open chromatin data from most tissues in most species is infeasible, so predictions might be the best OCR annotations that we can obtain. b To demonstrate that our models can accurately predict whether sequence differences between species are associated with open chromatin differences, in addition to the evaluations described in previous work [57], we evaluated our performance on species-specific open chromatin for a species not used in model training and clade-specific open and closed chromatin for clades not used in model training. Since such regions often comprise a minority of OCR orthologs, models could obtain good overall performance while obtaining poor performance on such regions. We also evaluated our performance on tissue-specific open and closed chromatin for a tissue not used in model training, where we expect models to predict 0 if model learns sequence signatures related to the tissue used in training. c Full mouse test set and lineage-specific OCR accuracy evaluations for mouse sequence-only brain model, illustrating that, even for the best of these models,](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:jkd2l647lviezhenqed454lh/bafkreicgkhegfuippjqhdt2tkku6dr74stuf5znohmtovfk5zojt5w7xkq)
November 7, 2025 at 2:28 PM
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
If anyone is interested, I've updated our take on a cellular basis of the mammalian nocturnal-diurnal switch @biorxivpreprint.bsky.social
We've refined the paper (for the better, hopefully!) - my fave updates are the results from a collab with Zoonomia (Fig 3)
www.biorxiv.org/content/10.1...
We've refined the paper (for the better, hopefully!) - my fave updates are the results from a collab with Zoonomia (Fig 3)
www.biorxiv.org/content/10.1...
A cellular basis for the mammalian nocturnal-diurnal switch
Early mammals were nocturnal until the Cretaceous-Paleogene extinction enabled diurnal niche expansion. Diurnality evolved multiple times independently, but the mechanisms driving this shift remain un...
www.biorxiv.org
April 24, 2025 at 10:29 AM
If anyone is interested, I've updated our take on a cellular basis of the mammalian nocturnal-diurnal switch @biorxivpreprint.bsky.social
We've refined the paper (for the better, hopefully!) - my fave updates are the results from a collab with Zoonomia (Fig 3)
www.biorxiv.org/content/10.1...
We've refined the paper (for the better, hopefully!) - my fave updates are the results from a collab with Zoonomia (Fig 3)
www.biorxiv.org/content/10.1...
In our annotation curation, we included lots of scATAC, cCREs from ENCODE, conservation from Zoonomia, pathogenicity from AlphaMissense, among others. Generally - PRSFNN "learns" that low-frequency SNPs in accessible chromatin are likely to have larger effect sizes (maybe not that surprising).
July 22, 2025 at 9:25 PM
In our annotation curation, we included lots of scATAC, cCREs from ENCODE, conservation from Zoonomia, pathogenicity from AlphaMissense, among others. Generally - PRSFNN "learns" that low-frequency SNPs in accessible chromatin are likely to have larger effect sizes (maybe not that surprising).
BREAKING BALTO NEWS.
“Now, decades later, the sequencing of Balto’s genome has laid to rest an old rumor that he was actually a wolf. “He was not a wolf,” Moon said. “He was just a good boy.”
https://www.washingtonpost.com/climate-environment/2023/04/27/balto-dog-mammals-zoonomia/
“Now, decades later, the sequencing of Balto’s genome has laid to rest an old rumor that he was actually a wolf. “He was not a wolf,” Moon said. “He was just a good boy.”
https://www.washingtonpost.com/climate-environment/2023/04/27/balto-dog-mammals-zoonomia/
April 28, 2023 at 1:50 PM
BREAKING BALTO NEWS.
“Now, decades later, the sequencing of Balto’s genome has laid to rest an old rumor that he was actually a wolf. “He was not a wolf,” Moon said. “He was just a good boy.”
https://www.washingtonpost.com/climate-environment/2023/04/27/balto-dog-mammals-zoonomia/
“Now, decades later, the sequencing of Balto’s genome has laid to rest an old rumor that he was actually a wolf. “He was not a wolf,” Moon said. “He was just a good boy.”
https://www.washingtonpost.com/climate-environment/2023/04/27/balto-dog-mammals-zoonomia/
Watch out—these saiga antelopes aren't just about their unique, bulbous noses! Known for their wild and dramatic arguments, they’re nature’s own drama queens. Bonus: Their genome was sequenced by the Zoonomia Project unlocking deep insights into their evolutionary story.
December 22, 2024 at 4:07 PM
Watch out—these saiga antelopes aren't just about their unique, bulbous noses! Known for their wild and dramatic arguments, they’re nature’s own drama queens. Bonus: Their genome was sequenced by the Zoonomia Project unlocking deep insights into their evolutionary story.
14. Consistent with much of the human genome comprising inactive and neutrally evolving TEs, studies typically find that less than 15% of the human genome is constrained by purifying selection (i.e., is functional), for example 10.7% in this recent study: www.science.org/doi/full/10....
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...
www.science.org
August 15, 2026 at 8:18 PM
14. Consistent with much of the human genome comprising inactive and neutrally evolving TEs, studies typically find that less than 15% of the human genome is constrained by purifying selection (i.e., is functional), for example 10.7% in this recent study: www.science.org/doi/full/10....
Kids these days be spoiled, what with their hundreds of Zoonomia genomes...back in my day, they just released the 7way multiz for vertebrates 🧬👨🏾💻🧬
November 22, 2024 at 12:03 AM
Kids these days be spoiled, what with their hundreds of Zoonomia genomes...back in my day, they just released the 7way multiz for vertebrates 🧬👨🏾💻🧬
Meet the proboscis monkey: nature's quirky comedian with a nose as big as its personality.
Its genome has been sequenced by the Zoonomia Project. Follow our LinkedIn for more indepth coverage on Zoonomia's publications.
www.linkedin.com/company/eart...
Its genome has been sequenced by the Zoonomia Project. Follow our LinkedIn for more indepth coverage on Zoonomia's publications.
www.linkedin.com/company/eart...
December 11, 2024 at 3:47 PM
Meet the proboscis monkey: nature's quirky comedian with a nose as big as its personality.
Its genome has been sequenced by the Zoonomia Project. Follow our LinkedIn for more indepth coverage on Zoonomia's publications.
www.linkedin.com/company/eart...
Its genome has been sequenced by the Zoonomia Project. Follow our LinkedIn for more indepth coverage on Zoonomia's publications.
www.linkedin.com/company/eart...