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Riley Mangan

@rimangan.bsky.social
94 followers 154 following 19 posts

Computational Biologist. Postdoc at MIT/Broad

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Reposted by Riley Mangan
Nature @nature.com · 23/09/2026
Nature research paper: The gene-regulatory evolution of the human skeleton go.nature.com/46GUxG8
go.nature.com
The gene-regulatory evolution of the human skeleton - Nature
Massively parallel reporter assays and human–ape hybrid skeletal cells are used to study the evolution of human cis-regulatory elements (CREs), revealing how differences in CREs have shaped the composition of human skeletal tissue.
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Riley Mangan @rimangan.bsky.social · 23/09/2026
I'm thrilled to share that a study I co-led leveraging T2T human and ape genomes to expand and refine our identification of rapidly evolved regions in the human genome is now published in Cell Genomics! Paper: doi.org/10.1016/j.xg...
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Reposted by Riley Mangan
EMBL Events @events.embl.org · 17/09/2026
Day 3 of #EESHuman with talks by riley mangan about deep learning prediction of cis-regulatory turnover in human evolution and Shop Mallick about the ultima ancient DNA resource 🧬🦴 Many discussions were sparked in the following coffee break 💫 @EMBO @EMBLEvents
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Reposted by Riley Mangan
bioRxiv Genomics @biorxiv-genomic.bsky.social · 28/08/2026
Sequence-to-function deep learning decodes human cis-regulatory evolution www.biorxiv.org/content/10.64898/20…
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Riley Mangan @rimangan.bsky.social · 28/08/2026
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...
Figure 1: Sequence-based deep learning prediction of lineage-specific cis-regulatory elements in human evolution  (a) Identification of lineage-specific cis-regulatory elements (linCREs). We generated diploid personalized genomes across 17 hominin and great ape short read sequencing libraries through reference-guided assembly. We used Enformer22 to predict genome-wide chromatin accessibility profiles across 100 epigenomic contexts across all 34 haplotypes. We compared chromatin accessibility at open chromatin elements to identify linCREs. (b) Six classes of linCREs, defined by the lineage and direction of differential accessibility. Schematics at top illustrate accessibility profiles defining each class. Total linCRE instances and the number of distinct loci are reported for each class. Predicted accessibility across all 34 haplotypes in a 3kb window centered on a representative example element of each class are shown below, colored by lineage.
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Reposted by Riley Mangan
Cedric Boeckx @cedricboeckx.bsky.social · 21/10/2025
“Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans” New work on HAQERs, by @rimangan.bsky.social Yanting Luo Craig Lowe @debbysilver.bsky.social @manoliskellis.bsky.social & colleagues 🧪🧬 www.biorxiv.org/content/10.1...
biorxiv.org
Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans
Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on single assemb...
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Reposted by Riley Mangan
Debby Silver @debbysilver.bsky.social · 14/05/2025
Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...
nature.com
A human-specific enhancer fine-tunes radial glia potency and corticogenesis - Nature
HARE5, a human accelerated region enhancer, modulates cortical development by influencing neural progenitor cell behaviour, leading to an enlarged neocortex with increased functional independence betw...
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Reposted by Riley Mangan
Adam Phillippy @aphillippy.bsky.social · 09/04/2025
A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...
A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.
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Reposted by Riley Mangan
bioRxiv Genomics @biorxiv-genomic.bsky.social · 09/02/2025
Genome Sequence of a Marine Threespine Stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet www.biorxiv.org/content/10.1101/202…
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Reposted by Riley Mangan
Anshul Kundaje @anshulkundaje.bsky.social · 08/01/2025
Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction. www.nature.com/articles/s41... 1/
nature.com
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics
Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.
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Reposted by Riley Mangan
Gencode Genes @gencodegenes.bsky.social · 21/11/2024
We're pleased to share our GENCODE 2025 NAR database paper: tinyurl.com/3etnfw4j Thanks to all our collaborators, friends and users. This is now the main citation for our resource, and hopefully also a good explanation of how and why we do what we do.
tinyurl.com
GENCODE 2025: reference gene annotation for human and mouse
Abstract. GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as n
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