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Tianxiong (Bear) Yu

@tianxiong-bear-yu.bsky.social
95 followers 179 following 15 posts

Instructor in UMass Chan Medical School. Focus on using Computational Methods to study transposons in human and koala genomes.

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Reposted by Tianxiong (Bear) Yu
Kaili Fan @kailifan.bsky.social · 05/10/2026
1/13 The human body runs on one genome—but every cell reads it differently. How? To find out, we need to measure both gene expression and chromatin accessibility in the same nucleus. So we did, across 21 adult tissues and nearly half a million nuclei. 🧵 🔗 www.biorxiv.org/content/10.6...
biorxiv.org
Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues
Diverse human cell types establish specialized functions through lineage- and context-specific regulatory programs. Interpreting non-coding genetic risk requires integrated multi-omic reference maps t...
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Tianxiong (Bear) Yu @tianxiong-bear-yu.bsky.social · 05/10/2026
Excited to share our latest paper in Genome Biology! We analyzed 405 wild koalas to reconstruct the ongoing invasion of KoRV-A, one of the few opportunities to observe ERV evolution in real time. Great work by all collaborators. @lubanlab.bsky.social link.springer.com/article/10.1...
link.springer.com
The trajectory of KoRV-A evolution suggests initial integration into the koala germline genome near Coffs Harbour in New South Wales - Genome Biology
Background Koala Retrovirus-A is a gamma-retrovirus that is spreading across wild koala populations through horizontal and vertical transmission, contributing significantly to genomic diversity across...
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Reposted by Tianxiong (Bear) Yu
The EMBO Journal @embojournal.org · 19/03/2026
How do meiotic gene promoters become accessible prior to prophase I? Deniz Özata, @tianxiong-bear-yu.bsky.social and coworkers find that NFYA primes timely gene activation by establishing a poised chromatin state with paused RNA polymerase II link.springer.com/article/10.1...
link.springer.com
Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice - The EMBO Journal
Meiotic prophase I, characterized by homologous recombination and synapsis, is a critical step in spermatogenesis. This process entails extensive changes to chromatin and transcription. Prior to proph...
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Reposted by Tianxiong (Bear) Yu
Alice Godden @alicegodden.bsky.social · 13/12/2025
Delighted to see our work picked up by @theguardian.com this is a real window of opportunity for us to reduce carbon emissions to give the bears a hope at survival before it really is too late.
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Reposted by Tianxiong (Bear) Yu
Alice Godden @alicegodden.bsky.social · 16/11/2025
🚨 New preprint alert! Our latest work from @immler.bsky.social lab 🐟🧬 Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells #TESky #TE #piRNA #miRNA #zebrafish #DanioDigest 🔗 Read here www.biorxiv.org/content/10.1... A thread 🧵...
biorxiv.org
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
Environmental fluctuations influence heritable phenotypes through complex molecular mechanisms. In zebrafish (Danio rerio), the interplay between temperature variation, transposable element (TE) activ...
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Reposted by Tianxiong (Bear) Yu
Toby Baril @tobybarilbio.bsky.social · 19/08/2025
At @eseb.bsky.social #ESEB2025 and want to connect with other researchers working on transposable elements? Take a look at the #TEWorldwide #TEsky feed: bsky.app/profile/did:...
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Reposted by Tianxiong (Bear) Yu
Prof Steven Lee @stevethechemist.bsky.social · 01/10/2025
Our work on visualising protein aggregates in human brain tissue in Parkinson's disease was published today in Nature Biomedical Engineering, well done to Becs, Bin and Christina for their hardwork! www.cam.ac.uk/research/new...
cam.ac.uk
Parkinson’s ‘trigger’ directly observed in human brain tissue for the first time
Scientists have, for the first time, directly visualised and quantified the protein clusters believed to trigger Parkinson’s, marking a major advance in the
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Tianxiong (Bear) Yu @tianxiong-bear-yu.bsky.social · 03/09/2025
As we age, our brains change at both the genomic and transcriptomic levels. 🧠✨ In our new Nature @nature.com paper, we map these changes at single-cell resolution in the human prefrontal cortex from infancy to centenarian. Honored to lead the data analysis and be co-first author on this work!
nature.com
Single-cell transcriptomic and genomic changes in the ageing human brain - Nature
Sequencing analyses of human prefrontal cortex from donors ranging in age from 0.4 to 104 years show that ageing correlates with an accumulation of somatic mutations in short housekeeping genes a...
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Reposted by Tianxiong (Bear) Yu
Michael Haslam @twigtechnology.bsky.social · 26/08/2025
New study led by Joanna Baker shows bigger brains and relatively longer thumbs coevolved in primates. Humans have huge thumbs, but only what our brain size (esp. neocortex) would predict. It’s NOT driven by tool use. A fantastic paper with a huge amount of work, and superb data presentation 🧪🏺👍🧠💀🐒🦧
nature.com
Human dexterity and brains evolved hand in hand - Communications Biology
Thumbs and brains coevolved in primates. Across living and extinct species, longer thumbs predict bigger brains, highlighting the neural cost of dexterity.
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Reposted by Tianxiong (Bear) Yu
Julius Brennecke @juliusbrennecke.bsky.social · 16/07/2025
Pls. share widely Calling all transposon fans & lovers of genetic innovation MOBILE GENOME welcomes you in Heidelberg, Nov. 4–7 2025 → Vibrant & friendly community → Cutting-edge talks from mechanisms to physiology → Plenty of surprises (TEs never stop innovating) submit abstract by July 29
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Tianxiong (Bear) Yu @tianxiong-bear-yu.bsky.social · 10/07/2025
Finally got my personal academia website done. I am glad it looks well-organized for both laptop and phone. Big shout to "Academia Pages" GitHub pages template. tianxiongbb.github.io
tianxiongbb.github.io
About me
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Reposted by Tianxiong (Bear) Yu
Selin Jessa @selinjessa.com · 03/05/2025
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
biorxiv.org
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
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Reposted by Tianxiong (Bear) Yu
Cell - a Cell Press journal @cp-cell.bsky.social · 17/04/2025
The new issue is out! 👉 cell.com/cell/current ⁠ In this issue of Cell, Yu et al. capture evolution of KoRV-A transcriptional silencing as the virus transitions from a pathogen to a stable endogenous retrovirus. The cover features an adult koala with a joey. 📷 Credit: Currumbin Wildlife Sanctuary
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Jim Johnson 🇨🇦 @jimjohnsonsci.bsky.social · 04/04/2025
www.nature.com/naturecareer... UBC LSI Job!!
nature.com
Assistant Professor (tenure track) – Chromatin, Epigenetics - Vancouver, British Columbia (CA) job with The University of British Columbia (UBC) | 12837841
Assistant Professor (tenure track) - Chromatin Regulation, Genetic Regulatory Mechanisms, Epigenetics, Epigenomics
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Nature @nature.com · 29/03/2025
🧪 A paralysed man can stand on his own after receiving an injection of neural stem cells to treat his spinal cord injury go.nature.com/4jaZ3RB
go.nature.com
Paralysed man stands again after receiving ‘reprogrammed’ stem cells
Nature - Another man also regained some movement, but two others experienced minimal improvement.
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Reposted by Tianxiong (Bear) Yu
Julius Brennecke @juliusbrennecke.bsky.social · 29/03/2025
We are seeking a new colleague to join us at the Vienna BioCenter, specifically at my beloved home institution, IMBA @imbavienna.bsky.social we value collegiality and a passion for curiosity driven science. Being a great and fun human being also helps!
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Reposted by Tianxiong (Bear) Yu
Dr. Tyler A. Elliott @transposableman.bsky.social · 21/03/2025
#TEsky The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition doi.org/10.7554/eLif...
doi.org
The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition
DNA hypomethylation in human tumor cells results in the activation of the LINE-1-derived RNA-binding protein L1TD1 and its interactions with LINE-1 transposons.
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Reposted by Tianxiong (Bear) Yu
@LaBonneLaB @labonnelab.bsky.social · 19/03/2025
Super exciting and beautiful new work from the talented @mathithiru.bsky.social www.nature.com/articles/s41...
nature.com
Repurposing of a gill gene regulatory program for outer-ear evolution - Nature
A study on the evolutionary origin of the mammalian outer ear finds that it shares genetic programs with the gills of fishes and amphibians, indicating that elements of an ancestral gill have been reu...
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Reposted by Tianxiong (Bear) Yu
Julius Brennecke @juliusbrennecke.bsky.social · 17/03/2025
In the ‘90s, Pelisson et al. found that gypsy retrotransposons in flies can go viral—literally—thanks to an envelope gene. Now, @mayavoichek.bsky.social uncovers a wild new path to retrotransposon infectivity. A fascinating story—see Maya's thread www.biorxiv.org/content/10.1101/2025.03.14.642691v2
biorxiv.org
Direct cell-to-cell transmission of retrotransposons
Transposable elements are abundant in host genomes but are generally considered to be confined to the cell in which they are expressed, with the notable exception of endogenous retroviruses. Here, we ...
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Reposted by Tianxiong (Bear) Yu
UMass Chan Medical School @umasschan.bsky.social · 17/03/2025
Working with a team at the University of Queensland, UMass Chan scientists have discovered that a population of koalas has evolved genomic immunity to a retrovirus: direc.to/mDfy #koalas @lubanlab.bsky.social @tianxiong-bear-yu.bsky.social
William E. Theurkauf, PhD; Jeremy Luban, MD; Tianxiong Yu, PhD; and Zhiping Weng, PhDA koala
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Saez-Rodriguez Group @saezlab.bsky.social · 14/03/2025
📄 Update on our preprint about Gene Regulatory Net (GRN) benchmarking 📄 We have included the original and decoupled version of SCENIC+, added a new metric and two more databases. Dictys and SCENIC+ outperformed others, but still performed poorly in causal mechanistic tasks. doi.org/10.1101/2024... 👇
Performance of multimodal GRN inference methods. SCENIC+ and Dictys outperform others.
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Reposted by Tianxiong (Bear) Yu
Wayo Matsushima @wayomayo.bsky.social · 10/03/2025
New preprint of my postdoc work! We found a novel group of zinc-finger proteins that rapidly evolved in a lineage-specific manner to repress regulatory activities of transposon-derived sequences through anchoring nucleosomes. #TEsky biorxiv.org/content/10.110…
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Tianxiong (Bear) Yu @tianxiong-bear-yu.bsky.social · 09/03/2025
I am thrilled to share our story online at @cellpress.bsky.social . Big thanks to all authors: Zhiping, Bill, @lubanlab.bsky.social, Keith & bluesky-less! authors.elsevier.com/c/1kjdaL7PXu... How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it. #Retrovirus #koala #piRNA More below 👇
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