Tianxiong (Bear) Yu
@tianxiong-bear-yu.bsky.social
Instructor in UMass Chan Medical School. Focus on using Computational Methods to study transposons in human and koala genomes.
Pinned
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...
www.nature.com
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!
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!
Reposted by Tianxiong (Bear) Yu
🚨 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 🧵...
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 🧵...
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...
www.biorxiv.org
November 16, 2025 at 10:18 AM
🚨 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 🧵...
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 🧵...
Reposted by Tianxiong (Bear) Yu
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:...
Take a look at the #TEWorldwide #TEsky feed:
bsky.app/profile/did:...
August 19, 2025 at 1:01 PM
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:...
Take a look at the #TEWorldwide #TEsky feed:
bsky.app/profile/did:...
Reposted by Tianxiong (Bear) Yu
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...
www.cam.ac.uk/research/new...
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
www.cam.ac.uk
October 1, 2025 at 12:09 PM
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...
www.cam.ac.uk/research/new...
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!
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!
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...
www.nature.com
September 3, 2025 at 5:46 PM
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!
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!
Reposted by Tianxiong (Bear) Yu
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 🧪🏺👍🧠💀🐒🦧
A fantastic paper with a huge amount of work, and superb data presentation 🧪🏺👍🧠💀🐒🦧
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.
www.nature.com
August 26, 2025 at 10:01 AM
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 🧪🏺👍🧠💀🐒🦧
A fantastic paper with a huge amount of work, and superb data presentation 🧪🏺👍🧠💀🐒🦧
Reposted by Tianxiong (Bear) Yu
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
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
⏰ Abstract deadline for 'The mobile genome' is 29 July!
👉 https://s.embl.org/mge25-01-bl
Join us 4–7 Nov 2025 at EMBL Heidelberg (or online) to explore the impact of TEs across biology. 🧬🔍
⭐🧑🏼🔬 24 talks + 15 flash talks from posters – don't miss out!
#EMBOMobileGenome
👉 https://s.embl.org/mge25-01-bl
Join us 4–7 Nov 2025 at EMBL Heidelberg (or online) to explore the impact of TEs across biology. 🧬🔍
⭐🧑🏼🔬 24 talks + 15 flash talks from posters – don't miss out!
#EMBOMobileGenome
July 16, 2025 at 8:43 AM
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
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
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
Big shout to "Academia Pages" GitHub pages template.
tianxiongbb.github.io
About me
tianxiongbb.github.io
July 10, 2025 at 4:44 PM
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
Big shout to "Academia Pages" GitHub pages template.
tianxiongbb.github.io
Reposted by Tianxiong (Bear) Yu
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 🧬🖥️
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...
www.biorxiv.org
May 3, 2025 at 6:27 PM
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 🧬🖥️
Reposted by Tianxiong (Bear) Yu
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
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
April 17, 2025 at 3:50 PM
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
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
Reposted by Tianxiong (Bear) Yu
www.nature.com/naturecareer... UBC LSI Job!!
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
www.nature.com
April 4, 2025 at 4:03 AM
www.nature.com/naturecareer... UBC LSI Job!!
Reposted by Tianxiong (Bear) Yu
🧪 A paralysed man can stand on his own after receiving an injection of neural stem cells to treat his spinal cord injury
https://go.nature.com/4jaZ3RB
https://go.nature.com/4jaZ3RB
Paralysed man stands again after receiving ‘reprogrammed’ stem cells
Nature - Another man also regained some movement, but two others experienced minimal improvement.
go.nature.com
March 29, 2025 at 12:13 PM
🧪 A paralysed man can stand on his own after receiving an injection of neural stem cells to treat his spinal cord injury
https://go.nature.com/4jaZ3RB
https://go.nature.com/4jaZ3RB
Reposted by Tianxiong (Bear) Yu
New preprint from our lab! Why is not everyone working on Transposons?
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
www.biorxiv.org/content/10.1...
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
www.biorxiv.org/content/10.1...
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and associated with the histone mark H3K9me3. Heterochromatin erosion is a hallmark of human ageing and H3K9me3 ...
www.biorxiv.org
March 29, 2025 at 10:05 AM
New preprint from our lab! Why is not everyone working on Transposons?
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
www.biorxiv.org/content/10.1...
Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
www.biorxiv.org/content/10.1...
Reposted by Tianxiong (Bear) Yu
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!
we value collegiality and a passion for curiosity driven science. Being a great and fun human being also helps!
IMBA is recruiting a Junior Group Leader! Are you interested in starting your own lab, pursuing curiosity-driven basic research in the life sciences? Apply now to our group leader position. The deadline is May 28. Link is below.
March 29, 2025 at 1:22 PM
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!
we value collegiality and a passion for curiosity driven science. Being a great and fun human being also helps!
Reposted by Tianxiong (Bear) Yu
#TEsky The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition doi.org/10.7554/eLif...
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.
doi.org
March 21, 2025 at 3:14 PM
#TEsky The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition doi.org/10.7554/eLif...
Reposted by Tianxiong (Bear) Yu
Super exciting and beautiful new work from the talented @mathithiru.bsky.social www.nature.com/articles/s41...
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...
www.nature.com
March 19, 2025 at 5:48 PM
Super exciting and beautiful new work from the talented @mathithiru.bsky.social www.nature.com/articles/s41...
Reposted by Tianxiong (Bear) Yu
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
www.biorxiv.org/content/10.1101/2025.03.14.642691v2
March 17, 2025 at 8:28 PM
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
www.biorxiv.org/content/10.1101/2025.03.14.642691v2
Reposted by Tianxiong (Bear) Yu
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
#koalas @lubanlab.bsky.social @tianxiong-bear-yu.bsky.social
March 17, 2025 at 1:54 PM
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
#koalas @lubanlab.bsky.social @tianxiong-bear-yu.bsky.social
Reposted by Tianxiong (Bear) Yu
📄 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... 👇
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... 👇
March 14, 2025 at 10:34 AM
📄 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... 👇
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... 👇
Reposted by Tianxiong (Bear) Yu
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…
biorxiv.org/content/10.110…
March 10, 2025 at 8:49 AM
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…
biorxiv.org/content/10.110…
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 👇
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇
March 9, 2025 at 2:35 AM
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 👇
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇