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Reposted by Xi Fu

David A Knowles @davidaknowles.bsky.social · Jul 2

New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman. www.biorxiv.org/content/10.1...

Perplexity as a Metric for Isoform Diversity in the Human Transcriptome

Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...

www.biorxiv.org

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Xi Fu @fuxialexander.bsky.social · May 5

My friend tried to ask what are some well known gene in Chr10/etc and guess what…

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Chao Hou @chaohou.bsky.social · Apr 17

We have updated our protein lanuage model trained on structure dynamics. Our new models show significant better zero-shot performance on mutation effects of designed and viral proteins compared to ESM2. check the new preprint here: www.biorxiv.org/content/10.1...

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Sara Mostafavi @saramostafavi.bsky.social · Apr 16

Some encouraging news for cross-gene generalization of allele effects in S2F models. www.biorxiv.org/content/10.1...

Deep genomic models of allele-specific measurements

Allele-specific quantification of sequencing data, such as gene expression, allows for a causal investigation of how DNA sequence variations influence cis gene regulation. Current methods for analyzin...

www.biorxiv.org

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Nature Biotechnology @natbiotech.nature.com · Apr 3

An engineered Cas12a enables higher-order combinatorial functional genomic screens using CRISPR interference go.nature.com/3UTnSXM
rdcu.be/ef95k

Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations - Nature Biotechnology

An engineered Cas12a enables higher-order combinatorial functional genomic screens using CRISPR interference.

go.nature.com

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Xi Fu @fuxialexander.bsky.social · Mar 26

much better with GPT

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Reposted by Xi Fu

zhoujt.bsky.social @zhoujt.bsky.social · Mar 25

1/10 Excited to share our latest - the first whole-body map of both DNA methylation and 3D genome at single-cell resolution.

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Xi Fu @fuxialexander.bsky.social · Mar 21

Biorxiv seems to be really slow nowadays. Is it just me? Curious whether it's due to some infra change or there are some AI Agents crawling the data...

Xi Fu @fuxialexander.bsky.social · Mar 18

Looks like a Tesla logo 😈 (I'm sorry...)

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Columbia University's Zuckerman Institute @zuckermanbrain.bsky.social · Mar 17

For decades, government funding “has positioned the United States as a global leader” in science, says scientist Tom Maniatis of @zuckermanbrain.bsky.social and the New York Genome Center. He highlights how a new #NIH policy cutting money for research “jeopardizes” this, in Cell tinyurl.com/ubw6uphe

We must act swiftly and decisively to safeguard the future of science in the US - Tom Maniatis, PhD

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Tuuli Lappalainen @tuuliel.bsky.social · Mar 6

Can someone send this to the NIH Director nominee who said yesterday under oath that he doesn’t know where the indirects go.

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Reposted by Xi Fu

Carolyn Ibberson @cbibberson.bsky.social · Feb 22

We are crowd sourcing reductions in graduate admissions and hiring freezes across biomedical research and higher ed in response to pauses in NIH funding and EO’s. If you have information if you could add to this spreadsheet, it would be greatly appreciated!: docs.google.com/spreadsheets...

Graduate Reductions Across Biomedical Sciences (2025)

docs.google.com

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Tuuli Lappalainen @tuuliel.bsky.social · Feb 12

This is very cool work (where I was fortunate to play a small part), providing creative and crucial solutions for secure and federated eQTL mapping. Bigger functional genetic studies with less administrative and legal hassle! 💪

Gamze Gürsoy @gamzeandgursoy.bsky.social · Feb 12

The world is on fire but we must continue doing science! With immense pride, I share the latest from my lab: privateQTL - a method for federated and secure eQTL mapping, led by my brilliant student Annie from @ColumbiaDBMI www.cell.com/cell-genomic...
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Secure and federated quantitative trait loci mapping with privateQTL

Choi et al. developed a novel tool for privacy-preserving cross-institutional eQTL mapping studies. The authors benchmarked their tool against meta-analysis and demonstrated that it achieves higher ac...

www.cell.com

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