Lightnews — Scholar-powered news

Reposted

Hanbin Lee @epigenci.bsky.social · 2d

Our paper (Brieuc Lehmann is the first author) is now online in Genetics.

academic.oup.com/genetics/adv...

On ARGs, pedigrees, and genetic relatedness matrices

Abstract. Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant se

academic.oup.com

11 18

Reposted

Aaron Roth @aaroth.bsky.social · 7d

To contribute to common knowledge :-) I too have been integrating AI tools closely into my research. This paper arxiv.org/abs/2507.09683 with @mkearnsphilly.bsky.social
and Emily was my first experiment with this, and it was just accepted to SODA. I'll describe the process in thread.

Networked Information Aggregation via Machine Learning

We study a distributed learning problem in which learning agents are embedded in a directed acyclic graph (DAG). There is a fixed and arbitrary distribution over feature/label pairs, and each agent or...

arxiv.org

1 3 22

Reposted

Mia Levine @levine-lab.bsky.social · 7d

Check out this new Levine-Lampson collaboration, led by the talented Hyuk-Joon Jeon.

We explored the consequences of inheriting long telomeres from dad and short telomeres from mom. Or the reciprocal. Turns out, parent-of-origin matters (in mice, at least).

authors.elsevier.com/c/1loW-3QW8S...

authors.elsevier.com

3 20 49

Reposted

Jae Young Choi @jychoi.bsky.social · 19d

Excited to share a new method developed from my group thats published at Genome Biology. This was an amazing effort by my grad student Linh @linhngk.bsky.social. We developed Topsicle, a method that analyzes long read data for telomere analysis and length measuring.
doi.org/10.1186/s130...

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data - Genome Biology

Telomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many...

doi.org

1 6 11

Reposted

Timothy Bredy @twbredy.bsky.social · 19d

We've been busy in the lab, and I'm super proud of the team right now. These three papers are great examples of "Night Science", creative, curiosity driven work at its best! All are works in progress.

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

Dynamic regulation of neuronal Vault trafficking and RNA cargo by the noncoding RNA, Vaultrc5

Vaults are large ribonucleoprotein complexes of unknown function in neurons. Here, we report that the Vault-associated noncoding RNA, Vaultrc5, is highly enriched at the synapse and is required for ac...

www.biorxiv.org

1 2 12

Reposted

Yun S. Song @yun-s-song.bsky.social · 19d

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

4 89 170

Reposted

PLOS Biology @plosbiology.org · 26d

The #Drosophila Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that #fitness & #immunity are the likely primary evolutionary drivers of Dscam1 isoform diversity in #arthropods @plosbiology.org 🧪 plos.io/4gp8cWd

Top: Dscam1 gene structure and isoform diversity in pancrustacean species. Top: Schematic diagrams of Drosophila melanogaster Dscam1 gene and protein structure. The variable exons or domains are shown in color, while the constant exons or domains are shown in gray. Middle: Phylogenetic distribution of Dscam1 isoform diversity. A phylogenetic tree of Pancrustacean species is shown in the lower panel. The upper panel shows distribution of the number of exons in variable exon 4, exon 6, or exon 9 clusters in Pancrustacean species, with variable exon clusters shown in different colors. The middle panel shows distribution of the number of potential ectodomains diversity, where species with a special number of diversities are highlighted. Bottom: Reducing the Dscam1 diversity affects adult survival upon Beauveria bassiana infection. Survival curves after Triton or B. bassiana infection for wild-type and exon 4 (left), exon 6 (middle), and exon 9 (right) mutants are shown, respectively. The Triton groups (control) are represented by solid lines, while the B. bassiana groups are represented by dashed lines.

10 19

Reposted

Yun S. Song @yun-s-song.bsky.social · Sep 11

SINGER, our ARG inference method, is finally published and freely available online:

doi.org/10.1038/s415...

It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics

SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.

doi.org

1 52 99

Reposted

Albert Vilella, PhD. @albertvilella.bsky.social · Sep 5

Pretty amazing observation in nature rdcu.be/eEebw

One mother for two species via obligate cross-species cloning in ants

Nature - In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from...

rdcu.be

3 14

Reposted

James Briscoe @jamesbriscoe.bsky.social · Aug 26

Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh

🧵

www.sciencedirect.com/science/arti...

Investigating morphogen and patterning dynamics with optogenetic control of morphogen production

Morphogen gradients provide the patterning cues that instruct cell fate decisions during development. Here, we establish an optogenetic system for the…

www.sciencedirect.com

7 40 140

junhyongkim.bsky.social @junhyongkim.bsky.social · Aug 25

The 2025 Cold Spring Harbor Labs, Single Cell Analysis Meetings are here. This is the longest running single cell meeting, started in 2009. Please register and send an abstract!

with
streetslab.berkeley.edu
‪@saukaspengler.bsky.social‬

meetings.cshl.edu/meetings.asp...

2 5

Reposted

Greg Egan @gregegansf.bsky.social · Aug 23

Here’s some Gemini gaslighting:

• giving a wrong answer to a puzzle
• giving Python code that could test its claim
• asserting it obtained results from the code supporting its claim
• but when I ran the code myself, it showed the claim was false.

g.co/gemini/share...

‎Gemini - Five Dimensions: A Dimensional Puzzle

Created with Gemini

g.co

3 6 36

junhyongkim.bsky.social @junhyongkim.bsky.social · Aug 14

I was just at the ICML AI/ML conference. Listening to the AGI related talks, I was thinking boy, it would be good to take some humanities courses.

Also, all the intellectually corrupt AI futurism that is killing us right now. If only they'd had better humanities training.

2

Reposted

Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

2 57 130

Reposted

Rita Strack @ritastrack.bsky.social · Aug 1

I have some BIG NEWS to share today!

Today I begin my next adventure as

Chief Editor of Nature Biomedical Engineering!!

(a thread) @natmethods.nature.com @natbiomedeng.nature.com @natureportfolio.nature.com

a bunch of balloons are flying in the sky .

ALT: a bunch of balloons are flying in the sky .

media.tenor.com

93 33 690

Reposted

Alex de Mendoza @alexdemendoza.bsky.social · Jul 28

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes

Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

academic.oup.com

6 51 100

junhyongkim.bsky.social @junhyongkim.bsky.social · Jul 26

With the hyper developed financial system, even the enshittified companies dying doesn't lead to self correcting markets.

Capital, like viruses, escapes the dead body and moves on to the next infection.

1 2

Reposted

Hanbin Lee @epigenci.bsky.social · Jul 19

My talk from this year's probgen is finally out.

Where do linear mixed models and random effects come from?

They emerge from *mutations* on Ancestral Recombination Graphs.

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 18

Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1

2 22 49

Reposted

Jonathan Kagan @jkagan1.bsky.social · Jul 17

Discovery of a pH sensor that regulates inflammation.
Zhou and Medzhitov provide a mechanistic tour-de-force in defining how BRD4 links changes in pH to inflammatory gene expression. Kudos to the authors on this exciting finding.
www.sciencedirect.com/science/arti...

Regulation of inflammatory responses by pH-dependent transcriptional condensates

Inflammation is an essential defense response but operates at the cost of normal tissue functions. Whether and how the negative impact of inflammation…

www.sciencedirect.com

2 3 22

Reposted

Rita Strack @ritastrack.bsky.social · Jul 16

Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...

Super-resolution stimulated X-ray Raman spectroscopy - Nature

A high-resolution spectroscopic tool is demonstrated using the stochastically fluctuating intensity spikes in time and energy domains of a self-amplified spontaneous emission X-ray free-electron laser...

share.google

5 29

Reposted

Yoav Gilad @ygilad.bsky.social · Jan 17

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.

It’s available on Amazon: tinyurl.com/mx2hewen

7 67 110

junhyongkim.bsky.social @junhyongkim.bsky.social · Jul 16

#ICML The issues surrounding AI alignment are fascinating, esp, what is it aligning to: your ave population, all people, or some ideal?

But, the more frightening thing is regardless how we think about alignment, AI embedded social norms and values are already here and will become pervasive.

2

junhyongkim.bsky.social @junhyongkim.bsky.social · Jul 16

So, there was a fascinating talk by Frauke Kreuter about aligning survey data. She mentioned that there are attempts to query LLM for surveys rather than people.

Reminded me of an old Asimov story about future voting will happen by an AI querying a single random voter.

1 1

junhyongkim.bsky.social @junhyongkim.bsky.social · Jul 16

At #ICML 2025 to present our paper on single cell lineage tracing.

Being one of "big 3, AI/ML", confs, I guess this is the ground zero of current AI. I'll have more to say about my obs, but one thing---it certainly is a lot more posh than your usual bio meetings.

acrobat.adobe.com/id/urn:aaid:...

Adobe Acrobat

acrobat.adobe.com

1 1

Reposted

Flavia Corsi @flaviacorsi.bsky.social · Jul 15

Happy to share my postdoc work—our new preprint is out! 🧬 It’s been a privilege to lead this project.

I'm immensely grateful to Anton @golobor.bsky.social for being such an inspiring and supportive supervisor. Also truly thankful to @danielgerlich.bsky.social for his guidance and collaboration.

Anton Goloborodko @golobor.bsky.social · Jul 15

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

3 7 36