@junhyongkim.bsky.social
A genomics cat, sometimes Christopher H. Browne Professor of Biology at Penn. All posts my opinion only.
Reposted
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
James Watson in his own words
“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…
liorpachter.wordpress.com
November 8, 2025 at 4:29 AM
Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...
liorpachter.wordpress.com/2018/05/18/j...
Reposted
After almost 30 years, the Tree of Life Web Project has been retired as an actively growing site. It will be unavailable until we can build a static site that contains its final content. More details at subulatepalpomere.com/2025/11/02/t...
The Passing of the Tree of Life Web Project
The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…
subulatepalpomere.com
November 3, 2025 at 6:28 PM
After almost 30 years, the Tree of Life Web Project has been retired as an actively growing site. It will be unavailable until we can build a static site that contains its final content. More details at subulatepalpomere.com/2025/11/02/t...
Reposted
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Our paper (Brieuc Lehmann is the first author) is now online in Genetics.
academic.oup.com/genetics/adv...
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
October 9, 2025 at 1:47 AM
Our paper (Brieuc Lehmann is the first author) is now online in Genetics.
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
Reposted
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.
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
October 4, 2025 at 6:47 PM
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.
and Emily was my first experiment with this, and it was just accepted to SODA. I'll describe the process in thread.
Reposted
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...
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
October 4, 2025 at 4:40 PM
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...
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...
Reposted
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...
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
September 22, 2025 at 2:18 PM
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...
doi.org/10.1186/s130...
Reposted
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...
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
September 21, 2025 at 10:50 PM
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
Reposted
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
September 15, 2025 at 8:44 AM
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
Reposted
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...
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
September 11, 2025 at 3:50 AM
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...
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...
Reposted
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
September 5, 2025 at 3:05 AM
Pretty amazing observation in nature rdcu.be/eEebw
Reposted
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...
🧵
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
August 26, 2025 at 8:28 AM
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...
🧵
www.sciencedirect.com/science/arti...
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...
with
streetslab.berkeley.edu
@saukaspengler.bsky.social
meetings.cshl.edu/meetings.asp...
August 25, 2025 at 2:53 PM
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...
with
streetslab.berkeley.edu
@saukaspengler.bsky.social
meetings.cshl.edu/meetings.asp...
Reposted
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...
• 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
August 23, 2025 at 11:29 AM
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...
• 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...
Reposted
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!
🧵
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!
🧵
August 4, 2025 at 1:52 PM
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!
🧵
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!
🧵
Reposted
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
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
August 1, 2025 at 2:27 PM
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
Today I begin my next adventure as
Chief Editor of Nature Biomedical Engineering!!
(a thread) @natmethods.nature.com @natbiomedeng.nature.com @natureportfolio.nature.com
Reposted
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
July 28, 2025 at 10:03 AM
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
Reposted
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.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1
July 19, 2025 at 1:04 AM
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.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Reposted
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...
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
July 17, 2025 at 8:21 PM
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...
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...
Reposted
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
July 16, 2025 at 8:49 PM
Wowee! Super-resolution stimulated X-ray Raman spectroscopy | Nature share.google/Mdn4Z0ddIy2t...
Reposted
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
It’s available on Amazon: tinyurl.com/mx2hewen
January 17, 2025 at 2:30 PM
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
It’s available on Amazon: tinyurl.com/mx2hewen
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:...
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
July 16, 2025 at 9:09 PM
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:...
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:...
Reposted
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.
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.
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/
www.biorxiv.org/content/10.1...
1/
July 15, 2025 at 12:23 PM
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.
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.
Reposted
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
July 15, 2025 at 1:28 PM
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...