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junhyongkim.bsky.social

@junhyongkim.bsky.social
340 followers 300 following 89 posts

A genomics cat, sometimes Christopher H. Browne Professor of Biology at Penn. All posts my opinion only.

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Maitreya Dunham @maitreya.bsky.social · 24/09/2026
Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.
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Xin Sun @xinsun-putiger.bsky.social · 24/09/2026
I’m deeply honored to receive the 2026 AGU Ocean Sciences Early Career Award! Thank you to AGU, the Ocean Sciences community, and my nominators for this recognition! [1/2]
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Steve Joffe @stevejoffe.bsky.social · 14/09/2026
Thrilled to share that Penn Medical Ethics @pennmehp.bsky.social is inviting applications for our 3-year National Human Genome Research Institute-funded postdoctoral fellowship in the ethical, legal, & social implications (ELSI) of genomics. Info @ medicalethicshealthpolicy.med.upenn.edu/elsipostdoc
medicalethicshealthpolicy.med.upenn.edu
Penn Medical Ethics and Health Policy | ELSI Genomics Postdoctoral Training Program
About the Fellowship The mission of the 3-year Penn Postdoctoral Training Program in the Ethical, Legal and Social Implications (ELSI) of Genetics and Genomics, supported by a training grant from...
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junhyongkim.bsky.social @junhyongkim.bsky.social · 12/07/2026
One of the most profound articles I've read. "Just try to be decent"
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Matthew Taliaferro @jmtali.bsky.social · 11/06/2026
New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵
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Christine Mayr @christinemayr.bsky.social · 08/06/2026
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
cell.com
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
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Caroline Bartman @cbartman.bsky.social · 20/05/2026
🚨first Bartman lab preprint! it's an LC-MS method to measure "total Coenzyme A" (sum of all acyl-CoAs). this will let us study coA synthesis flux using heavy-isotope tracing! huge congrats to first author Amelia Taylor and star coauthor @mzspectrum.bsky.social ! www.biorxiv.org/content/10.6...
biorxiv.org
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 06/04/2026
If you know a graduating undergraduate looking for the chance to spend 1-2 years in a lab before graduate school, we're hiring! Our lab explores morphogenesis, defining how the cell adhesion & cytoskeletal machinery work together to allow cells to change shape & move tarheels.live/peiferlab/ 1/n RT
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S Otto @sarperotto.bsky.social · 31/03/2026
Insightful summary of an extraordinary person being extraordinarily fired: "you don't silence a woman of color who raised concerns about racism by silencing her...The fingerprints are distributed perfectly across the system." www.linkedin.com/pulse/uclas-...
linkedin.com
UCLA's Most Decorated Ecologist Just Got Fired : Here's the sequence
In January of 2025, at the ICTP ICTS winter school at NCBS, Priyanga Amarasekare offered to take me and a few other students out for my birthday. She didn't have to do that.
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junhyongkim.bsky.social @junhyongkim.bsky.social · 28/03/2026
When the tech companies built their entire empire on algorithmically pushing what people want to hear to confirm their biases, why would they not do the same with LLMs
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Rita Strack @ritastrack.bsky.social · 25/03/2026
Well here's an answer to a question I hadn't thought of asking www.nature.com/articles/s41...
nature.com
Limitations of serial cloning in mammals - Nature Communications
Here they show that extended serial somatic cell cloning imposes a threefold increase in de novo mutations compared to natural reproduction, progressively reducing birth rates and ultimately limiting ...
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Mir Lab @mirlab.bsky.social · 20/03/2026
@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.
nature.com
A single cluster of RNA Polymerase II molecules is stably associated with active genes - Nature Communications
Live molecular-scale imaging in fly embryos shows that a single RNA Polymerase II cluster stays bound to active genes during transcription. Cluster formation requires initiation, and intensity represe...
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Colin Conine @colinconine.bsky.social · 19/03/2026
There is accumulating evidence that sperm miRNAs function to regulate embryonic gene expression and transmit inherited phenotypes to offspring but how does this work since sperm cargo is massively diluted in the egg upon fertilization. Here we directly address this ? www.biorxiv.org/content/10.6...
biorxiv.org
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Tugce Aktas @aktast.bsky.social · 25/02/2026
Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social doi.org/10.1016/j.ce... Read the thread👇 for the highlights of our findings.
doi.org
Redirecting
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junhyongkim.bsky.social @junhyongkim.bsky.social · 23/02/2026
Free markets are supposed to select for the good businesses and kill the bad. But, the hyper efficient capital markets allow transient feasting & abandoning the dying carcass. What we have now is a bunch of parasites on the economy evolving unbridled virulence. Now the viruses want to rule.
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Yun S. Song @yun-s-song.bsky.social · 21/02/2026
Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...
doi.org
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Seychelle Vos @voslab.org · 19/02/2026
🚨New preprint! We built a cell-free genomics platform (GATO-seq) to probe transcriptional regulation and discovered a “super pause” sequence that triggers a new Pol II active-site conformation. Huge shout-out to @robertovn.bsky.social for pulling off this monster of a project. tinyurl.com/superpause
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Lukasz Bugaj @bugajlab.bsky.social · 02/02/2026
Now in print at ACS Synbio! Introducing Aviatar: a concept for inducible translocation to any cell compartment using only a 1-component probe pubs.acs.org/doi/10.1021/...
pubs.acs.org
Optogenetic Translocation to Subcellular Compartments through Regulation of Protein Avidity
Inducible translocation to subcellular compartments is a common strategy for protein switches that control a variety of cell behaviors. However, existing switches achieve translocation through induced...
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The Warren Center for Network & Data Sciences @warrencenter.bsky.social · 27/01/2026
Warren Center faculty affiliate Greg Ridgeway has developed and tested a statistical model using real-world data that could help police departments take steps to prevent future excessive force. penntoday.upenn.edu/...
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Rita Strack @ritastrack.bsky.social · 23/01/2026
Well that's cool Source: Nature search.app/FLn5P
search.app
Quantum spin resonance in engineered proteins for multimodal sensing - Nature
A recently developed class of magneto-sensitive fluorescent proteins are engineered to alter the properties of their response to magnetic fields and radio frequencies, enabling multimodal sensing of b...
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 19/01/2026
This is how we first teach chirality to our undergrads !
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Heng Li @lh3lh3.bsky.social · 14/01/2026
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
hlilab.github.io
HLi Lab - Vacancies
Openings
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junhyongkim.bsky.social @junhyongkim.bsky.social · 14/01/2026
Since there are so much happenings that I can't breath, ill just have to take it out on this little irritant. What makes a workshop "prestigous" ? Does attending this give trainees prestige? Do organizers give themselves prestige for running it? Can we stop using language like this?
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Carl T. Bergstrom @carlbergstrom.com · 30/12/2025
Every week, Nature publishes yet another breathless puff piece about some AI startup, based only unpublished claims from the company and interviewing only those who work there. How can the leading scientific journal publish piece after piece that would make Kevin Roose blush? I think it's that...
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Russ Fischer @superelastic.bsky.social · 23/12/2025
and the winner of the "2025 best thing on Internet" has just arrived neal.fun/size-of-life/ @carlbergstrom.com
neal.fun
Size of Life
From an amoeba to a blue whale
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junhyongkim.bsky.social @junhyongkim.bsky.social · 22/12/2025
I just finished my 28th yr of teaching grad compbio. Following the inevitable trend, a 3rd of the course is now Deep Learning (DL). One activity we did was a deep dive into the AlphaGenome pre-print (www.biorxiv.org/content/10.1...). Question is, how do we evaluate it as a science paper? 1/n
biorxiv.org
AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model
Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence le...
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Nandita Garud @nanditagarud.bsky.social · 17/12/2025
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...
nature.com
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
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Mia Levine @levine-lab.bsky.social · 29/11/2025
Check out this terrific thread by first author, @sungyalin.bsky.social, whose creativity, bravery, exactitude, and perseverance made this project a reality.
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Mia Levine @levine-lab.bsky.social · 28/11/2025
How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...
science.org
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
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Maitreya Dunham @maitreya.bsky.social · 24/11/2025
Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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junhyongkim.bsky.social @junhyongkim.bsky.social · 22/11/2025
I feel irrationally annoyed at journals that ask for numerical scores and/or structured review responses. Assessing the reviews themselves is the job of the editors. I will refuse all review requests from journals who use such rubric devices for scientific papers as if they were term papers.
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Arjun Raj @arjunraj.bsky.social · 14/11/2025
So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...
cell.com
Single-cell susceptibility to viral infection is driven by variable cell states
Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...
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Lior Pachter @lpachter.bsky.social · 08/11/2025
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
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…
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David Maddison @bembidion.bsky.social · 03/11/2025
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...
subulatepalpomere.com
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…
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Jay Shendure @jshendure.bsky.social · 14/10/2025
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...
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Hanbin Lee @epigenci.bsky.social · 09/10/2025
Our paper (Brieuc Lehmann is the first author) is now online in Genetics. academic.oup.com/genetics/adv...
academic.oup.com
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
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Aaron Roth @aaroth.bsky.social · 04/10/2025
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.
arxiv.org
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...
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Mia Levine @levine-lab.bsky.social · 04/10/2025
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
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Jae Young Choi @jychoi.bsky.social · 22/09/2025
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
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...
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Timothy Bredy @twbredy.bsky.social · 21/09/2025
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...
biorxiv.org
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...
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
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)
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PLOS Biology @plosbiology.org · 15/09/2025
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.
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Yun S. Song @yun-s-song.bsky.social · 11/09/2025
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
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.
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Albert Vilella, PhD. @albertvilella.bsky.social · 05/09/2025
Pretty amazing observation in nature rdcu.be/eEebw
rdcu.be
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...
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James Briscoe @jamesbriscoe.bsky.social · 26/08/2025
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...
sciencedirect.com
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…
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junhyongkim.bsky.social @junhyongkim.bsky.social · 25/08/2025
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...
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Greg Egan @gregegansf.bsky.social · 23/08/2025
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...
g.co
‎Gemini - Five Dimensions: A Dimensional Puzzle
Created with Gemini
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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.
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Rita Strack @ritastrack.bsky.social · 01/08/2025
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
media.tenor.com
a bunch of balloons are flying in the sky .
ALT: a bunch of balloons are flying in the sky .
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Alex de Mendoza @alexdemendoza.bsky.social · 28/07/2025
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
academic.oup.com
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
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