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Stephen Rong

@alwaysrong.bsky.social
662 followers 1.6K following 1 posts

Computational biologist and genomic data scientist. Marie Skłodowska-Curie Actions Postdoc Fellow in Spivakov Lab at Imperial College. Formerly Postdoc Fellow in Reilly Lab at Yale University. The sounds of noncoding variants wake me from my slumber.

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Reposted by Stephen Rong
Ezequiel Galpern @eag91.bsky.social · 05/08/2026
1/ New preprint! with @solersanchisx.bsky.social @cwjpugh.bsky.social @federicobilleci.bsky.social @jonnyfrazer.bsky.social and Mafalda Dias, we introduce a scalable framework to improve stability prediction and separate folding from functional constraints. www.biorxiv.org/content/10.6...
biorxiv.org
Blending physics-based and inverse folding models to disentangle variant effects on stability and function
Protein sequences are constrained not only by the need to fold into stable structures, but also by specific functional requirements imposed by natural selection. Yet predictions of how amino-acid chan...
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Shicheng Guo @shihcheng.bsky.social · 29/07/2026
In a study of 78,664 participants, over 24,000 protein QTLs linked to 1,116 proteins were identified, revealing genetic effects on disease pathways and cell types. PMID:42097137, Cell 2026, @Cell www.cell.com/cell/fulltext/S0092-86… #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
cell.com
https://www.cell.com/cell/fulltext/S0092-8674(26)00385-5
No description available
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Shicheng Guo @shihcheng.bsky.social · 29/07/2026
AD brains show >1,000x enrichment of somatic SNVs in cancer driver genes, linked to clonal hematopoiesis, driving inflammation in microglia-like macrophages. PMID:42019491, Cell 2026, @Cell www.cell.com/cell/fulltext/S0092-86… #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
cell.com
https://www.cell.com/cell/fulltext/S0092-8674(26)00341-7
No description available
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Pedro Beltrao @pedrobeltrao.bsky.social · 20/07/2026
New lab preprint - Deep learning models are most often difficult to interpret black box models. What if we engineer them with interpretation in mind? Dennis Gankin carefully studied so-called biologically inspired neural networks and found an interesting phenomenon www.biorxiv.org/content/10.6...
biorxiv.org
Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity
Biologically inspired neural networks (BINNs) embed pathway, ontology, or protein-interaction structure directly into neural networks, promising interpretable disease prediction where hidden nodes map...
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Xavier Grau-Bové 🌾 @xgrau.bsky.social · 20/07/2026
I'm happy to share our latest on #coral single-cell biology: a transcriptomic timecourse of heat stress in Stylophora pistillata, from bleaching to recovery 🪸🌊 This project was spearheaded by Shani Levy and carried through in @arnausebe.bsky.social's lab at @crg.eu. www.biorxiv.org/content/10.6...
Stylophora pistillata colony from the Red Sea. Picture by Hagai Nativ.
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Ben Williamson @benpatrickwill.bsky.social · 18/07/2026
The anatomy of an AI-supported academic article is becoming more apparent. I desk reviewed ~70 manuscripts this week for our journal. Reckon 20ish had significant AI assistance. On top of hundreds of others recently I'm starting to see patterns. Are other editors are seeing the same or similar? 1/
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Loukas Theodosiou @bioinformatician.bsky.social · 19/07/2026
After four years, several updates and a handful of CRAN releases, 𝗹𝘁𝗰 𝗰𝗼𝗹𝗼𝗿 𝗽𝗮𝗹𝗲𝘁𝘁𝗲 𝗥-𝗽𝗮𝗰𝗸𝗮𝗴𝗲, reached a version I feel genuinely good about sharing with the community. github.com/loukesio/ltc...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Ekin Deniz Aksu @ekindea.bsky.social · 15/07/2026
I'm excited to share that Corgi is out in @natcomms.nature.com! We refine context-aware sequence-to-function models by using FiLM to condition the model on trans-regulator expression levels. This way Corgi can generalize to unseen cell types. www.nature.com/articles/s41... 🧵Thread 1/n
nature.com
Context-aware sequence-to-function model of human gene regulation - Nature Communications
This study introduces Corgi and Corgi+ , biology-inspired deep neural network models of regulatory DNA sequences that can generalize to unseen cell types. They accurately impute epigenomic d...
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Carlos Sarabia, PhD @carlossarabia.bsky.social · 28/06/2026
First taste at #SMBE2026: joining the intriguing GHIST2026 challenge as a participant. We have 6 months to see who will be the best at detecting selective sweeps, demographic changes and infer relatedness patterns. Let the Hunger Games begin.
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Shoa Clarke @shoaclarke.bsky.social · 02/07/2026
Really incredible work from the Tcheandjieu Lab that finally helps us to decipher what is going on at the 9p21 locus and its association with coronary disease on different ancestral backgrounds. www.cell.com/ajhg/fulltex...
cell.com
Linkage disequilibrium and allelic heterogeneity explain variation in coronary artery disease risk at 9p21 across populations and reduced effect in Africans
Using cross-ancestry fine-mapping across global and local ancestry groups, this study dissects the 9p21.3 coronary artery disease locus and shows how ancestry-specific haplotype structure shapes assoc...
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Nandita Garud @nanditagarud.bsky.social · 30/06/2026
We are very excited to share our latest. We thought that soft sweeps would be the only type of sweep spreading across human gut microbiomes. Turns out many are hard! Reach @peterlaurin.bsky.social 's thread on why! And tomorrow at #SMBE2026 I will share this work and more!
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Xinjun Zhang @zhanglabpopgen.bsky.social · 29/06/2026
Just in time for #SMBE2026! Here's DEEP for detecting ghost/superarchaic introgression: scalable, robust, and no ARG! We find ~0.5% genome with superarchaic ancestry in East Asians and Oceanians, plus a notable signal at HLA Come find our poster tonight (#241)! www.biorxiv.org/content/10.6...
biorxiv.org
Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations
Ghost introgression from unsampled hominin lineages has emerged as an increasingly important component of human evolutionary history. Recent studies suggest that deeply divergent hominin lineages may ...
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Cedric Boeckx @cedricboeckx.bsky.social · 28/06/2026
Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...
biorxiv.org
The Vertebrate Genomes Project Phase I: A global reference genome resource
The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...
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Mateja Hajdinjak @matejahajdi.bsky.social · 23/06/2026
Ancient human DNA from the cave walls! 🤯 Wonderful new paper led by Alba Bossoms Mesa and a great team of people that made this work possible.
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Carl T. Bergstrom @carlbergstrom.com · 20/06/2026
Gift link
nytimes.com
Opinion | The Science That Turned Lizard Venom Into GLP-1s Is Under Attack
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Karen James @kejames.bsky.social · 20/06/2026
Cool Sankey diagram of the ranked choice voting results of Maine’s Democratic gubernatorial primary. Think how transformative this could be if more states adopted it.
Colorful diagram showing the flow of votes after each round of elimination with the title, “Sankey diagram of the Democratic gubernatorial primary ranked choice tabulation”
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Matt Stata @mattstata.bsky.social · 10/06/2026
New review out in Current Biology with colleagues in the Plant Cell Atlas (@plantcellatlas.bsky.social)! We discuss how single-cell genomics is reshaping our understanding of plant cell-type identity and evolution across the Green Lineage. bit.ly/4eAip2Q
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Armita R. Manafzadeh @armanafzadeh.bsky.social · 16/06/2026
The secret's out – thrilled to share I’ve been selected as a member of the inaugural class of @sciam.bsky.social's Young American Scientists! It's been so fun to learn about the work of the other 27 awardees from around the country. www.scientificamerican.com/issue/sa/202...
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Cedric Boeckx @cedricboeckx.bsky.social · 12/06/2026
Awesome work led by Serena Tucci showing how ong-­ term isolation and archaic introgression shape functional genetic variation in Near Oceania @science.org 🧪🧬💀 www.science.org/doi/10.1126/...
science.org
Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania
Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity yet are drastically underrepresented in human genomics. We generated 177 high-coverage Near Oceanian whole genom...
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Nikhil Milind @nikhilmilind.dev · 27/05/2026
I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social). www.cell.com/cell-genomic... [1/n]
cell.com
Buffering of gene dosage response curves for human complex traits
Milind et al. explore why loss-of-function variants and duplications tend to have average effects in the same direction on 94 complex traits. Using gene dosage response curves (GDRCs), they gather evi...
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Alejandro Montenegro @aemonten.bsky.social · 26/05/2026
"(...) plasmids are chromatinized in an organized, sequence-dependent manner and adopt a heterogeneous and incomplete chromatin architecture relative to nuclear-encoded chromatin fibers" www.cell.com/molecular-ce...
cell.com
Chromatin architectures underlying plasmid-based assays for regulatory variant effects
Mallory et al. develop plasmid Fiber-seq to map chromatin architecture along individual transfected plasmids at near-nucleotide resolution, which reveals that plasmids adopt heterogeneous chromatin pa...
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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
npr.org
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
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Reese Richardson @reeserichardson.bsky.social · 21/05/2026
@johanduchene.bsky.social @sholtodavid.bsky.social Spent the last hour looking, found ten more apparently manipulated Western blots in Thermo Fisher's antibody verification data (across eight different catalogued products). Thread below. www.thermofisher.com/antibody/pro...
Apparent manipulation in the antibody verification data in Thermo Fisher's online catalog
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 13/05/2026
Beautiful new study from @elphegenoralab.bsky.social and Leonid Mirny's lab: Cohesin-bridged encounters mediate enhancer-promoter communication, predicting how enhancer effect scales with genomic distance and - for the first time - how CTCF sites modulate enhancer-promoter communciation! 🧵 below
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
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Nikolai Slavov @slavov-n.bsky.social · 12/05/2026
Single-cell proteomics illuminated new mechanisms of mammalian development. We found that spatially polarized protein distributions and intracellular protein gradients emerge during the earliest stages of mammalian embryogenesis and bias subsequent cell fate decisions. www.cell.com/cell/fulltex...
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Doudna Lab @doudna-lab.bsky.social · 12/05/2026
New pre-print 📣 “Undruggable” cancer mutations remain very hard to target with current modalities. What if we could instead sense mutant transcripts and convert that recognition into selective cell killing? Check out this work led by postdoc Jingkun Zeng: www.biorxiv.org/content/10.6...
biorxiv.org
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Julia Lazzari-Dean @jlazzaridean.bsky.social · 12/05/2026
We invented “triplet tumbling microscopy” (TTM) to track protein-protein interactions in living cells! Tag your protein with GFP and see it interact with *untagged* binding partners www.biorxiv.org/content/10.6...
A cartoon overview of triplet tumbling microscopy, comparing data from bound and unbound samples.
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Wendy Bickmore @wbickmor.bsky.social · 08/05/2026
Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...
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rain 🌦️ @sunshowers.io · 08/05/2026
Spoiler
(By the way, coming back to contraception, the person who popularized the no-technical-solution thing was Garrett Hardin, whose 1968 paper "The Tragedy of the Commons" had as its abstract: "The population problem has no technical solution; it requires a fundamental extension in morality." Hardin was a eugenicist and white nationalist who time has shown to be completely wrong in the specific instance he invoked the phrase in. It certainly wasn't "morality" that came to the rescue — it was a combination of technology in the form of the Green Revolution plus widespread availability of contraception, as well as improved standards of living.)
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Mike Feigin 🥯 @mikefeigin.bsky.social · 01/05/2026
I don’t know how to feel about grant rejections anymore. When you get a score that would have been funded at any other point in history, except right now, how bad can you feel? I see scores from friends and colleagues (and my own) and it just breaks my heart more than anything.
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Michael Hiller @hillermich.bsky.social · 08/05/2026
We now have genome browsers on our UCSC mirror at genome.senckenberg.de for the 1033 mammal and 866 bird assemblies, showing spliceAi, reference-based and ref-integrated TOGA2 tracks. Tables with links to all browsers are genome.senckenberg.de/TOGA2Mammali... & genome.senckenberg.de/TOGA2Aves.html
genome.senckenberg.de
Hiller Lab UCSC Genome Browser
Senckenberg Genome Browser
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Plant Science Spotlight @plant-sci.bsky.social · 05/05/2026
Don’t reach for ChatGPT Images or Nano Banana as your first option when creating scientific images There are multiple free and open-source images, icons, and tools for creating scientific illustrations. #plantscience @stephenturner.us blog.stephenturner.us/p/free-open-...
blog.stephenturner.us
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Takashi Fukaya @fukayalab.bsky.social · 03/05/2026
New preprint alert! Together with Tetsuya Yamamoto at Hokkaido University, we propose a “polymer micelle” model of transcriptional bursting. www.biorxiv.org/content/10.6...
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Maxim Greenberg @maxvcg.bsky.social · 01/05/2026
This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...
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Alfonso Martinez Arias @amartinezarias.bsky.social · 02/05/2026
A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵
cell.com
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...
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Harris Wang @harriswang.bsky.social · 01/05/2026
1/ Excited to share our new paper in Science @science.org: “Toward life with a 19-amino acid alphabet through generative artificial intelligence design.” A great collab w/ Sergey's group @sokrypton.org at MIT @columbiasysbio.bsky.social science.org/doi/10.1126/... 🦠🧬🛠️🖥️💥
science.org
Toward life with a 19–amino acid alphabet through generative artificial intelligence design
Because all known living organisms are made from at least 20 canonical amino acids, the feasibility of life using a more simplified alphabet remains unclear. In this work, we leveraged computational d...
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Simon Kozlov @sim0nsays.bsky.social · 01/05/2026
Yours truly is a proper scientist now! TL;DR: we used AI to redesign parts of essential cell machinery with only 19 canonical amino acids instead of 20. Why? Great thread by @harriswang.bsky.social provides more context and details. Let me talk a bit about the AI design part of this. 1/
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 15/02/2026
We are holding our annual Rising Stars in Genetics and Genomics Postdoc Symposium on September 24-25, 2026! Please nominate postdocs who are conducting cutting edge, creative work, and are likely to be a leader in their field. Please nominate by April 30, 2026: forms.gle/85NZaxFezUk8... (1/2)
forms.gle
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
This work was co-led by myself and Peter Yoon. Structure was led by Peter, @terryzzy.bsky.social , and Trevor Docter. Many thanks to our intrepid collaborators and special thanks to Jennifer for supporting us through this project. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
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Marcos Castro e Silva, PhD 🇧🇷 @macscastro.bsky.social · 22/04/2026
🚨 Check out our new paper in Nature! In our new study, we sequenced 128 high-coverage genomes from Indigenous peoples across Latin America and uncovered their unique genetic diversity and history. 👇🧵 www.nature.com/articles/s41...
nature.com
The evolutionary history and unique genetic diversity of Indigenous Americans - Nature
Analysis of 128 high-coverage Indigenous American genomes shows extensive diversity shaped by several South American dispersals, ancient Australasian admixture, archaic introgression and long-term ada...
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Minji Lee @m1nj2.bsky.social · 21/04/2026
We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 20/04/2026
A new study shows how different regulatory genetic elements coordinate the activity of a key developmental gene. The findings could explain subtle differences seen in patients with congenital limb malformations, for which the underlying disease mechanisms often remain unknown. Read more: ⬇️
molgen.mpg.de
Waves of regulation control an important developmental gene
In a new study published in Genes & Development, researchers from the labs of Stefan Mundlos (Max Planck Institute for Molecular Genetics and Charité, Berlin) and Lila Allou (MRC Laboratory of Medical...
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Eric Topol @erictopol.bsky.social · 20/04/2026
some data on the shrinkage
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Zamin Iqbal @zaminiqbal.bsky.social · 18/04/2026
"We identify at least three waves of "back-to-Africa" migrations starting ~14,000 years ago. Applying GhostBuster to deeper timescales..." V interesting new paper on human history
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Jason Rasgon @vectorgen.bsky.social · 17/04/2026
WAT www.science.org/doi/10.1126/...
science.org
Science | AAAS
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