Stephen Rong
@alwaysrong.bsky.social
Marie Skłodowska-Curie Actions postdoc in Spivakov Lab at Imperial College. Formerly postdoc at in Reilly Lab at Yale University. The sounds of noncoding variants wake me from my slumber.
Reposted by Stephen Rong
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression
Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases. Single cell-resolved measures of RNA levels and single-cell expre...
www.medrxiv.org
November 12, 2025 at 3:15 PM
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Reposted by Stephen Rong
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.
www.cam.ac.uk/jobs/faculty...
www.cam.ac.uk/jobs/faculty...
Faculty Position in Computational Biology
Applications are invited for an Assistant/ Associate Professorship in Computational Biology to commence on 1 April 2026 or shortly thereafter. This is a joint post between the Department of Applied
www.cam.ac.uk
November 11, 2025 at 9:05 PM
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.
www.cam.ac.uk/jobs/faculty...
www.cam.ac.uk/jobs/faculty...
Reposted by Stephen Rong
SYNTH is a radical departure from the classic pre-training recipe: what if we trained for reasoning and focused on the assimilation of knowledge and skill that matters? At its core it’s an upsampling of Wikipedia 50,000 “vital” articles. huggingface.co/datasets/Ple...
November 10, 2025 at 5:30 PM
SYNTH is a radical departure from the classic pre-training recipe: what if we trained for reasoning and focused on the assimilation of knowledge and skill that matters? At its core it’s an upsampling of Wikipedia 50,000 “vital” articles. huggingface.co/datasets/Ple...
Reposted by Stephen Rong
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
November 10, 2025 at 9:01 PM
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Reposted by Stephen Rong
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
November 10, 2025 at 11:11 AM
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
Reposted by Stephen Rong
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Effects of polygenic risk score communication on health outcomes: systematic review and meta-analysis
Abstract Objective. The purpose of this systematic review and meta-analysis is to summarize evidence from all RCTs to-date on the efficacy of polygenic risk score (PRS) communication in changing healt...
www.medrxiv.org
November 7, 2025 at 8:33 AM
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Reposted by Stephen Rong
BehaveAI is live!
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
November 6, 2025 at 10:09 AM
BehaveAI is live!
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Reposted by Stephen Rong
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Stephen Rong
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes https://www.biorxiv.org/content/10.1101/2025.11.05.686799v1
November 6, 2025 at 11:32 PM
Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes https://www.biorxiv.org/content/10.1101/2025.11.05.686799v1
Reposted by Stephen Rong
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - Nature Communications
The authors give a method for learning causal gene networks using Perturb-seq data. In K562 cells, they find a network with small-world and scale-free properties. Analysis shows a relationship between...
nature.com
November 3, 2025 at 7:09 PM
@brielin.bsky.social's fantastic work on causal gene network inference from Perturb-seq is published! We estimate total causal effects using guides as instruments, then deconvolve into direct & mediated effects with a directed analog of graphical lasso. Deets: nature.com/articles/s41467-025-64353-7
Reposted by Stephen Rong
50 years ago, King & Wilson published a foundational paper that underlies the cis-regulatory paradigm (CRP) of #DevoEvo #EvoDevo, i.e., that *almost* all morphological evolution is driven by mutations in regulatory elements, rather than proteins, and it all arose from simple misunderstanding 🧪 🧵
October 29, 2025 at 12:35 AM
Reposted by Stephen Rong
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reposted by Stephen Rong
🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social
October 21, 2025 at 9:59 AM
🚨 🚨 🚨 New preprint alert!!! 🚨 🚨 🚨
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social
In the past, we have learnt that Oct4 can induce nucleosome breathing on the mono-nucleosome level.
But what happens when you have a fibre of multiple nucleosomes?
www.biorxiv.org/content/10.1...
@rcollepardo.bsky.social @juliamaristany.bsky.social
Reposted by Stephen Rong
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 25, 2025 at 4:46 AM
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Reposted by Stephen Rong
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Simple scaling laws control the genetic architectures of human complex traits
Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely. This study shows that differences in architectures of highly polygenic traits arise mainly f...
journals.plos.org
October 24, 2025 at 1:51 AM
Why do complex traits differ in their genetic architecture?
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
In our new PLOS Biology paper, we will try to convince you that two simple scaling laws drive differences in the number, effect sizes and frequencies of causal variants affecting complex traits.
Thread:
journals.plos.org/plosbiology/...
Reposted by Stephen Rong
PhD students conduct most of the actual work in generating knowledge on college campuses. Cutting the number of students cuts the amount of research by that amount.
A huge divestment from future growth.
A huge divestment from future growth.
Wow. Harvard nuking its PhD programs
- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
Harvard FAS Cuts Ph.D. Seats By More Than Half Across Next Two Admissions Cycles | News | The Harvard Crimson
The Faculty of Arts and Sciences slashed the number of Ph.D. student admissions slots for the Science division by more than 75 percent and for the Arts & Humanities division by about 60 percent for th...
www.thecrimson.com
October 21, 2025 at 5:33 PM
PhD students conduct most of the actual work in generating knowledge on college campuses. Cutting the number of students cuts the amount of research by that amount.
A huge divestment from future growth.
A huge divestment from future growth.
Reposted by Stephen Rong
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
SAFE-LD: A novel method for the estimation of linkage disequilibrium from summary statistics
Genome-wide association studies (GWAS) have greatly advanced our understanding of the genetic architecture of complex traits. Downstream analyses of GWAS summary statistics require accurate in-sample ...
www.biorxiv.org
October 21, 2025 at 9:47 AM
I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini.
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
📄: shorturl.at/BgXqq
Github: shorturl.at/b49Wa
Reposted by Stephen Rong
🚨 Exciting opportunity! The Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard is recruiting exceptional postdocs for 2026 at the intersection of ML/math and biomedicine.
Shape the future of computational biology 🧵👇
Shape the future of computational biology 🧵👇
October 22, 2025 at 2:50 AM
🚨 Exciting opportunity! The Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard is recruiting exceptional postdocs for 2026 at the intersection of ML/math and biomedicine.
Shape the future of computational biology 🧵👇
Shape the future of computational biology 🧵👇
Reposted by Stephen Rong
Now #published as a Letter @physreve.bsky.social: "Geometry of T1 transitions in epithelia" doi.org/10.1103/kdnb-bxdx
My first single-author paper deploys a silly amount of Olympiad geometry on a fundamental biophysics problem, summarised in the attached thread!
@mpipks.bsky.social @mpi-cbg.de
My first single-author paper deploys a silly amount of Olympiad geometry on a fundamental biophysics problem, summarised in the attached thread!
@mpipks.bsky.social @mpi-cbg.de
October 9, 2025 at 2:31 PM
Now #published as a Letter @physreve.bsky.social: "Geometry of T1 transitions in epithelia" doi.org/10.1103/kdnb-bxdx
My first single-author paper deploys a silly amount of Olympiad geometry on a fundamental biophysics problem, summarised in the attached thread!
@mpipks.bsky.social @mpi-cbg.de
My first single-author paper deploys a silly amount of Olympiad geometry on a fundamental biophysics problem, summarised in the attached thread!
@mpipks.bsky.social @mpi-cbg.de
Reposted by Stephen Rong
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity
Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...
www.biorxiv.org
October 16, 2025 at 12:34 PM
Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...
Reposted by Stephen Rong
I think one of the saddest things about being a millennial is remembering a time when technology was advancing in a way that made life better and easier and more exciting instead of actively, intentionally worse
July 9, 2025 at 7:18 PM
I think one of the saddest things about being a millennial is remembering a time when technology was advancing in a way that made life better and easier and more exciting instead of actively, intentionally worse
Reposted by Stephen Rong
"You need an expansive political imagination, one that can anticipate the tyrant’s next move and understand its logic without obeying it."
My latest: sarahkendzior.substack.com/p/inventing-...
My latest: sarahkendzior.substack.com/p/inventing-...
Inventing Antifa
In 2005, the Uzbek government invented a group called “Akromiya” to justify massacring protesters. Now I worry the US government will do the same.
sarahkendzior.substack.com
October 19, 2025 at 2:37 PM
"You need an expansive political imagination, one that can anticipate the tyrant’s next move and understand its logic without obeying it."
My latest: sarahkendzior.substack.com/p/inventing-...
My latest: sarahkendzior.substack.com/p/inventing-...
Reposted by Stephen Rong
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes. #YeastGenomes #Pangenomes #GeneticVariation #StructuralVariants #LongRead #Sequencing @nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 19, 2025 at 7:32 AM
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes. #YeastGenomes #Pangenomes #GeneticVariation #StructuralVariants #LongRead #Sequencing @nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Stephen Rong
CogNeuroLanguage: new by @lauragwilliams.bsky.social & @jeanremiking.bsky.social (w Alec Marantz & me) shows how the brain maintains-updates continuously unfolding lang hierarchy during comprehension, anchoring ling theories to biological implementation
www.pnas.org/doi/10.1073/... #neuroskyence
www.pnas.org/doi/10.1073/... #neuroskyence
Hierarchical dynamic coding coordinates speech comprehension in the human brain | PNAS
Speech comprehension involves transforming an acoustic waveform into meaning. To do
so, the human brain generates a hierarchy of features that conv...
www.pnas.org
October 18, 2025 at 1:36 PM
CogNeuroLanguage: new by @lauragwilliams.bsky.social & @jeanremiking.bsky.social (w Alec Marantz & me) shows how the brain maintains-updates continuously unfolding lang hierarchy during comprehension, anchoring ling theories to biological implementation
www.pnas.org/doi/10.1073/... #neuroskyence
www.pnas.org/doi/10.1073/... #neuroskyence
Reposted by Stephen Rong
📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
October 18, 2025 at 6:59 PM
📢 New preprint:
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇
Experiment-guided AlphaFold3 resolves accurate protein ensembles.
doi.org/10.1101/2025...
AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇