Vijay Ramani
@vram142.bsky.social
PI @ Gladstone Institutes & UCSF. Molecular technologies & the genomics / molecular biology / biochemistry of gene regulation. Views here mine & do not represent those of my affiliated institutions.
Pinned
Vijay Ramani
@vram142.bsky.social
· Sep 20
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
Reposted by Vijay Ramani
🚨 Requesting help:
I am looking for an agent who can facilitate more speaking gigs, podcast appearances, and interviews with journalists
I want to more widely share my story and expertise as a trans geneticist who understands the reality and complexity of "biological sex" 🏳️⚧️🧬
Please signal boost?
I am looking for an agent who can facilitate more speaking gigs, podcast appearances, and interviews with journalists
I want to more widely share my story and expertise as a trans geneticist who understands the reality and complexity of "biological sex" 🏳️⚧️🧬
Please signal boost?
January 28, 2026 at 9:03 PM
🚨 Requesting help:
I am looking for an agent who can facilitate more speaking gigs, podcast appearances, and interviews with journalists
I want to more widely share my story and expertise as a trans geneticist who understands the reality and complexity of "biological sex" 🏳️⚧️🧬
Please signal boost?
I am looking for an agent who can facilitate more speaking gigs, podcast appearances, and interviews with journalists
I want to more widely share my story and expertise as a trans geneticist who understands the reality and complexity of "biological sex" 🏳️⚧️🧬
Please signal boost?
No justice, no science. Fuck ICE.
If you are a scientist funded by NIH and agree that if the HHS/NIH bill is held hostage by linkage for funding to DHS/ICE, we need to shutdown both and save lives, its time to speak up. Right now, with a few exceptions, the silence is deafening
As a someone with a 33 year NIH-funded lab whose grant is supposed to be reviewed this week, shut NIH down if that is what's needed to end ICE terrorism. Innocent lives are more important 🧪
January 26, 2026 at 6:33 PM
No justice, no science. Fuck ICE.
Reposted by Vijay Ramani
If you are a scientist funded by NIH and agree that if the HHS/NIH bill is held hostage by linkage for funding to DHS/ICE, we need to shutdown both and save lives, its time to speak up. Right now, with a few exceptions, the silence is deafening
As a someone with a 33 year NIH-funded lab whose grant is supposed to be reviewed this week, shut NIH down if that is what's needed to end ICE terrorism. Innocent lives are more important 🧪
The Senate may choose to vote together on the DHS and LHHS bills. Thus, a filibuster on DHS may mean no funding for NIH. What my colleagues are saying:
“Shut it down, public health will understand. I’ll work without pay again.”
- anonymous NIHer
“Shut it down, public health will understand. I’ll work without pay again.”
- anonymous NIHer
January 26, 2026 at 1:46 PM
If you are a scientist funded by NIH and agree that if the HHS/NIH bill is held hostage by linkage for funding to DHS/ICE, we need to shutdown both and save lives, its time to speak up. Right now, with a few exceptions, the silence is deafening
Reposted by Vijay Ramani
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
www.nature.com
January 21, 2026 at 9:14 PM
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Reposted by Vijay Ramani
Congratulations to @groth-anja.bsky.social on receiving the Novo Nordisk Foundation Jacobæus Prize 🏆 we’re proud to see Anja's mentorship, leadership, & pioneering work in epigenetic cell memory getting top recognition 👏 celebrating the contributions of past & present lab members to this work too 🥳
January 14, 2026 at 8:43 PM
Congratulations to @groth-anja.bsky.social on receiving the Novo Nordisk Foundation Jacobæus Prize 🏆 we’re proud to see Anja's mentorship, leadership, & pioneering work in epigenetic cell memory getting top recognition 👏 celebrating the contributions of past & present lab members to this work too 🥳
Reposted by Vijay Ramani
Stress controls epigenetic inheritance!
A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8
A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8
January 7, 2026 at 4:46 PM
Stress controls epigenetic inheritance!
A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8
A histone ubiquitylation-based regulatory hub links stress/environmental signaling to heterochromatin self-propagation and epigenetic inheritance-reshaping how we think about development, drug resistance, and cancer
👉 nature.com/articles/s41586-025-09899-8
Reposted by Vijay Ramani
Is arginine the new cysteine?! Check out our lab's latest in collaboration with @ianseiple.bsky.social's team where we introduce ninhydrin as a selective covalent warhead and probe targeting reactive arginines.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Ninhydrin as a covalent warhead for chemical proteomic-enabled discovery and selective engagement of reactive arginines
Covalent molecules have emerged as next-generation therapeutics and as powerful tools for perturbing fundamental biological processes. Chemical proteomic methods to screen for reactive proteinaceous a...
www.biorxiv.org
January 6, 2026 at 3:40 PM
Is arginine the new cysteine?! Check out our lab's latest in collaboration with @ianseiple.bsky.social's team where we introduce ninhydrin as a selective covalent warhead and probe targeting reactive arginines.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Vijay Ramani
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1
December 22, 2025 at 6:14 PM
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
And found a hidden RNA-decay axis from Piwi to the RNA exosome.
Reposted by Vijay Ramani
Ladies and gentlemen... the weekend. (also: you are important and are not alone 🧡)
December 20, 2025 at 12:00 AM
Ladies and gentlemen... the weekend. (also: you are important and are not alone 🧡)
Reposted by Vijay Ramani
Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones)
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
www.biorxiv.org
December 16, 2025 at 7:50 PM
Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones)
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :
www.biorxiv.org/content/10.6...
Reposted by Vijay Ramani
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Escape from X inactivation is directly modulated by Xist noncoding RNA
Nature Cell Biology - The authors show that increased Xist RNA levels can induce de novo silencing of genes that normally escape X inactivation. SPEN depletion prevents the silencing of escape...
rdcu.be
December 15, 2025 at 4:22 PM
Very happy to share our paper rdcu.be/eUImj out today in @natcellbio.nature.com 🎉🎉🎉
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
We uncover an unexpected role for endogenous Xist RNA in regulating X-linked genes that escape X-inactivation.
Reposted by Vijay Ramani
Reposted by Vijay Ramani
@science.org🧬Cohesin guides homology search during DNA repair using loops and sister chromatid linkages | Science www.science.org/doi/10.1126/... @fedeteloni.bsky.social @danielgerlich.bsky.social et al.
Cohesin guides homology search during DNA repair using loops and sister chromatid linkages
Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequenc...
www.science.org
December 5, 2025 at 8:50 PM
@science.org🧬Cohesin guides homology search during DNA repair using loops and sister chromatid linkages | Science www.science.org/doi/10.1126/... @fedeteloni.bsky.social @danielgerlich.bsky.social et al.
Reposted by Vijay Ramani
Oh hey, looks like I can upload longer videos here now!
Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.
Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.
December 4, 2025 at 1:20 AM
Oh hey, looks like I can upload longer videos here now!
Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.
Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.
Reposted by Vijay Ramani
Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.
December 3, 2025 at 8:42 PM
Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.
Reposted by Vijay Ramani
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
December 2, 2025 at 2:18 PM
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Reposted by Vijay Ramani
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
November 27, 2025 at 9:59 PM
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Man it would be so cool if, in the year 2025 of our lord, we could all just be chill and celebratory about nice professional things being announced for our colleagues in molecular biology.
Unrelated, anyone reading absolute Batman? Bc it slaps.
Unrelated, anyone reading absolute Batman? Bc it slaps.
November 29, 2025 at 10:30 AM
Man it would be so cool if, in the year 2025 of our lord, we could all just be chill and celebratory about nice professional things being announced for our colleagues in molecular biology.
Unrelated, anyone reading absolute Batman? Bc it slaps.
Unrelated, anyone reading absolute Batman? Bc it slaps.
Reposted by Vijay Ramani
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
POSTDOCTORAL FELLOW - Toronto (City), Ontario (CA) job with Taipale Lab, Donnelly Centre, University of Toronto | 12849004
The Taipale lab in the Donnelly CCBR and University of Toronto is looking for a highly motivated Postdoctoral Fellow
www.nature.com
November 19, 2025 at 5:51 PM
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
Reposted by Vijay Ramani
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Vijay Ramani
Read my full story here!
Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance
www.nature.com/articles/d41...
Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance
www.nature.com/articles/d41...
Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance
The Make America Healthy Again summit, attended by health secretary Robert F. Kennedy Jr and vice-president JD Vance, gave a sense of what’s driving US health policy.
www.nature.com
November 21, 2025 at 5:01 PM
Read my full story here!
Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance
www.nature.com/articles/d41...
Psychedelics and immortality: Nature went to a health summit starring RFK and JD Vance
www.nature.com/articles/d41...
Reposted by Vijay Ramani
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
November 19, 2025 at 4:24 PM
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
Reposted by Vijay Ramani
Very excited to present OpenCGChromatin🔥🔥🔥
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
November 18, 2025 at 3:07 PM
Very excited to present OpenCGChromatin🔥🔥🔥
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation
Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
Reposted by Vijay Ramani
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
www.biorxiv.org
November 18, 2025 at 2:51 PM
Major new direction in the lab: hacking human cell biology with pathogen effectors (eORFs) - amazing collaboration with @miketilapia.bsky.social lab. Huge congrats to first authors Tomas & He & all co-authors! Check out the pre-print on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...
Reposted by Vijay Ramani
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