Selin Jessa
@selinjessa.bsky.social
(she/her) Computational biologist and post-doc scientist in the Greenleaf and Kundaje labs at Stanford. Interested in understanding how cells know what to become (transcription factors, gene regulation, dev bio, open science) www.selinjessa.com
Reposted by Selin Jessa
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
November 5, 2025 at 3:09 PM
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Reposted by Selin Jessa
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 Selin Jessa
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread
dual activator-repressor function of transcription factors (TFs) and enables the model-guided
design of cell-state-sp...
www.cell.com
May 8, 2025 at 4:07 PM
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
Reposted by Selin Jessa
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
A highlight of my summer was this collab w/
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 7, 2025 at 6:38 PM
A highlight of my summer was this collab w/
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
Reposted by Selin Jessa
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 Selin Jessa
📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Genome Biology. We are particularly interested in researchers investigating the molecular and biophysical mechanisms underlying genome function and regulation. More details ➡️ tinyurl.com/3t7vvdct
November 5, 2025 at 10:59 AM
📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Genome Biology. We are particularly interested in researchers investigating the molecular and biophysical mechanisms underlying genome function and regulation. More details ➡️ tinyurl.com/3t7vvdct
Reposted by Selin Jessa
How does a “universal” transcription factor evolve to do species-specific jobs?
Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes.
Read it here 👉
www.biorxiv.org/content/10.1...
#MolecularEvolution #Transcription
Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes.
Read it here 👉
www.biorxiv.org/content/10.1...
#MolecularEvolution #Transcription
Molecular determinants underlying functional divergence of TBP homologs
The TATA-box binding protein (TBP) is a highly conserved basal transcription factor and a core component of the pre-initiation complex (PIC) for all three eukaryotic RNA polymerases (RNA Pols). Despit...
www.biorxiv.org
October 7, 2025 at 7:43 PM
How does a “universal” transcription factor evolve to do species-specific jobs?
Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes.
Read it here 👉
www.biorxiv.org/content/10.1...
#MolecularEvolution #Transcription
Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes.
Read it here 👉
www.biorxiv.org/content/10.1...
#MolecularEvolution #Transcription
Reposted by Selin Jessa
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
October 26, 2025 at 5:15 PM
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Reposted by Selin Jessa
Looking forward, I am launching my lab in the @mitkochinstitute.bsky.social and IMES at @mit.edu, and will continue studying how the unique regulatory landscape of ecDNA enables tumor evolution. We're looking for creative scientists to push this frontier - if you're interested, get in touch!
October 21, 2025 at 2:43 PM
Looking forward, I am launching my lab in the @mitkochinstitute.bsky.social and IMES at @mit.edu, and will continue studying how the unique regulatory landscape of ecDNA enables tumor evolution. We're looking for creative scientists to push this frontier - if you're interested, get in touch!
Reposted by Selin Jessa
Delighted to share our new study in @natcellbio.nature.com showing that the unique epigenetic landscape of ecDNA can enable the oncogenic enhancer activation of transposable elements! This was a great collaboration with @katerinakraft.bsky.social and @sedonamurphy.bsky.social. tinyurl.com/mwfbu4w4
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
tinyurl.com
October 21, 2025 at 2:43 PM
Delighted to share our new study in @natcellbio.nature.com showing that the unique epigenetic landscape of ecDNA can enable the oncogenic enhancer activation of transposable elements! This was a great collaboration with @katerinakraft.bsky.social and @sedonamurphy.bsky.social. tinyurl.com/mwfbu4w4
Reposted by Selin Jessa
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
October 23, 2025 at 5:10 PM
The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.
Reposted by Selin Jessa
My lab is seeking two PhD candidates to investigate the function and regulation of endogenous retroviruses in the early stages of human development 🦠👩🔬. Apply through the International Max Planck Research School (IMPRS) program: www.molgen.mpg.de/IMPRS/applic.... www.molgen.mpg.de/5094682/Fuey...
[2026] – Endogenous retroviruses in human embryogenesis
www.molgen.mpg.de
October 23, 2025 at 8:31 PM
My lab is seeking two PhD candidates to investigate the function and regulation of endogenous retroviruses in the early stages of human development 🦠👩🔬. Apply through the International Max Planck Research School (IMPRS) program: www.molgen.mpg.de/IMPRS/applic.... www.molgen.mpg.de/5094682/Fuey...
Reposted by Selin Jessa
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Reposted by Selin Jessa
🚨 We are recruiting postdocs! If you're interested in reproductive, stem cell/developmental biology, and/or women's health, please apply! 📝 Please repost! 🚩
More info here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
More info here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Postdoctoral Scientist - Zhang Lab
Primary Work Address: One Shields Avenue, Davis, CA, 95616 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute (HHMI) advances the discovery and s...
hhmi.wd1.myworkdayjobs.com
October 24, 2025 at 4:23 PM
🚨 We are recruiting postdocs! If you're interested in reproductive, stem cell/developmental biology, and/or women's health, please apply! 📝 Please repost! 🚩
More info here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
More info here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Reposted by Selin Jessa
(1/4) New Pre-print! 🌟
Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.
Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.
October 9, 2025 at 8:08 PM
(1/4) New Pre-print! 🌟
Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.
Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.
Reposted by Selin Jessa
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
Reposted by Selin Jessa
Faculty positions in animal morphogenesis that may be filled at the Assistant or Associate Professor level in one of my favorite Departments" Cell and Systems Biology at the University of Toronto. 1/n
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
October 6, 2025 at 6:09 PM
Faculty positions in animal morphogenesis that may be filled at the Assistant or Associate Professor level in one of my favorite Departments" Cell and Systems Biology at the University of Toronto. 1/n
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...
Reposted by Selin Jessa
The Vienna BioCenter PhD Program application deadline is approaching: October 10!
Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!
training.vbc.ac.at/phd-program/
#PhD #LifeSciences
Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!
training.vbc.ac.at/phd-program/
#PhD #LifeSciences
October 5, 2025 at 9:35 AM
The Vienna BioCenter PhD Program application deadline is approaching: October 10!
Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!
training.vbc.ac.at/phd-program/
#PhD #LifeSciences
Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!
training.vbc.ac.at/phd-program/
#PhD #LifeSciences
Reposted by Selin Jessa
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
DNA mutagenesis driven by transcription factor competition with mismatch repair
Competition between transcription factors and mismatch repair machinery drives localized
hypermutation at regulatory elements, with implications for cancer and genome evolution.
www.cell.com
October 2, 2025 at 11:37 PM
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
Reposted by Selin Jessa
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
A human-specific regulatory mechanism revealed in a pre-implantation model
Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.
rdcu.be
October 1, 2025 at 6:08 PM
Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD
Reposted by Selin Jessa
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
September 29, 2025 at 7:03 AM
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Selin Jessa
FINAL REGISTRATION DEADLINE!
Last day to register for the CEEHRC Annual Meeting is FRIDAY, OCTOBER 10!
Abstracts still being accepted for the poster sessions.
Speaker lineup and other details can be found at event.fourwaves.com/...
#epigenetics #epigenomics #ceehrc
Last day to register for the CEEHRC Annual Meeting is FRIDAY, OCTOBER 10!
Abstracts still being accepted for the poster sessions.
Speaker lineup and other details can be found at event.fourwaves.com/...
#epigenetics #epigenomics #ceehrc
CEEHRC 11th Annual Canadian Conference on Epigenetics
Fourwaves - CEEHRC 11th Annual Canadian Conference on Epigenetics
event.fourwaves.com
September 29, 2025 at 8:42 PM
FINAL REGISTRATION DEADLINE!
Last day to register for the CEEHRC Annual Meeting is FRIDAY, OCTOBER 10!
Abstracts still being accepted for the poster sessions.
Speaker lineup and other details can be found at event.fourwaves.com/...
#epigenetics #epigenomics #ceehrc
Last day to register for the CEEHRC Annual Meeting is FRIDAY, OCTOBER 10!
Abstracts still being accepted for the poster sessions.
Speaker lineup and other details can be found at event.fourwaves.com/...
#epigenetics #epigenomics #ceehrc
Reposted by Selin Jessa
Please help me to celebrate Mei Zhen, an innovator and tremendous collaborator, named to the Royal Society of Canada Academy of Science on September 4, 2025
September 6, 2025 at 5:56 PM
Please help me to celebrate Mei Zhen, an innovator and tremendous collaborator, named to the Royal Society of Canada Academy of Science on September 4, 2025
Reposted by Selin Jessa
Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...
HDAC3 prevents enhancer hyperactivation to enable developmental transitions
Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...
www.biorxiv.org
September 18, 2025 at 9:55 AM
Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...