Hamed Najafabadi
@hsnajafabadi.bsky.social
Associate Professor at McGill University. Gene regulation, genomics, and bioinformatics. https://csg.lab.mcgill.ca/
Reposted by Hamed Najafabadi
Transcriptional interferences ensure one olfactory receptor per ant neuron
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
October 22, 2025 at 8:40 PM
Transcriptional interferences ensure one olfactory receptor per ant neuron
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
www.nature.com/articles/s41...
Caviar for RNA-Seq nerds! Check this out
Reposted by Hamed Najafabadi
📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...
October 17, 2025 at 2:12 AM
📣 Attention #RNA #Splicing lovers! How is splicing of exons coordinated??🤔 ➡️ Exon Junction Complex (EJC) coordinates inclusion of blocks of neighboring exons!😯 Cool work by Alexandra Bergfort @karlaneugebauer.bsky.social lab - check it out! (we got to help a bit 😊) genesdev.cshlp.org/content/earl...
Reposted by Hamed Najafabadi
🚨 New paper alert on telomeres! 🚨
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
October 9, 2025 at 5:33 AM
🚨 New paper alert on telomeres! 🚨
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.
Reposted by Hamed Najafabadi
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 Hamed Najafabadi
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs
The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...
www.biorxiv.org
September 27, 2025 at 3:39 PM
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Reposted by Hamed Najafabadi
Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
August 18, 2025 at 12:23 PM
Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
Delighted to share our latest paper out @NatureComms. REST/NRSF is essential for muscle stem cell identity, blocking alternate cell fates—huge congrats to the first author @KorinSahinyan and the rest of the fantastic coauthors.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
REST/NRSF Preserves muscle stem cell identity by repressing alternate cell fate - Nature Communications
Here the authors show that REST/NRSF represses non-muscle lineage genes in muscle stem cells and progenitors, preserving their identity and differentiation capacity. Loss of REST disrupts gene silenci...
www.nature.com
August 12, 2025 at 8:44 PM
Delighted to share our latest paper out @NatureComms. REST/NRSF is essential for muscle stem cell identity, blocking alternate cell fates—huge congrats to the first author @KorinSahinyan and the rest of the fantastic coauthors.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Hamed Najafabadi
Is the annotation of viruses in the human genome accurate? We think not. Take a look at our new paper and let us know if you agree! www.science.org/doi/10.1126/...
A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage
A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.
www.science.org
July 21, 2025 at 1:51 PM
Is the annotation of viruses in the human genome accurate? We think not. Take a look at our new paper and let us know if you agree! www.science.org/doi/10.1126/...
Reposted by Hamed Najafabadi
I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology
Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.
nature.com
July 27, 2025 at 5:03 PM
I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)
@natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)
Reposted by Hamed Najafabadi
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression
Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...
www.science.org
July 4, 2025 at 11:00 AM
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Reposted by Hamed Najafabadi
Hello out there! Are you looking for a friendly community to share your RNA research and hear about some cool RNA biology? Register for @trendrna.bsky.social on July 10-11 now! Oral abstract deadline is May 30th! Co sponsored by @rnacanada.bsky.social!
We are excited to announce that registration for this year's Toronto RNA Enthusiasts' Day (TREnD) is now open!
July 10th, 1pm-4pm ET ONLINE for everyone
July 11th, 9am-7pm ET ONLINE across Canada and IN PERSON in Toronto
event.fourwaves.com/trend25/regi...
July 10th, 1pm-4pm ET ONLINE for everyone
July 11th, 9am-7pm ET ONLINE across Canada and IN PERSON in Toronto
event.fourwaves.com/trend25/regi...
May 23, 2025 at 9:06 PM
Hello out there! Are you looking for a friendly community to share your RNA research and hear about some cool RNA biology? Register for @trendrna.bsky.social on July 10-11 now! Oral abstract deadline is May 30th! Co sponsored by @rnacanada.bsky.social!
Reposted by Hamed Najafabadi
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Perspective on recent developments and challenges in regulatory and systems genomics
Abstract. Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regul
doi.org
May 13, 2025 at 4:59 PM
Our New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models.
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
🔗 doi.org/10.1093/bioa...
#Genomics #Bioinformatics #RegulatoryGenomics
Reposted by Hamed Najafabadi
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Reposted by Hamed Najafabadi
Delighted to see this out! Fun fact: I actually started my lab @ UCSF w/ goal of understanding tRNA txn regulation, which aligned perfectly w/ @genophoria.bsky.social & Sohail! 6+ years of amazing collaboration & stellar work by Siyu, Albertas, & co & we're making real progress w/ more to come!
Check out our latest preprint, led by Dr. Siyu Chen, that brings together an amazing team of scientists from several labs ( @vram142.bsky.social, Tavazoie, and Navickas) to tackle a fundamental problem in biology: how do cells regulate expression of their tRNAs? www.biorxiv.org/content/10.1...
Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis
Transfer RNAs (tRNAs), once viewed as static adaptors in translation, are now recognized as dynamic regulators of gene expression. While recent studies have illuminated roles for tRNA stability, the u...
www.biorxiv.org
May 1, 2025 at 3:22 AM
Delighted to see this out! Fun fact: I actually started my lab @ UCSF w/ goal of understanding tRNA txn regulation, which aligned perfectly w/ @genophoria.bsky.social & Sohail! 6+ years of amazing collaboration & stellar work by Siyu, Albertas, & co & we're making real progress w/ more to come!
Reposted by Hamed Najafabadi
Alternative splicing (AS) is common, but its impact on the proteome remains debated, especially in primary cells.
What determines which AS isoforms result in abundant proteins ?
We find that proteoform-specific ...
🧵
www.biorxiv.org/content/10.1...
What determines which AS isoforms result in abundant proteins ?
We find that proteoform-specific ...
🧵
www.biorxiv.org/content/10.1...
April 28, 2025 at 10:28 AM
Alternative splicing (AS) is common, but its impact on the proteome remains debated, especially in primary cells.
What determines which AS isoforms result in abundant proteins ?
We find that proteoform-specific ...
🧵
www.biorxiv.org/content/10.1...
What determines which AS isoforms result in abundant proteins ?
We find that proteoform-specific ...
🧵
www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
March 26, 2025 at 5:11 PM
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
Reposted by Hamed Najafabadi
Why do RBPs need multiple RNA-binding domains? We show transcriptome-wide that the endosomal mRNA transporter Rrm4 uses its three RRMs to differentiate functional binding sites from accessory ones. Great collaboration with @koenig-lab.bsky.social and Zarnack lab
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Dissecting the RNA binding capacity of the multi-RRM protein Rrm4 essential for endosomal mRNA transport
RNA-binding proteins (RBPs) utilize multiple RNA-binding domains (RBDs) to engage with extensive mRNA networks. Understanding the intricate interplay of modular RBDs is essential for uncovering RBP fu...
www.biorxiv.org
March 1, 2025 at 4:20 PM
Why do RBPs need multiple RNA-binding domains? We show transcriptome-wide that the endosomal mRNA transporter Rrm4 uses its three RRMs to differentiate functional binding sites from accessory ones. Great collaboration with @koenig-lab.bsky.social and Zarnack lab
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...
Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling
Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...
www.biorxiv.org
February 25, 2025 at 1:25 PM
@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
How do early lung tumors evolve?
Our latest preprint, led by Junbum Kim, maps early-stage cancer at single-cell resolution, revealing two key pathways:
🦠Driven by immune activity
🛠️ Driven by fibrosis
These insights could refine detection & treatment.
www.biorxiv.org/content/10.1...
Our latest preprint, led by Junbum Kim, maps early-stage cancer at single-cell resolution, revealing two key pathways:
🦠Driven by immune activity
🛠️ Driven by fibrosis
These insights could refine detection & treatment.
www.biorxiv.org/content/10.1...
Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression
Lung cancer remains the deadliest cancer in the United States, with lung adenocarcinoma (LUAD) as its most prevalent subtype. While computed tomography (CT)-based screening has improved early detectio...
www.biorxiv.org
February 24, 2025 at 3:34 PM
How do early lung tumors evolve?
Our latest preprint, led by Junbum Kim, maps early-stage cancer at single-cell resolution, revealing two key pathways:
🦠Driven by immune activity
🛠️ Driven by fibrosis
These insights could refine detection & treatment.
www.biorxiv.org/content/10.1...
Our latest preprint, led by Junbum Kim, maps early-stage cancer at single-cell resolution, revealing two key pathways:
🦠Driven by immune activity
🛠️ Driven by fibrosis
These insights could refine detection & treatment.
www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
Thrilled to share LUNA🌕 – our new generative AI model that reassembles tissue structures from dissociated cells! LUNA learns spatial priors over existing spatially resolved datasets with the aim to predict cell locations de novo.
Check out our paper here: www.biorxiv.org/content/10.1...
Check out our paper here: www.biorxiv.org/content/10.1...
February 24, 2025 at 3:29 PM
Thrilled to share LUNA🌕 – our new generative AI model that reassembles tissue structures from dissociated cells! LUNA learns spatial priors over existing spatially resolved datasets with the aim to predict cell locations de novo.
Check out our paper here: www.biorxiv.org/content/10.1...
Check out our paper here: www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
I love this insight on building teams from @genophoria.bsky.social, Core Investigator at Arc Institute, which just released Evo 2: the largest AI model for biology to date.
Catch the full conversation:
+ YouTube: youtu.be/sWcoslBueiE
+ Spotify: spoti.fi/4hLk3xo
+ Apple Podcasts: apple.co/40sQCu9
Catch the full conversation:
+ YouTube: youtu.be/sWcoslBueiE
+ Spotify: spoti.fi/4hLk3xo
+ Apple Podcasts: apple.co/40sQCu9
February 20, 2025 at 6:35 PM
I love this insight on building teams from @genophoria.bsky.social, Core Investigator at Arc Institute, which just released Evo 2: the largest AI model for biology to date.
Catch the full conversation:
+ YouTube: youtu.be/sWcoslBueiE
+ Spotify: spoti.fi/4hLk3xo
+ Apple Podcasts: apple.co/40sQCu9
Catch the full conversation:
+ YouTube: youtu.be/sWcoslBueiE
+ Spotify: spoti.fi/4hLk3xo
+ Apple Podcasts: apple.co/40sQCu9
Reposted by Hamed Najafabadi
Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin?
By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient!
#chromatin #3Dgenome #generegulation
www.science.org/doi/10.1126/...
👇
By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient!
#chromatin #3Dgenome #generegulation
www.science.org/doi/10.1126/...
👇
Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus
In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and a...
www.science.org
February 7, 2025 at 10:22 AM
Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin?
By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient!
#chromatin #3Dgenome #generegulation
www.science.org/doi/10.1126/...
👇
By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient!
#chromatin #3Dgenome #generegulation
www.science.org/doi/10.1126/...
👇
Reposted by Hamed Najafabadi
The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...
A generative framework for enhanced cell-type specificity in rationally designed mRNAs
mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...
www.biorxiv.org
January 2, 2025 at 1:10 PM
The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...
Reposted by Hamed Najafabadi
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Hamed Najafabadi
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:54 AM
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/