Dane Vassiliadis
@danevass.bsky.social
chromatin, transcription, lineage tracing & single cells
Reposted by Dane Vassiliadis
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
November 20, 2025 at 9:36 AM
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
Thrilled to be awarded this inspirational research grant for our work targeting hard to kill drug tolerant cells in ALK+ lung cancer. Many thanks to @alkpostitiveaust.bsky.social, the Thoracic Oncology Group of Australasia and all donors for generously supporting our work 🙏
Identifying ALK+ resistance pathways is at the very core of what is important to us all. That makes the announcement of Dr Vassiliadis as the recipient of the ALK Positive Australia/TOGA Inspirational Grant for 2026 so thrilling.
Every $ donated to ALK Positive Australia goes towards research.
Every $ donated to ALK Positive Australia goes towards research.
November 13, 2025 at 2:33 AM
Thrilled to be awarded this inspirational research grant for our work targeting hard to kill drug tolerant cells in ALK+ lung cancer. Many thanks to @alkpostitiveaust.bsky.social, the Thoracic Oncology Group of Australasia and all donors for generously supporting our work 🙏
Reposted by Dane Vassiliadis
I’m excited to highlight our latest paper, just published in Cell 🎉
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
RNA Pol II inhibition activates cell death independently from the loss of transcription
When RNA polymerase II (RNA Pol II) is inhibited, the inhibition is sensed and signaled
to mitochondria, leading to programmed cell death independently of the loss of RNA
Pol II transcription activity...
www.cell.com
August 15, 2025 at 6:35 PM
I’m excited to highlight our latest paper, just published in Cell 🎉
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
We report the existence of a previously uncharacterized signaling pathway that is responsible for activating cell death upon loss of gene expression.
1/n 🧪
www.cell.com/cell/fulltex...
Reposted by Dane Vassiliadis
EMBO workshop on Single cell Lineage Tracing!
Sept 18-21 in Sant Feliu, Girona, Spain.
Registration OPEN!!!!!
Tons of opportunities for talks (including some full length ones).
You don’t want to miss it!
meetings.embo.org/event/25-lin...
Sept 18-21 in Sant Feliu, Girona, Spain.
Registration OPEN!!!!!
Tons of opportunities for talks (including some full length ones).
You don’t want to miss it!
meetings.embo.org/event/25-lin...
Lineage tracing: Dynamics, cellular memory, and somatic evolution
Recent advances in high-resolution lineage tracing technologies and single-cell genomics are allowing researchers to quantify cell state dynamics at unprecedented scales. Across cancer and immunity, …
meetings.embo.org
April 8, 2025 at 6:36 PM
EMBO workshop on Single cell Lineage Tracing!
Sept 18-21 in Sant Feliu, Girona, Spain.
Registration OPEN!!!!!
Tons of opportunities for talks (including some full length ones).
You don’t want to miss it!
meetings.embo.org/event/25-lin...
Sept 18-21 in Sant Feliu, Girona, Spain.
Registration OPEN!!!!!
Tons of opportunities for talks (including some full length ones).
You don’t want to miss it!
meetings.embo.org/event/25-lin...
Reposted by Dane Vassiliadis
I'll be presenting this work this Friday (14 Feb), all are welcome 😃
See below for event details. Our colleague Ruqian will also present her spatial work on lung fibrosis: events.unimelb.edu.au/MIG/event/44...
See below for event details. Our colleague Ruqian will also present her spatial work on lung fibrosis: events.unimelb.edu.au/MIG/event/44...
February 12, 2025 at 12:25 AM
I'll be presenting this work this Friday (14 Feb), all are welcome 😃
See below for event details. Our colleague Ruqian will also present her spatial work on lung fibrosis: events.unimelb.edu.au/MIG/event/44...
See below for event details. Our colleague Ruqian will also present her spatial work on lung fibrosis: events.unimelb.edu.au/MIG/event/44...
Reposted by Dane Vassiliadis
📃 New preprint from the lab! 📃
Dr. Jiadong Mao extends Φ-Space for spatial transcriptomics. Φ-Space ST is fast, platform-agnostic, and segmentation-free—uncovering niche-specific cell states with high accuracy.
Read it here: www.biorxiv.org/content/10.1...
#SpatialTranscriptomics #singlecell
Dr. Jiadong Mao extends Φ-Space for spatial transcriptomics. Φ-Space ST is fast, platform-agnostic, and segmentation-free—uncovering niche-specific cell states with high accuracy.
Read it here: www.biorxiv.org/content/10.1...
#SpatialTranscriptomics #singlecell
Φ-Space ST: a platform-agnostic method to identify cell states in spatial transcriptomics studies
We introduce Φ-Space ST, a platform-agnostic method to identify continuous cell states in spatial transcriptomics (ST) data using multiple scRNA-seq references. For ST with supercellular resolution, Φ...
www.biorxiv.org
February 11, 2025 at 11:55 PM
📃 New preprint from the lab! 📃
Dr. Jiadong Mao extends Φ-Space for spatial transcriptomics. Φ-Space ST is fast, platform-agnostic, and segmentation-free—uncovering niche-specific cell states with high accuracy.
Read it here: www.biorxiv.org/content/10.1...
#SpatialTranscriptomics #singlecell
Dr. Jiadong Mao extends Φ-Space for spatial transcriptomics. Φ-Space ST is fast, platform-agnostic, and segmentation-free—uncovering niche-specific cell states with high accuracy.
Read it here: www.biorxiv.org/content/10.1...
#SpatialTranscriptomics #singlecell
Reposted by Dane Vassiliadis
‘A neoantigen vaccine generates antitumour immunity in renal cell carcinoma’
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A neoantigen vaccine generates antitumour immunity in renal cell carcinoma - Nature
A phase I trial of a neoantigen-targeting personalized cancer vaccine led to durable and polyfunctional T cell responses and antitumour recognition, and was associated with no recurrence in patie...
www.nature.com
February 8, 2025 at 8:44 AM
‘A neoantigen vaccine generates antitumour immunity in renal cell carcinoma’
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Dane Vassiliadis
🧵 1/ We’re excited to share that our new paper with @adrianbracken.bsky.social lab is out 🎉 In this study (which began over 10 years ago!), we explore the biology of PRC2 and PRC1 in non-dividing cells. We also explore the effects of PRC2 inhibitor drugs on these cells. Here’s what we found👇
January 14, 2025 at 10:57 PM
🧵 1/ We’re excited to share that our new paper with @adrianbracken.bsky.social lab is out 🎉 In this study (which began over 10 years ago!), we explore the biology of PRC2 and PRC1 in non-dividing cells. We also explore the effects of PRC2 inhibitor drugs on these cells. Here’s what we found👇
Reposted by Dane Vassiliadis
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
www.nature.com
January 8, 2025 at 1:30 PM
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Dane Vassiliadis
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 Dane Vassiliadis
My previous mentor and great friend Prof. Marc Mansour from UCL has joined Bluesky! 🎉 Do consider following him if you’re researching acute leukaemias and associated novel therapies!
bsky.app/profile/marc...
bsky.app/profile/marc...
bsky.app
January 6, 2025 at 9:48 AM
My previous mentor and great friend Prof. Marc Mansour from UCL has joined Bluesky! 🎉 Do consider following him if you’re researching acute leukaemias and associated novel therapies!
bsky.app/profile/marc...
bsky.app/profile/marc...
Reposted by Dane Vassiliadis
🔬Decoding Silencing: How Heterochromatin Transcribes to Silence Itself!
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
January 3, 2025 at 3:46 PM
🔬Decoding Silencing: How Heterochromatin Transcribes to Silence Itself!
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
Reposted by Dane Vassiliadis
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
January 3, 2025 at 7:25 PM
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
Reposted by Dane Vassiliadis
🧬 We’re excited to introduce D&D-seq, a single-cell technology that maps DNA:Protein interactions through molecular footprinting. Check it out here: biorxiv.org/content/10.1... #Genomics #Epigenetics
Single-cell mapping of regulatory DNA:Protein interactions
Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibil...
biorxiv.org
January 2, 2025 at 9:10 PM
🧬 We’re excited to introduce D&D-seq, a single-cell technology that maps DNA:Protein interactions through molecular footprinting. Check it out here: biorxiv.org/content/10.1... #Genomics #Epigenetics
Reposted by Dane Vassiliadis
Did you ever wonder why metastatic cancers often spread to the lungs? Amazing research from @ginevradoglioni.bsky.social! Many thanks to all collaborators, funders and patients. Wishing you all an enjoyable read and a happy new year and Ginevra a great next endeavor @salkinstitute.bsky.social
Beyond excited to share that the main work of my PhD on how aspartate signaling drives metastasis is finally out in @nature.com ✨
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
Aspartate signalling drives lung metastasis via alternative translation - Nature
Aspartate in the tumour environment activates the N-methyl-d-aspartate receptor in cancer cells to induce cellular programmes that increase the aggressiveness of metastasis.
go.nature.com
January 1, 2025 at 5:16 PM
Did you ever wonder why metastatic cancers often spread to the lungs? Amazing research from @ginevradoglioni.bsky.social! Many thanks to all collaborators, funders and patients. Wishing you all an enjoyable read and a happy new year and Ginevra a great next endeavor @salkinstitute.bsky.social
Reposted by Dane Vassiliadis
"Everything in epigenetics is circular". Here, we explore how memory that is stored locally on chromatin has a crucial role in stabilising cellular state, updating our view of the epigenetic landscape from one shaped by the genotype, to one moulded by experience
doi.org/10.1186/s130...
doi.org/10.1186/s130...
Chromatin-based memory as a self-stabilizing influence on cell identity - Genome Biology
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states...
doi.org
December 30, 2024 at 10:58 PM
"Everything in epigenetics is circular". Here, we explore how memory that is stored locally on chromatin has a crucial role in stabilising cellular state, updating our view of the epigenetic landscape from one shaped by the genotype, to one moulded by experience
doi.org/10.1186/s130...
doi.org/10.1186/s130...
Reposted by Dane Vassiliadis
Proud to share our paper on the impact of transcription inhibition on mRNA export in cancer.
A big thanks to collaborators, especially to Ewa Michalak, Vi Wickramasinghe, Jeff Chao and Mark Dawson @mafdawson.bsky.social. @fmiscience.bsky.social
A big thanks to collaborators, especially to Ewa Michalak, Vi Wickramasinghe, Jeff Chao and Mark Dawson @mafdawson.bsky.social. @fmiscience.bsky.social
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription
Transcription inhibitors also disrupt nuclear export. Here, Williams et al. reveal that mRNA export factors sense transcription inhibition and adapt by storing mature export-competent mRNA in nuclear speckles. This enables rapid release when transcription resumes and ensures retention of cellular identity and viability during a transient global transcription insult.
www.cell.com
January 2, 2025 at 10:55 PM
Proud to share our paper on the impact of transcription inhibition on mRNA export in cancer.
A big thanks to collaborators, especially to Ewa Michalak, Vi Wickramasinghe, Jeff Chao and Mark Dawson @mafdawson.bsky.social. @fmiscience.bsky.social
A big thanks to collaborators, especially to Ewa Michalak, Vi Wickramasinghe, Jeff Chao and Mark Dawson @mafdawson.bsky.social. @fmiscience.bsky.social
Reposted by Dane Vassiliadis
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription
Transcription inhibitors also disrupt nuclear export. Here, Williams et al. reveal that mRNA export factors sense transcription inhibition and adapt by storing mature export-competent mRNA in nuclear speckles. This enables rapid release when transcription resumes and ensures retention of cellular identity and viability during a transient global transcription insult.
www.cell.com
January 2, 2025 at 8:03 PM
Why can a human tolerate a drug that globally inhibits transcription? Why do transcription inhibitors not cure cancer? Our first paper of 2025 may help explain (some) of this!
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
So incredibly proud of @tobiaswilliams.bsky.social & Ewa Michalak who led the work!
www.cell.com/molecular-ce...
Reposted by Dane Vassiliadis
Beyond excited to share that the main work of my PhD on how aspartate signaling drives metastasis is finally out in @nature.com ✨
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
Aspartate signalling drives lung metastasis via alternative translation - Nature
Aspartate in the tumour environment activates the N-methyl-d-aspartate receptor in cancer cells to induce cellular programmes that increase the aggressiveness of metastasis.
go.nature.com
January 1, 2025 at 4:56 PM
Beyond excited to share that the main work of my PhD on how aspartate signaling drives metastasis is finally out in @nature.com ✨
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
-> go.nature.com/4gCYtuL
A huge thank to the @fendtlab.bsky.social and all our collaborators for the terrific team work 🙏
A brief 🧵
Reposted by Dane Vassiliadis
Stem cell-like states confer poor outcomes in blood cancer—but what mechanisms drive this and how can they be therapeutically targeted? In our new preprint, we show how a single TF represses one enhancer to maintain a subset of high-risk leukemias: 🧵👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 2, 2025 at 2:47 PM
Stem cell-like states confer poor outcomes in blood cancer—but what mechanisms drive this and how can they be therapeutically targeted? In our new preprint, we show how a single TF represses one enhancer to maintain a subset of high-risk leukemias: 🧵👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Dane Vassiliadis
new out in Nature www.nature.com/articles/s41...
Aspartate signalling drives lung metastasis via alternative translation - Nature
Aspartate in the tumour environment activates the N-methyl-d-aspartate receptor in cancer cells to induce cellular programmes that increase the aggressiveness of metastasis.
www.nature.com
January 2, 2025 at 6:03 PM
new out in Nature www.nature.com/articles/s41...
Reposted by Dane Vassiliadis
well well well. if it isn't all the things i said i'd do next year last year
January 1, 2025 at 4:27 PM
well well well. if it isn't all the things i said i'd do next year last year
Reposted by Dane Vassiliadis
Does anyone know the best and original references for absolute quantification of ChIP-Seq and RNA-Seq, using spike-in normalization?
November 26, 2024 at 5:45 PM
Does anyone know the best and original references for absolute quantification of ChIP-Seq and RNA-Seq, using spike-in normalization?
Reposted by Dane Vassiliadis
I don't know if this answers your specific question, but I found this recent commentary very useful www.nature.com/articles/s41...
The Wild West of spike-in normalization - Nature Biotechnology
The proper use of spike-in normalization in ChIP-seq improves sensitivity for detecting genome-wide changes between conditions, but improper use is common, calling some biological conclusions into que...
www.nature.com
November 26, 2024 at 6:05 PM
I don't know if this answers your specific question, but I found this recent commentary very useful www.nature.com/articles/s41...
Reposted by Dane Vassiliadis
(1/5) Traditionally, antibiotic discovery has centered on bacteria and fungi—until now.
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...
December 12, 2024 at 10:56 AM
(1/5) Traditionally, antibiotic discovery has centered on bacteria and fungi—until now.
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...