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...

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 🙏

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...

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...

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, …

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...

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...

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...

📃 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

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...

‘A neoantigen vaccine generates antitumour immunity in renal cell carcinoma’

www.nature.com/articles/s41...

Excellent work mate! Great to see it out.

🧵 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👇

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...

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...

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/...

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...

🔬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...

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⬇️

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...

🧬 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

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

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...

"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...

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

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.

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...

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.

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 🧵

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...

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.

new out in Nature www.nature.com/articles/s41...

well well well. if it isn't all the things i said i'd do next year last year

Does anyone know the best and original references for absolute quantification of ChIP-Seq and RNA-Seq, using spike-in normalization?

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...

I don't know if this answers your specific question, but I found this recent commentary very useful www.nature.com/articles/s41...

(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...

1. I feel like this is such obvious advice that it gets taken for granted & consequently no one says this to young scientists but READ PAPERS, read all the papers. As you move up in your career you will have less & less time to do this. Read everything that appeals to you not just in your field

Pol II degradation activates cell death independently from the loss of transcription https://www.biorxiv.org/content/10.1101/2024.12.09.627542v1

The lives of cells, recorded - Nature Reviews Genetics Recent advances in genome engineering are enabling the recording of cellular histories into genomes, with single-cell and spatial omics technologies enabling their reconstruction into cellular lineage...

"The lives of cells, recorded"--our new review on genomic recording systems and how they can reveal the dynamics of multicellular development. A pleasure to work on this with amazing colleagues from the Allen Discovery Center for Cell Lineage Tracing.
www.nature.com/articles/s41...

In case you did not see it the first time posted. If you are interested in how chromatin-based epimutations mediate resistance in fungi …… read our latest preprint…….