Matt Jones

I’m thrilled to share that I’m joining the faculty at the Stanford University School of Medicine. My lab and I will be relocating to Stanford this summer!

Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...

Out @nature.com: Clonal tracing with somatic epimutations

🧬 Single cell methylome encodes cell state & clonal identity

🔨 EPI-Clone reads out both (+mutations, +RNA) at scale

🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations

doi.org/10.1038/s415...
🧵

Our work on lineage tracing with somatic epimutations is finally out in @nature.com!

Check out the thread by @larsplus.bsky.social below.

EPI-clone is a revolutionary technique for lineage tracing and it will immediately impact how we trace clones everywhere.

Detailed protocols coming out soon!

A lot of fun teaming up with Hsin and Howard on this, with key contributions from @ruochiz.bsky.social, @zchiang.bsky.social, and @jbuenrostro.bsky.social on the tech dev and @mattjones.bsky.social, Natasha Weiser, and Paul Mischel on the ecDNA analysis. (5/5)

I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Delighted to have our Perturb-multiome paper, led by #JorgeMartinRufino and @hemagene.bsky.social from our lab, published today in @science.org. Please check out this powerful approach to decipher gene regulatory networks enriched for genetic variation: www.science.org/doi/10.1126/...

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 ...

@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...

A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites | Philosophical Transactions of the Royal Society B: Biological Sciences Analysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. Clustered regularly interspaced short palindromic repeats (CRISPR)-based dynamic lineage tracing relies ...

Quantification of developmental processes (here early Danio rerio development) with our novel Bayesian phylogenetic methodology - leveraging single cell lineage tracing data based on CRISPR/Cas9 technology royalsocietypublishing.org/doi/10.1098/... Antoine Zwaans @seidels.bsky.social Marc Manceau

Very excited to share the stellar speaker line-up at our ecDNA conference this June in London! 👇
If you're interested in #ecDNA and want to hear or present groundbreaking research, register now. Abstract submission deadline is 14 March.

Learn more: www.cancergrandchallenges.org/ecDNA-2025

Thank you for attending!

Transforming Pipeline Outputs into Biological Insights Curio Seeker Spatial Transcriptomics Kit, based on Slide-Seq technology, captures the mRNA in a tissue section using a spatially indexed monolayer of 10 µm beads.

Delighted to be presenting a webinar with Curio next Wed 2/19 on our recent work describing a spatially-resolved lineage-tracing technology and its application to the KP model of lung adenocarcinoma. Register here: hubs.ly/Q035NKqd0, and find our preprint here: www.biorxiv.org/content/10.1...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

I've started a list of people working on #cancer #evolution. Many more to be added, so do let me know if that is you. Also if you would like to be removed. go.bsky.app/QuAF4Mo

Wonderful, thank you!

Thank you for starting this - I’d love to be added!

Thanks for starting this! I’d love to be added

Getting in on the starter pack game for folks focusing on studying tumor-immune interactions during metastasis — DM/comment if you want to be added!

go.bsky.app/GyZxUDH

Cutaneous T cell lymphoma atlas reveals malignant TH2 cells supported by a B cell-rich tumor microenvironment - Nature Immunology Haniffa and colleagues provide diagnostic aids, potential biomarkers for disease staging and therapeutic strategies for cutaneous T cell lymphoma.

Thrilled to share our latest work on cutaneous T cell lymphoma. Check it out👇🏼

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

Cancer Immunology: bsky.app/starter-pack...
A repertoire of immunologists II: bsky.app/starter-pack...
Immunometabolism: bsky.app/starter-pack...
Immunoengineering: bsky.app/starter-pack...
A repertoire of immunologists: bsky.app/starter-pack...

The single-molecule accessibility landscape of newly replicated mammalian chromatin By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...

The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics

Registration now for the 2025 Cancer Genetics and Epigenetics GRC, a premier event for you to dive into groundbreaking research and network with leading experts in the field.

📅 Date: May 18-23, 2025
📍 Venue: Tuscany, Italy
🔗 Apply Now: www.grc.org/cancer-genet...

go.bsky.app/7xTwrrn

Thank you!

This is great! I’d love to be added, thanks for starting this

This is a great idea, thanks for starting this! I’d like to join

Ladder Rank Faculty Position – Assistant, Associate, or Full Professor University of California, San Francisco is hiring. Apply now!

My UCSF department, Biochemistry & Biophysics, is recruiting -- please repost & share! aprecruit.ucsf.edu/JPF04637

bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...