Matt Jones

Computational Immunologist - Boston, Massachusetts (US) job with Ragon Institute of MGH, MIT, & Harvard | 12849577 The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard in Cambridge MA, together with the Departmen

The @ragoninstitute.bsky.social is launching a new faculty search for a computational immunologist! Applications are open now and reviewed on a rolling basis. Please share broadly with your networks! #immunosky

www.nature.com/naturecareer...

Just about one more week to apply for our tenure-track opening in IMES at MIT! Come start your group in an outstanding community at MIT at the interface of medicine and engineering: faculty-searches.mit.edu/imes-search/

Genetic elements promote retention of extrachromosomal DNA in cancer cells - Nature A combination of genome-wide functional screening, imaging and chromatin profiling identifies a new class of highly prevalent genomic elements that help retain extrachromosomal DNA copies in dividing ...

Our paper is out in @nature.com! Oncogenes are often copy-number amplified on extrachromosomal DNA (ecDNA) in cancer, but how is ecDNA inherited by dividing cells? Here we identified elements within ecDNA that promote its retention in dividing cells. 1/11
www.nature.com/articles/s41...

@katerinakraft.bsky.social We have both a coffee corner and a mug with your name on it, whenever you're here! The long-read sequencer is en route ;-)

Thank you @benjaminwerner.bsky.social! Looking forward to catching up again sometime soon.

Thank you @fueyoraquel.bsky.social!

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!

This was a fun project that started on the first day of my postdoc as I chatted with @katerinakraft.bsky.social over coffee. Thanks to our advisors - Howard Chang and Paul Mischel - and the support of Team eDyNAmiC through @cancergrand.bsky.social for helping us push it across the finish line.

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...

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...

Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...

Our publication is out today!Big Thanks go to my amazing collaborators: @sedonamurphy.bsky.social for her imaging brilliance and @mattjones.bsky.social for his computational support.They both saw the potential in this project and helped me to explore what turned out to be an exciting discovery.

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

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...