Matt Jones
@mattjones.bsky.social
Incoming Assistant Professor @ MIT Biology, Koch Institute, and Institute for Medical Engineering and Science. Single-cell advisor to Vevo Therapeutics. Lineage tracing & cancer evolution. Website: thejoneslaboratory.com
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...
tinyurl.com
October 21, 2025 at 2:43 PM
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
Reposted by Matt Jones
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...
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...
www.nature.com
October 21, 2025 at 9:43 AM
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...
Reposted by Matt Jones
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.
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...
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...
www.nature.com
October 21, 2025 at 1:34 PM
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.
Reposted by Matt Jones
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.
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.
September 12, 2025 at 4:49 PM
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.
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.
Reposted by 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!
June 4, 2025 at 5:52 PM
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!
Reposted by Matt Jones
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...
🧵
🧬 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...
🧵
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...
doi.org
May 21, 2025 at 3:44 PM
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...
🧵
🧬 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...
🧵
Reposted by Matt Jones
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!
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!
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...
🧵
🧬 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...
🧵
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...
doi.org
May 21, 2025 at 4:06 PM
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!
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!
Reposted by Matt Jones
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)
April 18, 2025 at 6:36 PM
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)
Reposted by Matt Jones
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...
authors.elsevier.com
April 17, 2025 at 6:20 PM
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...
Reposted by Matt Jones
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/...
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...
www.science.org
April 3, 2025 at 11:57 PM
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/...
Reposted by Matt Jones
@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 Matt Jones
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
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 ...
royalsocietypublishing.org
February 21, 2025 at 8:37 AM
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
Reposted by Matt Jones
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
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
February 24, 2025 at 10:29 AM
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
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
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...
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.
hubs.ly
February 11, 2025 at 1:56 AM
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...
Reposted by Matt Jones
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.
February 8, 2025 at 9:21 PM
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.
Reposted by Matt Jones
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
November 12, 2024 at 11:49 AM
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
Reposted by Matt Jones
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
go.bsky.app/GyZxUDH
November 21, 2024 at 6:28 PM
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
go.bsky.app/GyZxUDH
Reposted by Matt Jones
Thrilled to share our latest work on cutaneous T cell lymphoma. Check it out👇🏼
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
November 22, 2024 at 4:23 AM
Thrilled to share our latest work on cutaneous T cell lymphoma. Check it out👇🏼
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matt Jones
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...
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...
November 17, 2024 at 7:41 PM
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...
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...
Reposted by Matt Jones
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
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...
www.cell.com
November 15, 2024 at 3:35 PM
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
Reposted by Matt Jones
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...
📅 Date: May 18-23, 2025
📍 Venue: Tuscany, Italy
🔗 Apply Now: www.grc.org/cancer-genet...
2025 Cancer Genetics and Epigenetics Conference GRC
The 2025 Gordon Research Conference on Cancer Genetics and Epigenetics will be held in Lucca (Barga), Lucca Italy. Apply today to reserve your spot.
www.grc.org
November 17, 2024 at 1:21 PM
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...
📅 Date: May 18-23, 2025
📍 Venue: Tuscany, Italy
🔗 Apply Now: www.grc.org/cancer-genet...
Reposted by Matt Jones
November 9, 2024 at 5:07 PM
Reposted by Matt Jones
My UCSF department, Biochemistry & Biophysics, is recruiting -- please repost & share! aprecruit.ucsf.edu/JPF04637
Ladder Rank Faculty Position – Assistant, Associate, or Full Professor
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
October 11, 2023 at 2:00 PM
My UCSF department, Biochemistry & Biophysics, is recruiting -- please repost & share! aprecruit.ucsf.edu/JPF04637
Reposted by Matt Jones
bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...
September 28, 2023 at 2:27 PM
bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...