Jonathan Mitchel
@j-e-mitchel.bsky.social
PhD candidate at Harvard-MIT HST program. Working on computational methods to make sense of genomics data. Member of Kharchenko and Sunyaev labs.
Overall, this work has spurred many new hypotheses by pinpointing which genes and contexts are relevant for each disease. As usual, this project was not without it's challenges - I have to give a huge shoutout to my PhD mentors Shamil Sunyaev + Peter Kharchenko and all of our fantastic collaborators
October 15, 2025 at 7:49 PM
Overall, this work has spurred many new hypotheses by pinpointing which genes and contexts are relevant for each disease. As usual, this project was not without it's challenges - I have to give a huge shoutout to my PhD mentors Shamil Sunyaev + Peter Kharchenko and all of our fantastic collaborators
Our method found evidence explaining ~2x the number of GWAS loci compared to pseudobulk eQTLs. We dove deep into several disease-specific findings, especially relating to Parkinson's disease (TRPV2 may be a protective gene, supported by recent studies).
October 15, 2025 at 7:49 PM
Our method found evidence explaining ~2x the number of GWAS loci compared to pseudobulk eQTLs. We dove deep into several disease-specific findings, especially relating to Parkinson's disease (TRPV2 may be a protective gene, supported by recent studies).
Therefore, our method leverages eQTL models with continuous cell state interactions. While such models are now more commonly used, we specially adapted their output to enable eQTL-GWAS colocalization testing across the cell state space.
October 15, 2025 at 7:49 PM
Therefore, our method leverages eQTL models with continuous cell state interactions. While such models are now more commonly used, we specially adapted their output to enable eQTL-GWAS colocalization testing across the cell state space.
Uniquely, scJLIM does NOT require clustering cells before eQTL mapping. Arbitrary clustering cutoffs can kill statistical power for detecting eQTLs when you cluster too finely or too coarsely, and we typically don't know the expected resolution to look at a priori.
October 15, 2025 at 7:49 PM
Uniquely, scJLIM does NOT require clustering cells before eQTL mapping. Arbitrary clustering cutoffs can kill statistical power for detecting eQTLs when you cluster too finely or too coarsely, and we typically don't know the expected resolution to look at a priori.
Super excited that my paper describing the scJLIM single-cell genetic colocalization tool is finally out on bioRxiv! scJLIM enables you to identify the specific cell states where GWAS genetic variants impact gene expression. Check it out! www.biorxiv.org/content/10.1...
A single-cell genetic colocalization test improves power and resolves disease-mediating cell types
Statistical colocalization testing methods can determine if the same single-nucleotide polymorphism (SNP) underlies both a genome-wide association study (GWAS) locus as well as an expression quantitat...
www.biorxiv.org
October 15, 2025 at 7:49 PM
Super excited that my paper describing the scJLIM single-cell genetic colocalization tool is finally out on bioRxiv! scJLIM enables you to identify the specific cell states where GWAS genetic variants impact gene expression. Check it out! www.biorxiv.org/content/10.1...
Reposted by Jonathan Mitchel
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
December 29, 2024 at 9:50 AM
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
Reposted by Jonathan Mitchel
1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch
Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer
Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet its adaptation upon standard chemotherapy remains poorly und…
www.sciencedirect.com
December 10, 2024 at 11:48 AM
1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch
Reposted by Jonathan Mitchel
Delighted to introduce our new spatial transcriptomics tool, SpottedPy, allowing the identification of tumour hotspots at different scales and the exploration of distances and overlap with tumour microenvironment niches: genomebiology.biomedcentral.com/articles/10....
December 2, 2024 at 12:00 PM
Delighted to introduce our new spatial transcriptomics tool, SpottedPy, allowing the identification of tumour hotspots at different scales and the exploration of distances and overlap with tumour microenvironment niches: genomebiology.biomedcentral.com/articles/10....
Reposted by Jonathan Mitchel
1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...
November 27, 2024 at 5:58 PM
1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...
Reposted by Jonathan Mitchel
Cancer escapes immunotherapies by mutating its surface, meaning even groundbreaking #CARTCell therapies fail too often. But what if #GenerativeAI could design CAR-T with de novo binders faster, targeting resistant tumors? 🧵 www.biorxiv.org/content/10.1... (1)
November 26, 2024 at 1:36 PM
Cancer escapes immunotherapies by mutating its surface, meaning even groundbreaking #CARTCell therapies fail too often. But what if #GenerativeAI could design CAR-T with de novo binders faster, targeting resistant tumors? 🧵 www.biorxiv.org/content/10.1... (1)
Reposted by Jonathan Mitchel
ctDNA isn't great at detecting small, early stage cancers which don't shed much DNA. Could the systemic anti-cancer immune response be used for early detection? Interesting data here from colorectal cancer
Paper found with researchbriefing.com.
Paper found with researchbriefing.com.
Human blood cell transcriptomics unveils dynamic systemic immune modulation along colorectal cancer progression
Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. CRC deaths can be reduced with prevention and early diagnosis. Circulating tumor DNA-based liquid…
buff.ly
November 27, 2024 at 9:00 AM
ctDNA isn't great at detecting small, early stage cancers which don't shed much DNA. Could the systemic anti-cancer immune response be used for early detection? Interesting data here from colorectal cancer
Paper found with researchbriefing.com.
Paper found with researchbriefing.com.
Reposted by Jonathan Mitchel
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
November 23, 2024 at 3:50 PM
🎨 In case anyone need…
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!
Check it out 👇
bioart.niaid.nih.gov
Reposted by Jonathan Mitchel
#paperoftheweek @jackiheraudfarlow.bsky.social & Co report that GGNBP2-CNOT10/11 complex formation promotes MDA5 sensing of immunogenic self dsRNAs, upon ADAR1 mutation. Congrats to all involved! 👏🏻
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
GGNBP2 regulates MDA5 sensing triggered by self double-stranded RNA following loss of ADAR1 editing
GGNBP2, CNOT10, and CNOT11 are required for innate immune response after the loss of ADAR1-mediated editing of self dsRNA.
www.science.org
November 24, 2024 at 12:32 PM
#paperoftheweek @jackiheraudfarlow.bsky.social & Co report that GGNBP2-CNOT10/11 complex formation promotes MDA5 sensing of immunogenic self dsRNAs, upon ADAR1 mutation. Congrats to all involved! 👏🏻
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Jonathan Mitchel
Reposted by Jonathan Mitchel
Now online in Cancer Discovery: PKN2 Is a Dependency of the Mesenchymal-like Cancer Cell State - by Shane Killarney, Kris Wood and colleagues doi.org/10.1158/2159...
November 20, 2024 at 3:00 PM
Now online in Cancer Discovery: PKN2 Is a Dependency of the Mesenchymal-like Cancer Cell State - by Shane Killarney, Kris Wood and colleagues doi.org/10.1158/2159...
Reposted by Jonathan Mitchel
Researchers at the Crick and UCL have developed a tool to analyse genes linked to the ability of tumours to hide from the immune system.
The findings were led by first author Clare Puttick as part of the TRACERx study funded by Cancer Research UK
www.crick.ac.uk/news-and-rep...
The findings were led by first author Clare Puttick as part of the TRACERx study funded by Cancer Research UK
www.crick.ac.uk/news-and-rep...
New tool reveals how breast and lung tumours avoid immune detection
Researchers at the Francis Crick Institute and UCL have developed a tool to analyse a key set of genes linked to the ability of cancer cells to hide from the body’s immune system.
www.crick.ac.uk
October 3, 2024 at 8:44 AM
Researchers at the Crick and UCL have developed a tool to analyse genes linked to the ability of tumours to hide from the immune system.
The findings were led by first author Clare Puttick as part of the TRACERx study funded by Cancer Research UK
www.crick.ac.uk/news-and-rep...
The findings were led by first author Clare Puttick as part of the TRACERx study funded by Cancer Research UK
www.crick.ac.uk/news-and-rep...
Reposted by Jonathan Mitchel
That's a really interesting system from Georgia Tech. Immune Organoids! The research team used synthetic hydrogels which can make a microenvironment for B cells, isolated from human tonsils and blood, to mature and produce antibodies.
Published in Nature Materials.
news.gatech.edu/news/2024/11...
Published in Nature Materials.
news.gatech.edu/news/2024/11...
Lab-Grown Human Immune System Model Uncovers Weakened Response in Cancer Patients
To better understand why some cancer patients struggle to fight off infections, Georgia Tech researchers have created tiny lab-grown models of human immune systems.
news.gatech.edu
November 15, 2024 at 5:57 PM
That's a really interesting system from Georgia Tech. Immune Organoids! The research team used synthetic hydrogels which can make a microenvironment for B cells, isolated from human tonsils and blood, to mature and produce antibodies.
Published in Nature Materials.
news.gatech.edu/news/2024/11...
Published in Nature Materials.
news.gatech.edu/news/2024/11...
Reposted by Jonathan Mitchel
Hot off the press: @mathonco.bsky.social members, including
Anna Gaffney, Matt Froid, and yours truly, working with the Lynch lab, use #MathOnco #ABM models to describe the bone ecosystem in Multiple #Myeloma:
link.springer.com/article/10.1...
Anna Gaffney, Matt Froid, and yours truly, working with the Lynch lab, use #MathOnco #ABM models to describe the bone ecosystem in Multiple #Myeloma:
link.springer.com/article/10.1...
The bone ecosystem facilitates multiple myeloma relapse and the evolution of heterogeneous drug resistant disease - Nature Communications
Multiple myeloma (MM) is an osteolytic malignancy that is incurable due to the emergence of treatment resistant disease. Defining how, when and where myeloma cell intrinsic and extrinsic bone microenv...
link.springer.com
March 19, 2024 at 5:58 PM
Hot off the press: @mathonco.bsky.social members, including
Anna Gaffney, Matt Froid, and yours truly, working with the Lynch lab, use #MathOnco #ABM models to describe the bone ecosystem in Multiple #Myeloma:
link.springer.com/article/10.1...
Anna Gaffney, Matt Froid, and yours truly, working with the Lynch lab, use #MathOnco #ABM models to describe the bone ecosystem in Multiple #Myeloma:
link.springer.com/article/10.1...
Reposted by Jonathan Mitchel
This one dramatically increased my awareness of how much we might be wrong with our current view of gene regulation by chromatin - and genesdev.cshlp.org/content/36/1...
The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter
communication
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
November 14, 2024 at 9:40 AM
This one dramatically increased my awareness of how much we might be wrong with our current view of gene regulation by chromatin - and genesdev.cshlp.org/content/36/1...
Reposted by Jonathan Mitchel
Reposted by Jonathan Mitchel
Spatialomics reveals T cell behaviors in metastatic breast cancer: infiltration vs. exclusion. Cool work from @KlughammerLab www.nature.com/articles/s41...
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features - Nature Medicine
Single-nucleus and single-cell RNA sequencing plus spatial profiling with four methods of core biopsies from 60 patients with metastatic breast cancer reveal patient-specific gene expression programs ...
www.nature.com
November 13, 2024 at 8:33 PM
Spatialomics reveals T cell behaviors in metastatic breast cancer: infiltration vs. exclusion. Cool work from @KlughammerLab www.nature.com/articles/s41...
Reposted by Jonathan Mitchel
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment www.sciencedirect.com/science/arti...
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with abundant cancer-associated fibroblasts (CAFs) creating hallmark desmoplasia t…
www.sciencedirect.com
November 13, 2024 at 9:31 PM
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment www.sciencedirect.com/science/arti...
Reposted by Jonathan Mitchel
Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...
November 13, 2024 at 4:46 PM
Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...
Reposted by Jonathan Mitchel
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
November 13, 2024 at 12:46 PM
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
Reposted by Jonathan Mitchel
Exciting to see the SciTwitter community rebuild and take off this week at Blue Sky.
We are interested in 3D Genome Structure and Function and long-range gene regulation.
Reposting from Twitter some of the things that came out of the lab ( www.ashansenlab.com ) over the last year or so.
We are interested in 3D Genome Structure and Function and long-range gene regulation.
Reposting from Twitter some of the things that came out of the lab ( www.ashansenlab.com ) over the last year or so.
Hansen Lab
The official lab website of Anders Sejr Hansen at MIT Department of Biological Engineering
www.ashansenlab.com
November 11, 2024 at 6:02 PM
Exciting to see the SciTwitter community rebuild and take off this week at Blue Sky.
We are interested in 3D Genome Structure and Function and long-range gene regulation.
Reposting from Twitter some of the things that came out of the lab ( www.ashansenlab.com ) over the last year or so.
We are interested in 3D Genome Structure and Function and long-range gene regulation.
Reposting from Twitter some of the things that came out of the lab ( www.ashansenlab.com ) over the last year or so.