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Jonathan Mitchel

@j-e-mitchel.bsky.social
317 followers 1.1K following 5 posts

PhD candidate at Harvard-MIT HST program. Working on computational methods to make sense of genomics data. Member of Kharchenko and Sunyaev labs.

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Jonathan Mitchel @j-e-mitchel.bsky.social · 15/10/2025
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...
biorxiv.org
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...
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MRC-LMB Cell Biology Division @cellbiol-mrclmb.bsky.social · 29/12/2024
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.
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Färkkilä Laboratory @farkkilab.bsky.social · 10/12/2024
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
sciencedirect.com
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…
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Maria Secrier @mariasecrier.bsky.social · 02/12/2024
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....
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Anna Obenauf @obenaufa.bsky.social · 27/11/2024
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...
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Andrea Schmidts @schmidts.bsky.social · 26/11/2024
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)
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Adam Pennycuick @adampennycuick.bsky.social · 27/11/2024
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.
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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…
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Reposted by Jonathan Mitchel
Jon Lim, FRCP PhD @drjonlim.bsky.social · 23/11/2024
🎨 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
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Jonathan Mannion @jmannion1.bsky.social · 24/11/2024
#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/...
science.org
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.
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Michael Ward @michael-e-ward.bsky.social · 21/11/2024
www.nature.com/articles/d41...
nature.com
Common genetic variants contribute more to rare diseases than previously thought
Assessing the influence of common mutations on rare disease risk.
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Elizabeth McKenna @elizsmckenna.bsky.social · 20/11/2024
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...
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The Francis Crick Institute @crick.ac.uk · 03/10/2024
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...
crick.ac.uk
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.
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Piotr Jung-Sillah @jung-sillah.bsky.social · 15/11/2024
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...
news.gatech.edu
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.
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David Basanta @cancerevo.org · 19/03/2024
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...
link.springer.com
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...
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David Suter @davidsuter.bsky.social · 14/11/2024
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...
genesdev.cshlp.org
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
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zack chiang @zchiang.bsky.social · 14/11/2024
wake up babe, new george church skincare routine just dropped www.biorxiv.org/content/10.1...
biorxiv.org
Human skin rejuvenation via mRNA
Aging is characterized by a gradual decline in function, partly due to accumulated molecular damage. Human skin undergoes both chronological aging and environmental degradation, particularly UV-induce...
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oZgun Gokce @gokcegroup.bsky.social · 13/11/2024
Spatialomics reveals T cell behaviors in metastatic breast cancer: infiltration vs. exclusion. Cool work from @KlughammerLab www.nature.com/articles/s41...
nature.com
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 ...
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Victor Javier @vjsanchez.bsky.social · 13/11/2024
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Matthew Taliaferro @jmtali.bsky.social · 13/11/2024
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/...
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Jay Hinton @jayhinton.bsky.social · 13/11/2024
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...
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Anders Sejr Hansen @andersshansen.bsky.social · 11/11/2024
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.
ashansenlab.com
Hansen Lab
The official lab website of Anders Sejr Hansen at MIT Department of Biological Engineering
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Will Ratcliff @wcratcliff.bsky.social · 26/10/2024
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
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Mubashar “Mubs” Iqbal @mubashariqbal.com · 11/11/2024
Starter packs are genius, but I was surprised there wasn't a list of them for people to find. So I built it: blueskydirectory.com/starter-pack... The website monitors the packs being shared and adds the ones it finds to the database. Missed your stater pack? Message me and I'll get it added.
blueskydirectory.com
All - Bluesky Directory
A curated collection of all things relating to the Blue Sky social media platform.
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