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Matt Mulè

@mattmule.bsky.social
593 followers 439 following 17 posts

mattpm.net –> my research website Systems immunology & Clinical pathology PhD - Cambridge NIH OxCam | MD - UNC Chapel Hill ('25)

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Reposted by Matt Mulè
Vincent van Unen @vincentvanunen.bsky.social · 19/06/2026
I am still kinda new on BlueSky. Interested in #IBD, #Tcells, #TCR ? I would kindly appreciate Reposts! :-) insight.jci.org/articles/vie...
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John Trant @trantteam.bsky.social · 04/04/2026
I essentially took the entirety of the first 2.5 years of my PhD, 55 hours/week and set them on fire. Nothing productive or useful arose. Those years are also the years that made me a very good scientist. Grunt work and failure and friction IS the work. There is no way around learning.
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Simon Fisher @profsimonfisher.bsky.social · 24/03/2026
“I shall send off the manuscript today or Monday. It is an extremely poor affair; I must say something & have nothing worth saying. Lock it up carefully, I hate it to that extent it would break my heart to write it again.” Charles Darwin captures the joy of academia in a letter to his daughter, 1871
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Stephen Turner @stephenturner.us · 22/03/2026
Nature Genetics: The polygenic, omnigenic and stratagenic models of complex disease risk www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2AE
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Quanta Magazine @quantamagazine.org · 19/03/2026
The central limit theorem is a mathematical truth so powerful that it often strikes newcomers as impossible, like a magic trick of nature. Through it, the most random chaos can lead to striking predictability.
quantamagazine.org
The Math That Explains Why Bell Curves Are Everywhere | Quanta Magazine
The central limit theorem started as a bar trick for 18th-century gamblers. Now scientists rely on it every day.
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Caleb Lareau @caleblareau.bsky.social · 28/01/2026
Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...
nature.com
Population-scale sequencing resolves determinants of persistent EBV DNA - Nature
Population-scale WGS reveals genetic determinants of persistent EBV DNA, linking immune regulation—especially antigen processing and MHC class II variation—to EBV persistence and heterogeneous di...
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Matt Mulè @mattmule.bsky.social · 27/01/2026
More interesting findings from the Casanova group on IFN neutralizing antibodies
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Casanova Lab @casanovalab.bsky.social · 26/01/2026
1/ We are excited to share our new report in PNAS: all three cases of encephalitis triggered by the live-attenuated chikungunya (CHIKV) vaccine (IXCHIQ®) are due to pre-existing autoantibodies neutralizing type I IFN (AAN-I-IFN) (doi.org/10.1073/pnas...).
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Iannacone Lab @iannaconelab.bsky.social · 24/01/2026
Great story from the Nieswandt lab in Science: uncovering a non-classical platelet mechanism that drives inflammation via integrin- and tetraspanin-rich tethers. A fresh angle on thrombo-inflammation. Happy to be part of this work! www.science.org/doi/10.1126/...
science.org
Platelet-derived integrin- and tetraspanin-enriched tethers exacerbate severe inflammation
Platelet integrin αIIbβ3 is essential for hemostasis, thrombosis, and inflammation. We found that ligation of αIIbβ3 by von Willebrand factor or fibrin under flow triggered its accumulation in plasma ...
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 13/01/2026
PCA is one of those techniques that sounds unreasonable (yeah sure we all want to fit a p-dimensional ellipsoid to our data) but turns out to be a reasonable solution to a wide range of problems. Also: I do hope stackexchange has been archived, because it is my gen's library of alexandria
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Wolfgang Huber @wkhuber.bsky.social · 20/01/2026
Can confirm.
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Kilian Schober @kischober.bsky.social · 03/11/2025
Dear single-cell bluesky community: We’re running Cell Ranger (5’ scRNA-seq) on sorted human CD8+ T cells with a custom library. Custom seqs (27–133 bp) appear in FASTQs + BAM but aren’t mapped. They are filtered out by STAR for being too short—any way to lower the length limit or workaround?
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Matt Mulè @mattmule.bsky.social · 15/06/2025
Which output is on when both switches are open? And can you guess why ChatGPT's 03 reinforcement learning model got this wrong initially? #reinforcementlearning #ai
An image of a wiring diagram showing a 2-line to 4-line decoder
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Reposted by Matt Mulè
Dr. Lucky Tran @luckytran.com · 09/06/2025
"We are speaking on behalf of hundreds of NIH staff who are standing up together to say: WE DISSENT. I am so scared about doing this but I am trying to be brave for my kids because it's only gonna get harder to speak up." Thank you to Dr. Jenna Norton and NIH scientists for your courage!
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Hadley Wickham @hadley.nz · 03/06/2025
At Posit, we love @typst.app: ⚡ Make PDFs in milliseconds, not minutes ✨ The power of LaTeX with today's technologies ✍️ Modern typography (including emojis!) 🧠 Clear mental model So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a... #rstats
posit.co
Posit
We’re happy to announce that we’re supporting Typst by funding one of their full-time engineers.
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Dawid Zyla @dzyla.bsky.social · 16/02/2025
I've been developing a semantic search tool that covers not just bioRxiv and medRxiv, but the entire PubMed database. This means you can search across a massive collection of biomedical research using keywords, questions, hypotheses, or even full abstracts. Try it out: mssearch.xyz
mssearch.xyz
Streamlit
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Nick Borcherding @thehumanborch.bsky.social · 31/12/2024
scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling www.biorxiv.org/content/10.1...
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Ellen Foxman @ellenfoxman.bsky.social · 25/11/2024
The measles vaccine is given as a shot but it is surprisingly good at inducing protective immunity in the respiratory tract (mucosal IgA). Our new study provides some clues about why...a thread (1/8) #IDSky #MedSky #lungs #immunology #ImmunoSky academic.oup.com/jid/advance-...
academic.oup.com
Validate User
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Kat Mayer-Barber,PhD @mayerbarber.bsky.social · 06/12/2024
Best #Nikolaus 🎅! Our paper on how the 🫁 microenvironment can shape #innate immunity against #viruses is out @sciimmunology.bsky.social This was a herculean effort brilliantly led by @pauljbaker.bsky.social who singlehandedly established the model in the lab during the pandemic. 🧪 #Immunosky 1/9
Graphical summary of our paper.  In mice, prior lower airway exposure to diverse inflammatory stimuli, including chronic bacterial infections such as M. tuberculosis, acute bacterial infections such as pulmonary S. aureus, viral infections such as Influenza A, type-II allergic responses such as the OVA-Alum model, activation of pulmonary TLR9 by CpG or pulmonary TLR1/2 by Pam3CSK4
 leads to reduced viral burden upon subsequent infection with SARS-CoV-2 (SCV2). (2) This SCV2 restriction occurs prior to induction of SCV2-specific adaptive immune responses 
and is mediated through innate immune responses, including the induction of IFN-I, TNFα and IL-1 and sustained changes to the TRM (Tissue resident macrophage) cellular 
compartment and the pulmonary epithelium. (3) Innate cytokine and TLR signaling to both recruited immune cells and the pulmonary epithelium creates a microenvironment in the 
lung that limits early replication of SCV2. IFN-I signaling to pulmonary ECs (epithelial cells) increases expression of interferon-stimulated genes, that likely cell-intrinsically limit viral
 replication. TNF- or IL-1 suppress SCV2 independently of IFN-I signaling. TNF acts exclusively through radio-resistant cell types such as the lung epithelium, whereas IL-1 affords 
control both direct and indirectly, through either stromal and hematopoietic cell types, to restrict overall early SCV2 burden.
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Albert Vilella, PhD. @albertvilella.bsky.social · 06/12/2024
Parse Bio GigaLab and Vevo Therapeutics Tahoe-100 experiment open.substack.com/pub/albertvi...
open.substack.com
Parse Bio GigaLab and Vevo Therapeutics Tahoe-100 experiment
100 million cells assayed over 60,000 conditions and 1,200 drug treatments across 50 different tumor models
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Jamie Heather @jamieheather.bsky.social · 29/11/2024
Re-pinging for new arrivals: here's a starter pack of researchers who work on variable immune receptors: let's all have nice repertoire chats together. go.bsky.app/Gi2dcGd
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Nikolai Slavov @slavov-n.bsky.social · 30/11/2024
Prioritized mass spec data acquisition increases proteomic data completeness & coverage depth. The increase is largest for the most challenging proteins. When using TMTpro, data completeness reaches 93% for all proteins across multiple sets. nature.com/articles/s41...
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Alex Rubinsteyn @alexr.bsky.social · 13/11/2024
New de-novo TCR design preprint from @dkarthikey1.bsky.social just dropped: TCR-TRANSLATE: Conditional Generation of Real Antigen Specific T-cell Receptor Sequences www.biorxiv.org/content/10.1...
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Matt Mulè @mattmule.bsky.social · 29/11/2024
Nice paper using an inverse covariance / partial correlation network analysis with graphical Lasso to identify direct associations with an outcome variable.
cell.com
Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques
Multi-modal datasets can be beset by spurious connections due to indirect impacts propagating through an unmapped biological network. We applied Markov fields to eliminate spurious correlations in a d...
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Matt Mulè @mattmule.bsky.social · 27/11/2024
Hello, world! We don’t routinely measure the immune system in the clinical laboratory. I’m working to make immune-based clinical tests a cornerstone of treatment selection, prognostication, and strategies to reprogram immunity across immune-mediated disease. Snapshot of my past work so far:
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Hannah Isles @hannah-isles.bsky.social · 23/11/2024
New in #ScienceImmunology: Research from @boztugk.bsky.social and team identifies an inborn error of #immunity caused by human LTβR deficiency, resulting in defective stromal cell signaling and impaired humoral immune responses. Read more: www.science.org/doi/10.1126/...
science.org
LTβR deficiency causes lymph node aplasia and impaired B cell differentiation
Loss-of-function mutations in LTBR result in a stromal defect, leading to dysfunctional secondary lymphoid organs and combined immunodeficiency in humans.
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Sander Wuyts, PhD 🧬 @swuyts.bsky.social · 26/11/2024
Anyone knows a good set of validated T-cell epitopes? Meaning epitopes that definitely showed a good T-cell response. I've used IEDB in the past but maybe there are other valuable resources? #Immunosky
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Greifflab @victorgreiff.bsky.social · 06/11/2023
Curious about what a blood sample can reveal about humoral immunity? Our latest work combined sequencing methods and mass spectrometry to explore BCR and antibody repertoires and assess their synergistic potential. www.biorxiv.org/content/10.1...
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John Tsang @tsanglab.bsky.social · 17/11/2024
I created a starter pack for systems immunology - let me know if you would like to be added. Excited to be here on @bsky.app go.bsky.app/PjH2Fuj
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