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Joel Babdor

@joelbabdor.bsky.social
6.3K followers 498 following 138 posts

Asst. Prof. University of Pennsylvania Systems Immunology and Microbiome Medicine lab #Academia #Immunology #Microbiome #SystemsBiology Mentorship | Science communication | Research culture Lab website: Babdorlab.com

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Joel Babdor @joelbabdor.bsky.social · 06/05/2026
Hi. Congrats on your PhD. Thanks for connecting. I have some Microbiome-MAIT data you might be interested in. As part of our recent work www.cell.com/cell/fulltex... we have seen an interesting MAIT phenotype that didn't make it to the final version of the paper. I'd love to chat.
cell.com
Immune-microbiome coordination defines interferon setpoints in healthy humans
A comprehensive multi-omic analysis of healthy humans reveals two major axes of immunological variation characterized by interferon responses, one of which is coordinated with the microbiome and its m...
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Joel Babdor @joelbabdor.bsky.social · 13/04/2026
I would love that. Check your DMs
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Joel Babdor @joelbabdor.bsky.social · 10/04/2026
Really cool work Joel
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Raes Lab @raeslab.org · 23/03/2026
We’re hiring! We are looking for a Clinical Studies Coordinator to support our microbiome research at the Raes lab (KU Leuven). Work on international clinical studies, from ethics and documentation to coordination with partners. Apply by 2 April 2026 via KU Leuven: www.kuleuven.be/personeel/jo...
kuleuven.be
Medewerker klinische studies
Ondersteun nationaal en internationaal klinisch onderzoek
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Ultimately, understanding how the microbiome shapes immune baselines may help us better define immune health and explain why individuals differ in disease susceptibility and response to treatment.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
My lab at Penn continues to build on these findings to understand the molecular mechanisms through which microbial signals shape immune activity.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
This project began during my postdoctoral training in Matthew Spitzer’s lab at UCSF and grew into a long collaboration with the Fragiadakis lab and my research group at the Perelman School of Medicine at the University of Pennsylvania.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Understanding these microbiome-associated immune states could have important implications. Baseline inflammation influences susceptibility to infections, autoimmune diseases, and cancer, yet the biological drivers of these differences remain unclear.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
These findings challenge the long-held assumption that healthy immune systems operate from a uniform baseline. Instead, immune activity appears to exist along a spectrum of immune states that differ across individuals.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Our paper is now out in Cell: www.cell.com/cell/fulltex...
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Importantly, this immune state was associated with specific microbiome features and circulating microbial metabolites. This suggests that signals originating from gut microbes may shape the immune system’s resting tone.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
One immune state we identified showed coordinated activation of interferon-stimulated genes and inflammatory mediators, even though participants were clinically healthy.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
We found that baseline inflammatory activity varies across individuals and that these immune states remain stable over time. In other words, each person’s immune system appears to operate from its own characteristic baseline.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Using single-cell immune profiling together with deep microbiome and metabolome analysis, we characterized immune and microbial activity simultaneously through an integrative multimodal computational approach.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
In the ImmunoMicrobiome Study, we profiled the immune system and the gut microbiome in 110 healthy individuals, analyzing blood and stool samples collected from each participant.
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Joel Babdor @joelbabdor.bsky.social · 11/03/2026
Even among healthy people, immune systems operate at different baseline levels. In our new Cell paper, we show that these immune states are stable over time and are associated with the gut microbiome. 🧵 @cp-cell.bsky.social #Immunology #SystemsImmunology
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Joel Babdor @joelbabdor.bsky.social · 09/03/2026
Happy Bday!
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Institute for Immunology and Immune Health (I3H) @i3h-upenn.bsky.social · 09/03/2026
A new CRISPR tool used directly in patients’ cancer cells can pinpoint genes driving acute myeloid leukemia (AML) — helping identify drug targets and uncover why some cancers resist treatment. Published by Penn Medicine & CHOP in Molecular Cell. bit.ly/4cqeZiB
bit.ly
First CRISPR-based platform to pinpoint leukemia drivers | Penn Today
The new toolkit, developed by Penn Medicine and Children’s Hospital of Philadelphia, allows researchers to test potential cancer targets directly in patient leukemia cells.
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Hutlab @hutlab.bsky.social · 23/10/2025
NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data! www.nature.com/articles/s41... 🧵⬇️ 1/8
nature.com
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
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Thomas Lin Pedersen @thomasp85.com · 11/09/2025
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
tidyverse.org
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
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Joel Babdor @joelbabdor.bsky.social · 06/08/2025
Excited to receive the Lupus Research Alliance Career Development Award. This award will support my lab at Penn studying how the microbiome shapes immune states in lupus. Honored to join amazing colleagues in pushing lupus research forward. #LupusResearch #Microbiome #Immunology bit.ly/LRA-ELR25
bit.ly
Lupus Research Alliance Announces 2025 Empowering Lupus Research Award Recipients to Support Breakthroughs
Today, the Lupus Research Alliance (LRA), the world’s largest private funder of lupus research, announced the recipients of the 2025 Empowering Lupus
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Andrea Sinz 🧪 @sinzandrea.bsky.social · 25/06/2025
‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT www.verwaltung.uni-halle.de/dezern3/Auss... #Academicsky #Chemsky #teammassspec
verwaltung.uni-halle.de
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Johanna Joyce @johannajoyce.bsky.social · 23/06/2025
Are you looking to start your #lab in a fantastic scientific 🧪environment, with great colleagues, and in a spectacular place to live? Then check out our open #junior #faculty position at the Department of Oncology, University of Lausanne, Switzerland: www.unil.ch/dof/en/home/... ⏰ Deadline 27 June
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Segata Lab @cibiocm.bsky.social · 11/06/2025
The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...
forum.biobakery.org
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
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Katherine Maki, PhD, NP-BC @katherine-maki1.bsky.social · 14/05/2025
👀👀 Looking for recs 👀👀 Are there any summer/fall workshops on multi-omic, pathway or microbiome analyses where the application period has not already passed? Looking for some good options for my trainees! Appreciate any leads in advance #AcademicSky #Bioinformatics
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Evangelos Giampazolias @giampazolias.bsky.social · 26/03/2025
💥Exciting new #postdoc opportunities in my lab at @cruk-mi.bsky.social i.bsky.social to study #NutrientHostMicrobiome interactions in #CancerImmunity in mice and humans. #CancerImmunology#MucosalImmunology#Microbiome ⏰Deadline: 4 April 2025 Apply👇 www.cruk.manchester.ac.uk/career/mi-24... ⏩RT
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Richard Sever @richardsever.bsky.social · 11/03/2025
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
openrxiv.org
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
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Kashif Shaikh @kashifshaikh.bsky.social · 04/03/2025
I am excited to share that I am starting as a postdoctoral researcher in the labs of @hajera-amatullah.bsky.social and @joelbabdor.bsky.social at University of Pennsylvania
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Richard Sever @richardsever.bsky.social · 27/02/2025
Calling all bioRxiv affiliates - bat signal is up as we have a big backlog. If you have time to screen some papers, we'd be eternally grateful! 🙏
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Jamie Heather @jamieheather.bsky.social · 25/02/2025
Dear TCR researchers of #immunosky, you may be interested to know that our tool Stitchr - for the automated production of full-length T cell receptor sequences - has just had a nice little update: jamieheather.github.io/stitchr/
jamieheather.github.io
stitchr — stitchr documentation
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Ran Blekhman @blekhman.bsky.social · 20/02/2025
These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today. We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe www.cell.com/cell/current...
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Nature Microbiology @natmicrobiol.nature.com · 18/02/2025
OUT NOW: ILC3s regulate the gut microbiota via host intestinal galactosylation to limit pathogen infection in mice #microsky #immunosky www.nature.com/articles/s41...
nature.com
ILC3s regulate the gut microbiota via host intestinal galactosylation to limit pathogen infection in mice - Nature Microbiology
Akkermansia muciniphila can promote intestinal pathogen infection in mice via microbial metabolite succinate production, but the expansion of A. muciniphila is strictly controlled by ILC3s through the...
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Christian Diener @cdiener.com · 18/02/2025
Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:
nature.com
Metagenomic estimation of dietary intake from human stool - Nature Metabolism
Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.
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Jerry Chen @jcsalterego.bsky.social · 04/02/2025
at least it's friday
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Joel Babdor @joelbabdor.bsky.social · 04/02/2025
It’s #WorldCancerDay 🎗🌍 I’m thinking of my family members who survived cancer thanks to the work of doctors & scientists. Fighting cancer is 1 of the reasons I became a researcher Today I’m proud to join our Cancer Center as an official member @pennmedicine.bsky.social, committed to fight & win!
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Joel Babdor @joelbabdor.bsky.social · 02/02/2025
This looks like a fantastic event! What a lineup! And why do I want to frame the poster so much!?
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Joel Babdor @joelbabdor.bsky.social · 02/02/2025
📌
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Karen Peralta Martínez @karenyperalta.bsky.social · 29/01/2025
So excited this work is out! 🦠🧫🐾🥼🧪 If you want to cultivate and isolate bacteria from sensible microbial samples collected in the field and needed to be transporters to the lab, take a look at the study we conducted using multiple preservation solutions with or without cryoprotectants.
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Immunity @cp-immunity.bsky.social · 21/01/2025
Share your #cancer #immunology research w/ #CSCancerImmunity2025 organizers Ignacio Melero, Ira Mellman, Fabiola Rivas @cp-immunity.bsky.social & Montse Rojo de la Vega @cp-cancercell.bsky.social . hubs.li/Q033hK4y0
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David Usharauli @davidusharauli.bsky.social · 23/01/2025
This epic study, which took more than three years to get published, deserves special consideration. #immunology #microbiome #allergy
nature.com
RELMβ sets the threshold for microbiome-dependent oral tolerance - Nature
RELMβ mediates a gut immune–epithelial circuit regulating tolerance to food antigens, offering targetable candidates for the prevention and treatment of food allergies.
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The Dunn School, Oxford @dunnschool.bsky.social · 22/01/2025
ICYMI We are recruiting a new Associate Professor in cell and molecular biology, with a preference for immunology, inflammation and/or infection - all defined broadly Come and be our colleague! Deadline 28 Feb, please spread the word! www.path.ox.ac.uk/vacancy/asso...
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Holden Thorp @holdenthorp.bsky.social · 22/01/2025
All - @science.org now has a @bsky.app share button! Enjoy!
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Eduardo Villablanca @ejvillablanca.bsky.social · 25/01/2025
Dear mucosal immunologists! Registration for the European Mucosal Immunology Group (EMIG) meeting in Aachen, Germany is now open. Register and see you this July in Aachen! 👇🏼 emig2025.de @petterbrodin.bsky.social @wiag.bsky.social @mucosalimmunol.bsky.social @societymucosalimm.bsky.social
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Altmetric @altmetric.com · 18/11/2024
We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics
docs.bsky.app
Action Intent Links | Bluesky
Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...
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Joel Babdor @joelbabdor.bsky.social · 25/01/2025
I love this positive story of scientists who find ways to collaborate instead of competing. It takes some work, open communication and keen awareness of everyone's interest but the positive outcome makes it worth the effort! A good read in these trying times.
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Eric Topol @erictopol.bsky.social · 24/01/2025
How our gut microbiome regulates sugar preference nature.com/articles/s41...
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Society for Mucosal Immunology @societymucosalimm.bsky.social · 24/01/2025
It's Coming! The Mucosal Immunology Podcast to launch on MONDAY! 🌟 Explore groundbreaking insights and inspiring stories in the world of mucosal immunology - brought to you by SMI and @mucosalimmunol.bsky.social. #MucosalImmunology #SciencePodcast #ImmunologyResearch #PodcastLaunch
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Samantha Graham @samanthagraham.bsky.social · 22/01/2025
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
cell.com
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...
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Emily Wissel, PhD @ewiss.bsky.social · 20/01/2025
Hi everyone! I'm looking for next job ✨ I'm looking for a Data Scientist, Data Analyst, or Bioinformatics role. I'd like to dive deep into multi-omics integration in life science data & focus on using existing tools, rather than building new bioinf tools. More & my CV below!
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