I would love that. Check your DMs

Really cool work Joel

New research out @cellpress.bsky.social in finds that immune-microbiome coordination defines interferon setpoints in healthy humans ft. @joelbabdor.bsky.social, @klkoser.bsky.social, Kristen Krip, @kashifshaikh.bsky.social & @hajera-amatullah.bsky.social www.cell.com/cell/fulltex...

Medewerker klinische studies Ondersteun nationaal en internationaal klinisch onderzoek

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...

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.

My lab at Penn continues to build on these findings to understand the molecular mechanisms through which microbial signals shape immune activity.

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.

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.

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.

Our paper is now out in Cell:
www.cell.com/cell/fulltex...

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.

One immune state we identified showed coordinated activation of interferon-stimulated genes and inflammatory mediators, even though participants were clinically healthy.

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.

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.

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.

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

Happy Bday!

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.

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. https://bit.ly/4cqeZiB

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.

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

ggplot2 4.0.0 A new major version of ggplot2 has been released on CRAN. Find out what is new here.

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

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

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

‼️ 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

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

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...

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-...

👀👀 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

💥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

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

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

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! 🙏

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/