Joel Babdor

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/

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...

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...

OUT NOW: ILC3s regulate the gut microbiota via host intestinal galactosylation to limit pathogen infection in mice

#microsky #immunosky

www.nature.com/articles/s41...

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.

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:

at least it's friday

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!

This looks like a fantastic event! What a lineup! And why do I want to frame the poster so much!?

📌

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.

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

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.

This epic study, which took more than three years to get published, deserves special consideration.

#immunology
#microbiome
#allergy

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...

All - @science.org now has a @bsky.app share button! Enjoy!

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

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...

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

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.

How our gut microbiome regulates sugar preference nature.com/articles/s41...

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

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...

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...