LungMAP

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases - Nature Biomedical Engineering UNAGI deciphers cellular dynamics from human disease time-series single-cell data and facilitates in silico drug perturbations to discover drugs potentially active against complex human diseases.

🚀 Off the press! Deep generative AI and multi-omics datasets are revolutionizing drug screening. Check out the findings here: www.nature.com/articles/s41.... It was incredible to be part of this endeavor. Learn more about UNAGI here🐡 🐍: medicine.yale.edu/news-article... @kaminskimed.bsky.social

Anne-Karina Perl, MSci, PhD, ATSF, an AJRCMB associate editor, will receive the Distinguished Achievement Award at the ATS 2025 International Conference in San Francisco. Congratulations! #AJRCMB #PBST

cincinnatichildrens.org/perl

@cincyresearch.bsky.social
@atscommunity.bsky.social

The AJRCCM 2025 ATS International Conference Abstract Issue is live! This year, it contains nearly 7,000 citable abstracts, organized by 36 pulmonary, critical care, and sleep medicine categories. #ATS2025

🔗 www.atsjournals.org/toc/ajrccm/2...

The Use of Computed Tomography Densitometry for the Assessment of Emphysema in Clinical Trials: A Position Paper from the Fleischner Society

CT densitometry is a reliable tool for diagnosis, prognosis, and disease monitoring of emphysema

www.atsjournals.org/doi/full/10....

Cell Population–resolved Multiomics Atlas of the Developing Lung

🔗 tinyurl.com/bdds9z7s

Endothelial ENaC-α Restrains Oxidative Stress in Lung Capillaries in Murine Pneumococcal Pneumonia–associated Acute Lung Injury

Novel mechanism applies to microvascular endothelial cells and develops therapeutic agents towards pneumonia-associated ARDS
#medsky

tinyurl.com/yhaj8cbj

Temporal Exploration of COPD Phenotypes: Insights from the COPDGene and SPIROMICS Cohorts

The authors present a method that phenotypes and models disease trajectories in a large population of COPD patients
@atscommunity.bsky.social #medsky

🔗 tinyurl.com/yvru6rp2

New publication 🫁 📊 🔬 ! We performed proteomics and transcriptomics of lung sorted cells from human (0 to 8 years). We discovered new cell markers and pathway modulated during development. A must-read for #teamMassSpec enthusiasts focused on development www.atsjournals.org/doi/abs/10.1...

FGF21 Signaling Exerts Antifibrotic Properties during Pulmonary Fibrosis
@atscommunity.bsky.social #medsky

🔗 tinyurl.com/m5ctz4wn

our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!

key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity

many are "negative regulators" & misexpressed in cancer

www.sciencedirect.com/science/arti...

Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses!

@davisjmcc.bsky.social

www.biorxiv.org/content/10.1...

The Complex Immune Cell Composition and Cellular Interaction in the Alveolar Compartment of Patients with Acute Respiratory Distress Syndrome
@atscommunity.bsky.social #medsky

🔓 Open Access

🔗 tinyurl.com/d5cwfyaf

Segger logo

Message passing intuition behind the segger’s link-prediction model and the network architecture

1/ New preprint! 🍳

@elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins!

doi.org/10.1101/2025...

Macrophage peroxisomes guide alveolar regeneration and limit SARS-CoV-2 tissue sequelae Peroxisomes are vital but often overlooked metabolic organelles. We found that excessive interferon signaling remodeled macrophage peroxisomes. This loss of peroxisomes impaired inflammation resolutio...

We are thrilled to share our new manuscript @science.org , in which we uncovers a critical role for macrophage peroxisomes in lung repair after viral infection. Could targeting peroxisomes be the key to mitigating long COVID?! www.science.org/doi/10.1126/...

Please join us for our ATS Postgraduate course, to learn best practices for the analysis and integration of lung single-cell and spatial multiomics data using new (published and unpublished) AI enabled workflows. May 17th, San Francisco #ATS2025. Apply here: bit.ly/4gvFhOY

Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition Nature Genetics - Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies...

Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition www.nature.com/articles/s4...

Synonymous mutations promote tumorigenesis by disrupting m6A-dependent mRNA metabolism The impact of synonymous mutations remains elusive. Here, the authors demonstrate that synonymous mutations can promote tumorigenesis by disrupting post-transcriptional m6A modification. The findings ...

This is a beautiful, important new paper that forges a link between mRNA epitranscriptomes, cancer variants, and response to therapy.

This should be on everyone's reading list.

#RNAsky
#CANsky
#genomics
#bioinformatics
#GENEsky
🧬 💻
🧪

www.cell.com/cell/fulltex...

FastCCC: A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies www.biorxiv.org/content/10....

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

In this issue of Nature Genetics, LungMAP Phase 3 investigators @nebanovich.bsky.social, Jen Sucre and Jon Kropski, leverage spatial transcriptomics (Xenium) to characterize lung distal remodeling and niche dysregulation in 26 pulmonary fibrosis patients and controls. www.nature.com/articles/s41...

The latest data release has been posted in the LungMAP OMICS Data Browser (data-browser.lungmap.net/projects), including CITE-Seq of COVID Lungs, Pulmonary Alveolar Microlithiasis, Alveolar Capillary Dysplasia, Bronchiolitis Obliterans Syndrome Bronchpulmonary Dysplasia and linked viewers.

New updates at LungMAP.net! Check our new collection of ShinyCell and CellxGene viewers, including post-viral lung regeneration (@morriseylab.bsky.social), Bronchopulmonary Dysplasia (Sun and Sucre labs) and Interstitial Lung Disease subtypes (@nebanovich.bsky.social), now live.

Submissions are now open for our ATS Postgraduate course PG15 Integrative Lung Bioinformatics: From Data to Discovery, May 17th, San Francisco at #ATS2025. Apply here: bit.ly/4gvFhOY

Fabulous and powerful workflow for the discovery of know and novel regulatory elements and transcriptional regulatory networks!

A panoramic view of cell population dynamics in mammalian aging | Science
a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, sexes, and genotypes.
www.science.org/doi/10.1126...

📣 The AJRCCM invites scientists to submit their original research for consideration in this special issue on airway diseases
@atscommunity.bsky.social #medsky

FIND OUT MORE HERE: tinyurl.com/4abynsnv

SUBMIT HERE: tinyurl.com/3hezurez

Important guidelines on the incredible and growing international resource of pluripotent stem cells for research and therapeutic development. #itsthecells!

One week from today! Remember to submit your Assembly Awards nominations by December 2nd!

Pylustrator offers an interactive interface to find the best way to present your data in a figure for publication. Added formatting and styling can be saved by automatically generated code. https://pylustrator.readthedocs.io/en/latest/ #python

Parental Report of Indoor Air Pollution Is Associated with Respiratory Morbidities in Bronchopulmonary Dysplasia - The Journal of Pediatrics