Lungmap

Please join us for our ATS Postgraduate course, to learn best practices for analysis and integration of lung single-cell and spatial multiomics data using new (published and unpublished) AI enabled workflows.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

In this issue of Nature Genetics, LungMAP Phase 3 investigators @NeBanovich @sucre_jen and @JKropski, leverage spatial transcriptomics (Xenium) to characterize lung distal remodeling and niche dysregulation in 26 pulmonary fibrosis patients and 9 controls. nature.com/articles/s4158…

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), Bronchopulmonary Dysplasia (@lab_xin and @sucre_jen) and Interstitial Lung Disease subtypes (@NeBanovich), 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

Join us today at 4pm EST for our LungMAP DCC Office Hours! 🚨 Yan Xu from the LungMAP DCC presenting her current research: Decoding Lymphangioleiomyomatosis (LAM): Cellular Heterogeneity, Niche Environment and Treatment Obstacles 📷Register here: forms.gle/KLcPUnenvZNNyz…

Join us for our second LungMAP DCC Office Hours! 🚨Exploring Genes, Cell types, and Pathways of the Lung 📷 Time: Thursday 4 PM - 5 PM EST (August 22nd 2024) 📷Register here: forms.gle/tpiWkNLvnjqP9T… #LungMAP #CellAtlas #OpenScience

Join us for our first LungMAP DCC Office Hours! 🚨 Single-cell omics and imaging tools for Lung Biology 🗓️ Date: August 14th (Wednesday) ⏰ Time: 4 PM - 5 PM EST 📋 Register here: forms.gle/V7k4TEiwUpYHh7… #LungMAP #CellAtlas #OpenScience

LungMAP Phase 3 has begun! Focused on pathways and novel therapeutic targets in lung disease. Let us know what you want to see in this exciting new phase.

Please come and hear from our LungMAP Data Coordination team on the comprehensive analytical web tools and interfaces available to understand existing lung datasets and analyze your own data.

LungMAP is pleased to announce our new Portal Ecosystem, now described in @AJRCMB. The ecosystem includes a redesigned web portal, comprehensive single-cell Azimuth, ShinyCell and cellxgene reference atlases for mouse and human lung... and much more. doi.org/10.1165/rcmb.2…

@cartalop @MC_Nawijn @LungMAP @humancellatlas @cziscience Yes. We are summarizing now and will post at lungmap.net soon (will update this tweet).

Today, LungMAP hosted a cross-consortia discussion at #UCSD on standardization of lung cell nomenclature, strategies for alignment, and future coordination. Summary to be posted online soon with additional input and help to be solicited from the broader lung community.

biologists.com/stories/reunit… @GRClung2021 @IPFdoc @dtschump1 @jhorowitzMD

A census of the lung: CellCards from LungMAP, is now online at Developmental Cell. CellCards provides a functional annotation of cell types within the lung and single cell data for a rigorous catalogue of cell lineages as an evolving online resource. cell.com/developmental-…

Quietly remembering the 8,000 people who died of progressive pulmonary fibrosis (IPF and similar diseases) in the UK in 2021. As the year comes to an end, our thoughts are with their families and friends. @ActionPFcharity #CurePF

We invite active contribution of new datasets and knowledge (i.e., CellCards) to better serve the lung research community and to promote new discoveries. Tutorials for these new portals and analysis tools can be found at: lungmap.net/tutorials

First, LungMAP.net now serves as gateway portal to a series of omics centric portals (single-cell, bulk, proteomics, metabolomics) and a new enhanced image analysis portal (omero.lungmap.net).

LungMAP is happy to share our recent preprint describing a series of interconnected LungMAP web portals to provide supervised single-data analyses, exploration of integrated datasets and new community resources. biorxiv.org/content/10.110…

These solutions are complemented by advanced lung analysis platforms, including ToppCell (toppcell.cchmc.org) and LUNGENS (research.cchmc.org/pbge/lunggens/…), providing analyses of the same and independent datasets.

Fourth, we provide a series of community and LungMAP single-cell browsers for exploration of disease, development and regional gene expression differences, leveraging cellxgene (@cziscience), ShinyCell and HighCharts solutions.

Third, we introduce the LungMAP Data Browser (data-browser.lungmap.net) for faceted search of Lung genomics datasets using the HCA metadata schema. This browser is links to Terra for immediate reprocessing and integration of datasets in the cloud.