LungMAP
@lungmap-dcc.bsky.social
LungMAP seeks to improve human health by providing the research community with tools and resources to understand LungMAP Disease biology and improve outcomes.
Reposted by LungMAP
🚀 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
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.
www.nature.com
June 20, 2025 at 8:43 PM
🚀 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
Reposted by LungMAP
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
cincinnatichildrens.org/perl
@cincyresearch.bsky.social
@atscommunity.bsky.social
May 13, 2025 at 3:20 PM
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
cincinnatichildrens.org/perl
@cincyresearch.bsky.social
@atscommunity.bsky.social
Reposted by LungMAP
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...
🔗 www.atsjournals.org/toc/ajrccm/2...
May 2, 2025 at 8:45 PM
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...
🔗 www.atsjournals.org/toc/ajrccm/2...
Reposted by LungMAP
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....
CT densitometry is a reliable tool for diagnosis, prognosis, and disease monitoring of emphysema
www.atsjournals.org/doi/full/10....
May 3, 2025 at 6:19 PM
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....
CT densitometry is a reliable tool for diagnosis, prognosis, and disease monitoring of emphysema
www.atsjournals.org/doi/full/10....
Reposted by LungMAP
May 2, 2025 at 8:09 PM
Reposted by LungMAP
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
Novel mechanism applies to microvascular endothelial cells and develops therapeutic agents towards pneumonia-associated ARDS
#medsky
tinyurl.com/yhaj8cbj
April 4, 2025 at 6:48 PM
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
Novel mechanism applies to microvascular endothelial cells and develops therapeutic agents towards pneumonia-associated ARDS
#medsky
tinyurl.com/yhaj8cbj
Reposted by LungMAP
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
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
April 2, 2025 at 7:11 PM
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
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
Reposted by LungMAP
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...
Increased Pulmonary GM-CSF Causes Alveolar Macrophage Accumulation. Mechanistic Implications for Desquamative Interstitial Pneumonitis
www.atsjournals.org
December 6, 2024 at 6:08 PM
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...
Reposted by LungMAP
FGF21 Signaling Exerts Antifibrotic Properties during Pulmonary Fibrosis
@atscommunity.bsky.social #medsky
🔗 tinyurl.com/m5ctz4wn
@atscommunity.bsky.social #medsky
🔗 tinyurl.com/m5ctz4wn
March 26, 2025 at 8:57 PM
FGF21 Signaling Exerts Antifibrotic Properties during Pulmonary Fibrosis
@atscommunity.bsky.social #medsky
🔗 tinyurl.com/m5ctz4wn
@atscommunity.bsky.social #medsky
🔗 tinyurl.com/m5ctz4wn
Reposted by LungMAP
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...
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...
March 26, 2025 at 5:11 PM
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...
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...
Reposted by LungMAP
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
March 26, 2025 at 6:04 PM
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
Reposted by LungMAP
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
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/d5cwfyaf
March 22, 2025 at 7:25 AM
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
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/d5cwfyaf
Reposted by LungMAP
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...
@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...
March 18, 2025 at 2:48 PM
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...
@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...
Reposted by LungMAP
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/...
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...
www.science.org
March 6, 2025 at 8:35 PM
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
unify
bit.ly
March 3, 2025 at 5:59 PM
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
Reposted by LungMAP
Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition www.nature.com/articles/s4...
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...
www.nature.com
February 15, 2025 at 3:00 AM
Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition www.nature.com/articles/s4...
Reposted by LungMAP
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...
This should be on everyone's reading list.
#RNAsky
#CANsky
#genomics
#bioinformatics
#GENEsky
🧬 💻
🧪
www.cell.com/cell/fulltex...
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 ...
www.cell.com
February 14, 2025 at 12:35 PM
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...
This should be on everyone's reading list.
#RNAsky
#CANsky
#genomics
#bioinformatics
#GENEsky
🧬 💻
🧪
www.cell.com/cell/fulltex...
Reposted by LungMAP
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....
February 12, 2025 at 3:00 AM
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....
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...
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.
www.nature.com
February 8, 2025 at 12:05 AM
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.
Projects - LungMAP Data Explorer
data-browser.lungmap.net
February 7, 2025 at 10:56 PM
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.
February 7, 2025 at 10:47 PM
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
February 7, 2025 at 10:38 PM
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!
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
December 27, 2024 at 1:38 AM
Fabulous and powerful workflow for the discovery of know and novel regulatory elements and transcriptional regulatory networks!
Reposted by LungMAP
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...
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...
December 10, 2024 at 3:15 PM
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...
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...
Reposted by LungMAP
📣 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
@atscommunity.bsky.social #medsky
FIND OUT MORE HERE: tinyurl.com/4abynsnv
SUBMIT HERE: tinyurl.com/3hezurez
December 10, 2024 at 10:59 PM
📣 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
@atscommunity.bsky.social #medsky
FIND OUT MORE HERE: tinyurl.com/4abynsnv
SUBMIT HERE: tinyurl.com/3hezurez