@niklasjlang.bsky.social
MD student with Herbert Schiller @www.helmholtz-munich.de | MSc Bioinformatics @edinburgh-uni.bsky.social | aspiring physician scientist - interested in PCCM, lung fibrosis, and single cell omics | mountaineering enthusiast | Views are my own
Reposted
Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts https://www.biorxiv.org/content/10.1101/2025.09.26.678416v1
September 29, 2025 at 3:35 PM
Spatial and Single-cell Transcriptomics Reveal Programs Governing Fibroblastic Foci Fibroblasts https://www.biorxiv.org/content/10.1101/2025.09.26.678416v1
Reposted
Drs. Michael Welsh, Jesús González, and Paul Negulescu have won the 2025 Lasker–DeBakey Clinical Medical Research Award for their roles in developing treatments for cystic fibrosis. Learn more: nej.md/41L3UCI
#MedSky #PulmSky #Genetics
#MedSky #PulmSky #Genetics
September 11, 2025 at 1:07 PM
Drs. Michael Welsh, Jesús González, and Paul Negulescu have won the 2025 Lasker–DeBakey Clinical Medical Research Award for their roles in developing treatments for cystic fibrosis. Learn more: nej.md/41L3UCI
#MedSky #PulmSky #Genetics
#MedSky #PulmSky #Genetics
Reposted
#WeekendRead! #InterferonsFriendsOrFoes?! @ruthfranklinlab.bsky.social, Medzhitov, Hoagland, Rodriguez-Morales &co show @science.org that macrophage-derived oncostatin M overcomes type I IFN detrimental responses during severe influenza lung infection by driving AT-II epithelial cell proliferation!
Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage
Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the patho...
www.science.org
July 12, 2025 at 2:10 PM
#WeekendRead! #InterferonsFriendsOrFoes?! @ruthfranklinlab.bsky.social, Medzhitov, Hoagland, Rodriguez-Morales &co show @science.org that macrophage-derived oncostatin M overcomes type I IFN detrimental responses during severe influenza lung infection by driving AT-II epithelial cell proliferation!
Reposted
This is remarkable
Nikkei found academics had written "give a positive review only" and "do not highlight any negatives" in white text or tiny font on 17 preprints to combat AI peer reviews.
asia.nikkei.com/Business/Tec...
asia.nikkei.com/Business/Tec...
'Positive review only': Researchers hide AI prompts in papers
Instructions in preprints from 14 universities highlight controversy on AI in peer review
asia.nikkei.com
July 3, 2025 at 6:56 PM
This is remarkable
Intruiging preprint using #singlecell genomic profiles of treated and untreated #IPF patients to identify a "therapeutic gap" of established anti-fibrotic treatments and implicating STAT3 in IPF pathogenesis. Have a look 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 24, 2025 at 12:56 PM
Intruiging preprint using #singlecell genomic profiles of treated and untreated #IPF patients to identify a "therapeutic gap" of established anti-fibrotic treatments and implicating STAT3 in IPF pathogenesis. Have a look 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Finally out as reprint!!!
"Alveolar epithelial cell plasticity & injury memory in human pulmonary fibrosis".
Glad to share the results of our single nuc-seq & single cell ATAC-seq analyses of human IPF & PCLS before peer review - see the key findings in 🧵👇🏽
www.biorxiv.org/content/10.1...
"Alveolar epithelial cell plasticity & injury memory in human pulmonary fibrosis".
Glad to share the results of our single nuc-seq & single cell ATAC-seq analyses of human IPF & PCLS before peer review - see the key findings in 🧵👇🏽
www.biorxiv.org/content/10.1...
June 15, 2025 at 1:11 PM
Finally out as reprint!!!
"Alveolar epithelial cell plasticity & injury memory in human pulmonary fibrosis".
Glad to share the results of our single nuc-seq & single cell ATAC-seq analyses of human IPF & PCLS before peer review - see the key findings in 🧵👇🏽
www.biorxiv.org/content/10.1...
"Alveolar epithelial cell plasticity & injury memory in human pulmonary fibrosis".
Glad to share the results of our single nuc-seq & single cell ATAC-seq analyses of human IPF & PCLS before peer review - see the key findings in 🧵👇🏽
www.biorxiv.org/content/10.1...
Reposted
Finally! The Pulmonary Fibrosis Drug Connectome is on #IPFCellAtlas!! If you want to know if a drug is antifibrotic, which cells it targets, or what drugs target a gene you like, in what cells - go to ipfcellatlas.com click on the Connectome tab. Enjoy - It's Free!!!
#DataSharing
#CurePF4All
#DataSharing
#CurePF4All
May 7, 2025 at 4:39 PM
Finally! The Pulmonary Fibrosis Drug Connectome is on #IPFCellAtlas!! If you want to know if a drug is antifibrotic, which cells it targets, or what drugs target a gene you like, in what cells - go to ipfcellatlas.com click on the Connectome tab. Enjoy - It's Free!!!
#DataSharing
#CurePF4All
#DataSharing
#CurePF4All
Huge personal milestone today: thesis submitted 🎉 @lmumuenchen.bsky.social @www.helmholtz-munich.de — and first day of clinical training @ University Hospital Basel 🇨🇭! Grateful and excited for what’s ahead 🙌
May 5, 2025 at 7:06 PM
Huge personal milestone today: thesis submitted 🎉 @lmumuenchen.bsky.social @www.helmholtz-munich.de — and first day of clinical training @ University Hospital Basel 🇨🇭! Grateful and excited for what’s ahead 🙌
Reposted
I enjoyed reading this very cool preprint over the weekend - congratulations @graycamplab.bsky.social and Laurian Cabon, should be a very powerful tool for the field 😍
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment
Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated[1][1]. Current in vitro organoid mo...
www.biorxiv.org
March 3, 2025 at 1:16 PM
I enjoyed reading this very cool preprint over the weekend - congratulations @graycamplab.bsky.social and Laurian Cabon, should be a very powerful tool for the field 😍
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
On my reading list for the weekend:
Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis | @naturebiotech.bsky.social
With some intruiging insights into Heřmanský–Pudlák Syndrome
www.nature.com/articles/s41...
Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis | @naturebiotech.bsky.social
With some intruiging insights into Heřmanský–Pudlák Syndrome
www.nature.com/articles/s41...
Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis - Nature Biotechnology
Human pluripotent cells are differentiated into lung progenitors and alveolar type 1 cells.
www.nature.com
February 28, 2025 at 6:29 AM
On my reading list for the weekend:
Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis | @naturebiotech.bsky.social
With some intruiging insights into Heřmanský–Pudlák Syndrome
www.nature.com/articles/s41...
Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis | @naturebiotech.bsky.social
With some intruiging insights into Heřmanský–Pudlák Syndrome
www.nature.com/articles/s41...
Reposted
Reposted
Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!
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 4, 2025 at 2:11 PM
Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!
Reposted
Great to be front page news! Congratulations @jennydickens41.bsky.social Read the paper here: www.embopress.org/doi/full/10....
February 4, 2025 at 10:43 AM
Great to be front page news! Congratulations @jennydickens41.bsky.social Read the paper here: www.embopress.org/doi/full/10....
Super cool an intriguing work by the group of @hansclevers.bsky.social - A human organoid model of alveolar regeneration reveals distinct epithelial response to interferon-gamma
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 4, 2025 at 9:00 AM
Super cool an intriguing work by the group of @hansclevers.bsky.social - A human organoid model of alveolar regeneration reveals distinct epithelial response to interferon-gamma
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Looking for sc or snRNA-seq datasets/studies in humans that specifically profile #eosinophils or contain a substantial number of them!
If you have any leads, please share! And if you don’t but know someone who might, please re-post so it reaches the right people :)
Many, many thanks!
If you have any leads, please share! And if you don’t but know someone who might, please re-post so it reaches the right people :)
Many, many thanks!
January 29, 2025 at 7:48 PM
Looking for sc or snRNA-seq datasets/studies in humans that specifically profile #eosinophils or contain a substantial number of them!
If you have any leads, please share! And if you don’t but know someone who might, please re-post so it reaches the right people :)
Many, many thanks!
If you have any leads, please share! And if you don’t but know someone who might, please re-post so it reaches the right people :)
Many, many thanks!
Reposted
Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep
Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...
tinyurl.com
January 23, 2025 at 8:42 AM
Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep
Reposted
Precision-Cut Lung Slices: Emerging Tools for Preclinical and Translational Lung Research: An Official American Thoracic Society Workshop Report
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/mwxrej45
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/mwxrej45
January 10, 2025 at 7:53 PM
Precision-Cut Lung Slices: Emerging Tools for Preclinical and Translational Lung Research: An Official American Thoracic Society Workshop Report
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/mwxrej45
@atscommunity.bsky.social #medsky
🔓 Open Access
🔗 tinyurl.com/mwxrej45
Reposted
Thought-provoking review by Paul Martin et al. including @ipfdoc.bsky.social on how imperfect epithelial repair sets the stage for chronic disease 🧪
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Imperfect wound healing sets the stage for chronic diseases
Although the age of the genome gave us much insight about how our organs fail with disease, it also suggested that diseases do not arise from mutations alone; rather, they develop as we age. In this R...
www.science.org
January 9, 2025 at 7:40 PM
Thought-provoking review by Paul Martin et al. including @ipfdoc.bsky.social on how imperfect epithelial repair sets the stage for chronic disease 🧪
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted
Yimin's paper on a a novel visualization paradigm and implementation of cross-layout visualizations is now published in the journal Genome Biology (genomebiology.biomedcentral.com/articles/10....). Check it out at github.com/Marsilea-viz...
January 7, 2025 at 8:23 AM
Yimin's paper on a a novel visualization paradigm and implementation of cross-layout visualizations is now published in the journal Genome Biology (genomebiology.biomedcentral.com/articles/10....). Check it out at github.com/Marsilea-viz...
Reposted
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted
To all interested in all things related to Pulmonary Fibrosis - the #CureFibrosis starter pack is ready for 2025 - please let me know if you wish to be included and ofcourse follow - use #CurePF4All #CureIPF #CureFibrosis etc
#HappyNewYear
go.bsky.app/6hgNDdr
#HappyNewYear
go.bsky.app/6hgNDdr
December 26, 2024 at 6:05 PM
To all interested in all things related to Pulmonary Fibrosis - the #CureFibrosis starter pack is ready for 2025 - please let me know if you wish to be included and ofcourse follow - use #CurePF4All #CureIPF #CureFibrosis etc
#HappyNewYear
go.bsky.app/6hgNDdr
#HappyNewYear
go.bsky.app/6hgNDdr
Reposted
Delighted 2 share latest preprint evaluating fibrotic niche in #IPF using spatial transcriptomics & Hyperion mass cytometry. We believe it raises some interesting questions about IPF pathogenesis IPF.
@nebanovich.bsky.social @kaminskimed.bsky.social
www.biorxiv.org/content/10.1...
@nebanovich.bsky.social @kaminskimed.bsky.social
www.biorxiv.org/content/10.1...
Multiscale single-cell assessment of the fibrotic niche in idiopathic pulmonary fibrosis
Background: Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal disease characterized by excessive extracellular matrix deposition within the lung. Recent advances in single-cell ...
www.biorxiv.org
December 13, 2024 at 10:29 AM
Delighted 2 share latest preprint evaluating fibrotic niche in #IPF using spatial transcriptomics & Hyperion mass cytometry. We believe it raises some interesting questions about IPF pathogenesis IPF.
@nebanovich.bsky.social @kaminskimed.bsky.social
www.biorxiv.org/content/10.1...
@nebanovich.bsky.social @kaminskimed.bsky.social
www.biorxiv.org/content/10.1...
Exciting paper in Nature CVR: venous ECs branch and differentiate into capillary ECs to regenerate the alveolar gas exchange unit following lung injury - but NOT in fibrotic (KRT5+) or AT1 depleted regions - food for thought and of potential relevance for #cureIPF
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Dynamic behavior and lineage plasticity of the pulmonary venous endothelium - Nature Cardiovascular Research
Wong et al. identify Slc6a2 as a marker of pulmonary venous endothelial cells and demonstrate that these cells differentiate into capillary endothelial cells during vascular regeneration after lung in...
www.nature.com
December 16, 2024 at 8:10 PM
Exciting paper in Nature CVR: venous ECs branch and differentiate into capillary ECs to regenerate the alveolar gas exchange unit following lung injury - but NOT in fibrotic (KRT5+) or AT1 depleted regions - food for thought and of potential relevance for #cureIPF
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Reposted
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
December 13, 2024 at 10:33 AM
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
