Axel Künstner
@knstnr.bsky.social
Bioinformatician. Statistician. Data squeezer. Omics-addicted with strong focus on #microbiome and #cancer.
Preprint: In PD-L1-gain EBV+ DLBCL, T cells get close to tumour cells but rarely touch them; a spatial "decoupling" of proximity and engagement. Fibroblast barriers, metabolic suppression, and T cell exhaustion together block anti-tumour immunity. 🧵1/5 doi.org/10.64898/202...
Really nice interactive here. Also, tax these killing machines into obscurity. www.nytimes.com/interactive/...
The Deadly Rise of Giant Trucks and S.U.V.s (Gift Article)
The vehicles on American roads have grown larger — and they are killing thousands more pedestrians, a Times investigation found.
nytimes.com
🧬 EaCoN v0.5.0 "Parallel Universe" is out! A modernized fork of Bastien Job's (@gustaveroussy.fr) copy number analysis package for Affymetrix arrays: → foreach/doParallel fully replaced with furrr/future + purrr/dplyr → R ≥ 4.2.0 compatible → OncoScan, CytoScan, SNP6 github.com/kunstner/EaCoN
GitHub - kunstner/EaCoN: Easy Copy Number !
Easy Copy Number ! Contribute to kunstner/EaCoN development by creating an account on GitHub.
github.com
Now published: journals.plos.org/plosbiology/...
What sets the mutation rate of a cell type in an animal species?
Mutation rates per generation are strikingly similar across germlines of animals and across at least one somatic cell type, suggesting a key role for natural selection in shaping mutation rates. This ...
journals.plos.org
Molly Przeworski@mollyprz.bsky.social · 8mo agoHappy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n
🦁 New preprint! We developed LION — a manufacturer-independent, 109-gene liquid biopsy panel for pan-cancer ctDNA analysis to support clinical decision-making. 📄 Preprint on medRxiv: www.medrxiv.org/content/10.6... #LiquidBiopsy #ctDNA #CancerGenomics #NGS #Oncology #Bioinformatics
A liquid biopsy-centered, pan-cancer, open next generation sequencing panel to support clinical decision-making (LION panel)
Cancer treatment has shifted toward personalized therapy based on molecular profiling, particularly in advanced disease. Existing circulating tumor DNA panels are often broad, generating many non-acti...
medrxiv.org
🧠 New paper out in Cancers! We profiled 49 solid tumor brain metastases and found that the adenosine pathway (CD39/CD73) is a frequent immune escape mechanism - often operating independently of PD-L1. #BrainMetastases #CancerGenomics #Oncology #OpenAccess www.mdpi.com/2072-6694/18...
mdpi.com
🧬 New paper out in @Cancers_MDPI! We show that Regnase-1 is a prognostic biomarker in high-grade soft tissue sarcoma — favorable in UPS, but flipped in adjuvantly irradiated patients. Context matters! 👉 www.mdpi.com/2072-6694/18... #SarcomaResearch #CancerBiomarkers #Immunology
mdpi.com
Preprint alert! 🚨 www.preprints.org/manuscript/2... High-grade soft tissue sarcomas (STS) lack robust biomarkers—but we may have a new signal. #Sarcoma #Immunology #CancerResearch #TumorMicroenvironment #Biomarkers #Oncology
preprints.org
Fresh from the press www.nature.com/articles/s41...
Exploring the underlying gene expression profiles of differences of sex development phenotypes through transcriptome analysis - Scientific Reports
Scientific Reports - Exploring the underlying gene expression profiles of differences of sex development phenotypes through transcriptome analysis
nature.com
Some news from the press www.nature.com/articles/s41...
Colonic spatial single-cell proteomics and murine models link mitochondrial dysfunction to dimeric IgA-secreting plasma cell deficiency in Crohn’s disease - Nature Communications
Crohn’s disease is associated with disturbances in the B-cell compartment and secreted antibodies. Here, the authors reveal impaired colonic dimeric IgA responses in patients with Crohn’s disease and ...
nature.com
Fresh from the press with some minor contribution from our group onlinelibrary.wiley.com/doi/10.1111/...
Immune Training of the Interleukin 6 Gene in Airway Epithelial Cells is Central to Asthma Exacerbations
This study aims to investigate how immune activation influences the epigenetic regulation and expression of the Interleukin-6 (IL-6) gene during asthma exacerbations. By examining molecular mechanism...
onlinelibrary.wiley.com
📢 Just out: Our study reveals the molecular secrets of primary renal DLBCL (prDLBCL) @bloodadvances.bsky.social #DLBCL #Lymphoma #Genomics 🧵 ashpublications.org/bloodadvance...
Molecular profiling of primary renal diffuse large B-cell lymphoma unravels a proclivity for immune-privileged tropism
Key Points. Primary renal DLBCL shows molecular parallels to immune-privileged B-cell lymphomas, with frequent MHC class I/II aberrations.Genomic and trans
ashpublications.org
📢 New Research Alert: #Lymphoma #Genomics #RenalMZL @bloodadvances.bsky.social Primary renal marginal zone lymphoma (prMZL) is extremely rare (and often misdiagnosed). We published the largest molecular study to date on this entity. 🔗 ashpublications.org/bloodadvance... Main findings 🧵👇
Molecular profiling of primary renal Marginal Zone Lymphoma reveals overlapping features with extranodal Marginal Zone Lymphoma
Axel Künstner, Vera von Kopylow, Philipp Lohneis, Matthias Kümmel, Hanno M. Witte, Dr, Veronica Bernard, Dr, Stephanie Stölting, Kathrin Kusch, Sivahari Pr
ashpublications.org
PICRUSt2 received an updated database academic.oup.com/bioinformati...
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2
AbstractSummary. PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference gen
academic.oup.com
Another one this week with contribution of our working group elifesciences.org/articles/98970 @uniluebeck.bsky.social
Diet modulates the therapeutic effects of dimethyl fumarate mediated by the immunometabolic neutrophil receptor HCAR
elifesciences.org
Fresh from the press: www.embopress.org/doi/full/10.... #microbiome
Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota | Molecular Systems Biology
imageimageThe gut microbiome supports health through balanced metabolic exchanges, but in type 2 diabetes rising blood glucose shifts interactions from cooperation to competition, altering cross-feedi...
embopress.org
Today's #Microbiome digest microbiomedigest.com/2025/04/06/a... @elisabethbik.bsky.social #microbiomesky 🦠
April 08, 2025
General microbiome Conserved genetic basis for microbial colonization of the gut – Liu et al. – Cell Human skin microbiome Confounders of the skin microbiome and wound healing in burn p…
microbiomedigest.com
New to data science with #RStats or need a refresher? I always recommend R for Data Science (r4ds.hadley.nz) – a free online book by @hadley.nz that takes you from importing data to statistical modeling in a gentle, beginner-friendly way. #datascience #rladies #r4ds
R for Data Science (2e)
r4ds.hadley.nz
6 days left to apply to the Post-doc opening in our lab @ebi.embl.org to develop&apply #bioinformatics & #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data: embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Postdoctoral fellow - Saez-Rodriguez Group
Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...
embl.wd103.myworkdayjobs.com
Are you a bioinformatician looking for an exciting opportunity in Melbourne? Is cancer genomics your passion? Apply now! www.nature.com/naturecareer...
Post-Doctoral Researcher - Parkville, Melbourne (AU) job with Peter MacCallum Cancer Centre – Parkville | 12837536
Exciting opportunity to join a research program led by Sarah-Jane Dawson at the Peter MacCallum Cancer Centre (www.thedawsonlab.com).
nature.com
🧬 Just published in Annals of Hematology! Thanks to the H. Witte, N. Gebauer, T. Hahn and others for pushing this study forward. link.springer.com/article/10.1... #HodgkinLymphoma #CancerGenomics #HematologyResearch #LymphomaGenetics #PrecisionOncology
The mutational landscape and its longitudinal dynamics in relapsed and refractory classic Hodgkin lymphoma - Annals of Hematology
In classic Hodgkin-lymphoma (cHL), only a few cases recur, and only a limited fraction of patients is primary-refractory to standard-polychemotherapy. Underlying genomic features of unfavorable clinic...
link.springer.com
I don't know how many Swedish speaking contacts I reach here, but if anyone is interested in wolfs and conservation genomics, I'll give a popular science evening lecture about it next Thursday! That is European evening time. In Swedish..🇸🇪 www.studieframjandet.se/uppsala-lan/...
Linnéa Smeds: Djupdykning i vargens genetik
Forskaren Linnéa Smeds berättar om vargstammens historia, genetiska utmaningar och sin forskning om inavel och skadliga mutationer. Föreläsningen lyfter ho
studieframjandet.se
Beyond prostate cancer: Androgen receptor signaling plays a key role in multiple malignancies. Dotto & collegues explore AR’s context-dependent functions in cancer cells & the TME, and highlight AR-targeting cancer trials. 📖 👇
Androgen receptor signalling in non-prostatic malignancies: challenges and opportunities - Nature Reviews Cancer
go.nature.com
📢 We’re looking for a new Team Leader! @enasequence.bsky.social is recruiting a Team Leader to shape the strategy and direction for the ENA and Biosamples open data resources. Interested?👇
Do you love software engineering for exciting biological applications, open science,open source, R, Bioconductor, modern web, cloud& ML technologies? We're looking for a software engineer to work on R/Bioconductor tools for biological data science and AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
I joined the Microbiome Digest team in 2018 (thanks to @elisabethbik.bsky.social) and what a journey it's been! Learned so much about microbiome science and connected with amazing researchers along the way. Looking to contribute? Come join our community!
Svetlana Ugarcina Perovic@svetlanaup.bsky.social · 2y ago📣 Come join the microbiome digest team & write microbiome research news! It's a great experience & you're gonna learn a lot. microbiomedigest.com/sample-page/...
My new book ‘The Cancer Roadmap’ was launched today It’s for anyone affected by cancer It tells you what is it, what causes it, how it’s treated, who to trust, how to understand risk + spot red flags on social media when it comes to alternative cures. Get yours here lnk.to/TheCancerRoa...
