Happy (belated) Valentine's Day from our lab to yours 💕 Image credit: @loggas.bsky.social and Lisa Künstler

🔬🏥 Gesundheitsforschung für die Menschen im InnoLÄND! In der Health + Life Science Alliance Heidelberg Mannheim wird zu zentralen Gesundheitsfragen geforscht. Mit der Innovationscampus-Förderung ermöglichen wir Grundlagenforschung mit Potenzial für biomedizinische Durchbrüche. 🔗 youtu.be/LZN-Sx9wfVQ

THE InnoLÄND: Innovationscampus Health & Life Science Alliance Heidelberg Mannheim

YouTube video by Ministerium für Wissenschaft, Forschung und Kunst

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I collected all of what I could find about the upcoming Illumina Spatial Transcriptomics technology, with some predictions about costs and sensitivity compared to 10x Genomics Visium HD www.batcheffect.com/p/the-giant-...

The giant wakes up: Illumina goes spatial

Predictions on the upcoming Illumina spatial transcriptomics technology

batcheffect.com

Introducing Count COMET 🧛🧛‍♀️ Happy Halloween! 🎃

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online: academic.oup.com/bib/article/... Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings. Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

This guy really dedicated his life to science: www.sciencedirect.com/science/arti... www.science.org/content/arti...

Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies

Snake envenomation is a neglected tropical disease, with 600 species causing over 100,000 deaths and 300,000 permanent disabilities in humans annually…

sciencedirect.com

I am excited to share my first work in @schapirolab.bsky.social on Multiple Myeloma (MM) in collaboration with the Standal Lab from NTNU Norway. We use Imaging Mass Cytometry (IMC) on bone marrow biopsies from MM and precursor patients (details below): www.biorxiv.org/content/10.1...

Highly multiplexed imaging recovers immune and metabolic niches in multiple myeloma associated with disease progression and bone involvement

Multiple myeloma (MM) is a cancer arising from genetically aberrant plasma cells (PCs) that remain dependent on the bone marrow (BM) microenvironment for disease establishment and progression. Here, w...

biorxiv.org

Nature Method: Temporal and spatial omics technologies for 4D profiling www.nature.com/articles/s4...

Temporal and spatial omics technologies for 4D profiling

Nature Methods - This Perspective explores advances and future directions in spatiotemporal omics methods for four-dimensional profiling.

nature.com

And for anyone who has considered contributing to an open source package: don't be scared to propose changes. Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.

For people like me who don't have a team behind a package like CellCharter, contributions like these mean a lot. So thank you Lukas :) And congratulations, it's not always easy to jump into an existing codebase and propose changes.

RCS measures how large a cell niche (aka spatial domain aka spatial cluster) is compared to what would be normally expected. This pushed me to completely rewrite the system for generating and plotting boundaries for cell niches. The new system is now more efficient, consistent, and visually clear.

A few weeks ago, we released CellCharter v0.3.5. Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social ! He designed a new metric called Relative Component Size (RCS).

GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter

github.com

Spotted: @loggas.bsky.social and @arojhada.bsky.social teaching phenotyping to our Advanced Systems Biology students

🖥️🧬 I used to have to tell my students not to bother with differential expression analysis in a language outside of R. Recently, with pydeseq2 and now InMoose, this is changing! bmcbioinformatics.biomedcentral.com/articles/10....

Differential expression analysis with inmoose, the integrated multi-omic open-source environment in Python - BMC Bioinformatics

Background Differential gene expression analysis is a prominent technique for the analysis of biomolecular data to identify genetic features associated with phenotypes. Limma—for microarray data –, an...

bmcbioinformatics.biomedcentral.com

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data

Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

biorxiv.org

An alternative to tSNE & UMAP for more accurate data visualization: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data. The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.

In addition to the two #SpatialBiology posts in the thread below, we're now also advertising for a Research Software Engineer #RSE to help us take #MuSpAn to the next level - come and join us! my.corehr.com/pls/uoxrecru... #academic #jobs #softwaredeveloper #compsci

Joshua Bull@joshuabull.bsky.social · last yr.

Are you looking for a postdoc position in #SpatialBiology? We're advertising roles in both mathematical method development and in spatial data analysis @ox.ac.uk in colorectal precancer spatial biology! Method Development: tinyurl.com/4vcbdjcy 🧮 Data Interpretation: tinyurl.com/yzsp729s 🧪

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

Big updates for the Nextflow @vscode.dev extension! 🚀 🔍 Workflow view – Visualize logical structure of pipelines ⚙️ Process view – See all processes in one place 🌐 Seqera view – Manage connected CEs directly in the IDE 📚 Resources view – Quickly access Copilot, AI tools & training

Miso made in space tastes nuttier! Researchers successfully make miso at the #InternationalSpaceStation, confirming that making fermented foods in space is possible. www.cell.com/iscience/ful... @medialab.bsky.social Maggie Coblentz @novo-nordisk.bsky.social Joshua D. Evans @cp-cell.bsky.social

Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!

Nature Biotechnology@natbiotech.nature.com · last yr.

High-dimensional imaging using combinatorial channel multiplexing and deep learning go.nature.com/4hGPfO0

Science is an investment that pays enormous dividends. So if you’re business-minded, it’s an offer you can’t refuse! Here's my full speech from the Stand Up For Science rally in DC today: www.youtube.com/watch?v=eemj...

🧵 We are excited to share our new paper, showcasing micronuclAI, which leverages #AI and #ComputerVision to detect #chromosomal_instability #CIN #micronuclei Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.

Communications Biology@commsbio.nature.com · last yr.

@arojhada.bsky.social, @miguelib.bsky.social, @denisschapiro.bsky.social, @schapirolab.bsky.social

The March issue is out! This week: TOX-inducible-KO 🐁show how #TOX maintains #exhausted CD8 #Tcell epigenetic fate; visualizing temporal & spatial #STING expression; & UVB-driven #mitochondrial Z-🧬complexed w ZBP1 fuels #autoimmune #photosensitivity via cGAS-STING! science.org/toc/sciimmunol/10/105

In an unprecedented move, the US National Institutes of Health has begun mass terminations of research grants that fund active scientific projects because they no longer meet “agency priorities”. https://go.nature.com/4bpG2It

Exclusive: NIH to terminate hundreds of active research grants

Studies that touch on LGBT+ health, gender identity and DEI in the biomedical workforce could be terminated, according to documents obtained by Nature.

go.nature.com

One week to go!

Heidelberg University Postdoc Network@heidelbergpostdoc.bsky.social · 2y ago

Are you a postdoc at @uniheidelberg.bsky.social? Don't forget to sign up!

Does anyone have a good universal membrane marker besides NaKATPase and CD98, that ideally stains epithelium/cancer similarly strong as stroma/immune cells? Antibody will be used for spatial proteomics (cyclic IF), goal is a good whole cell segmentation downstream

Gemini Code Assist now free: blog.google/technology/d... VSCode: marketplace.visualstudio.com/items?itemNa... Positron: open-vsx.org/extension/Go... #Rstats

Society, patients and clinicians welcome a much-needed non-opioid pain medication. Vertex’s first-in-class analgesic Journavx could soon be followed by a new generation of addiction-free pain drugs acting at NaV1.8 sodium channels www.nature.com/articles/s41...

Vertex’s opioid-free drug for acute pain wins FDA approval - Nature Biotechnology

Society, patients and clinicians welcome a much-needed non-opioid pain medication. Vertex’s first-in-class analgesic Journavx could soon be followed by a new generation of addiction-free pain drugs ac...

nature.com

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : 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