The challenges of single cell transcriptomics on difficult human tissue: the placenta Demand for the application of single cell transcriptomics on difficult tissues, processed and stored in disparate conditions, has led to the development of various single cell modalities. We focus on ...

Interested in applying #singlecelltranscriptomics to a difficult tissue? Please check out this #new preprint from our group and led by Dorian Xenakis. Important read for experimental design and analysis!

www.biorxiv.org/content/10.1...

Spatially resolved fetal and maternal cell contributions to severe Preeclampsia The molecular and cellular pathophysiology of the fetal-maternal interface in preeclamsia remains poorly understood, but it is increasingly clear that both fetus and mother make independent contributi...

🚨 New preprint out!
“Spatially resolved fetal and maternal cell contributions to severe preeclampsia”
Years of work using single-cell + spatial transcriptomics to study the fetal-maternal interface.
Proud to share: www.biorxiv.org/content/10.1...
🧬🤰🧪@uclpophealthsci.bsky.social

Vaccination in pregnancy to protect the newborn - Nature Reviews Immunology In this Review, Male and Jones provide an overview of the current vaccines that are offered during pregnancy and to newborns, explaining the rationale behind the different vaccination programmes and t...

👶🏼 Many #vaccines are not effective in newborns. So how do we protect them from infectious disease?

🤰🏽 By vaccination in #pregnancy!

Here we review…

💉 Established campaigns vs whooping cough, flu, COVID

💡 New approaches to RSV, GBS

🌈 Future challenges, opportunities

#ReproSky #ImmunoSky #IDSky

Ever wondered how organs take shape? Join us to find out!
The Organ Mechanobiology Lab @ncbsbangalore.bsky.social is recruiting Graduate Trainees. Perfect for final-year students curious about tissue mechanics, development & cell biology.
Check out the ad below 👇 Please RT! Thanks🙏

Short read sequencing

Excited to share our new study revealing the intricate dynamics of pregnancy & postpartum physiology! We analyzed 40M lab tests from 300K pregnancies and 160K women (cross-sectional) and mapped week-by-week changes starting from preconception to months-long postpartum recovery.

Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer Metastasis is the leading cause of cancer deaths; nonetheless, how tumor cells adapt to vastly different organ contexts is largely unknown. To investigate this question, we generated a transcriptomic ...

1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...

Are you the recipient of a Travelling Fellowship? Tell us your story - the Node Did you know that The Company of Biologists’ journals -  Development, Journal of Cell Science, Journal of Experimental Biology and

Have you received a Travelling Fellowship from @biologists.bsky.social to visit another lab?

We're collecting stories from you, our community, about your experience and how this has impacted your career. #biologists100

Share your story by sending us a digital 'message in a bottle'✍️

Supporting Scientific Research to Cure All Diseases We’re investing in new technology and collaborative research to cure all disease by 2100

I’m disappointed by @cziscience.bsky.social’s decision to discontinue the Science Diversity Leadership Award

chanzuckerberg.com/rfa/science-... no longer exists. But we exist & science needs us❤️‍🔥

👀 previous info at web.archive.org/web/20250130...

I’m among those who had written a Letter of Intent

Disease diagnostics using machine learning of B cell and T cell receptor sequences Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...

Disease diagnostics using machine learning of B cell and T cell receptor sequences

www.science.org/doi/10.1126/...

TL;DR: BCRs ARE ALL YOU NEED!

(Well actually .... keep reading) 1/

Should biology put complexity first? The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing damage to its complex nature? The answer might be foun...

"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models

+1

www.cell.com/cell-systems...

I am absolutely gutted to be moving away from @dev-journal.bsky.social & its wonderful community. I'll still be focussing on Development for the next few months, & I'll still be very involved in the journal in my new job, but I'm really going to miss hanging out with you all at #devbio meetings!

Attention Attention Attention

If anyone knows clinicians or patients who have knowledge of pediatric patients with the very rare cancer interdigitating dendritic cell sarcoma (IDCS) or other (non-LCH) dendritic or histiocytoc sarcomas please contact Sri

There’s a simple rule about giving a presentation: if you don’t practice it’s not going to be a good one. Students know this but many professors seem to have forgotten.

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 ...

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...

which one do you want to be?

The cover image portrays a human composed of proteins who is examining their health status (represented by the ECG monitoring interface) with the assistance of artificial intelligence (represented by the chip and binary codes).

Something you don't see every day!
Digitizing the human proteome in >53,000 individuals with 15-year follow-up and, with machine learning, unraveling nearly 500 disease-causing proteins
www.cell.com/cell/fulltex...
open-access

very happy to share our latest preprint, led by Michaela Unger: www.biorxiv.org/content/10.1... We are using Deep Learning to improve the detection of biomarkers in cancer genomic data 👇 This is an emerging field, much more to come.

Exciting work! A mitochondrial perspective of scRNAseq datasets!

BIH PhD Program - Call for PhD candidates 2025 - News - BIH at Charité The BIH PhD program aims to promote interdisciplinarity and support young translational talents. The program co-funds PhD positions for excellent translational projects that fit one of the four BIH re...

Do you also think that #SpatialTranstriptomics and #AI will give rise to #DigitalPathology 2.0? We have an open PhD position for the HISTOMAP (Histology-based Molecular Analysis Platform) project to accelerate biomarker detection. Please apply here: www.bihealth.org/en/notices/b....
Spread the word!

Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳

www.nature.com/articles/s41...

LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.

Some highlights⬇️

Come join us as a group leader:
www.jobs.cam.ac.uk/job/49356/
Happy to answer queries.

Continuing the peer review discussion: @katherine-brown.bsky.social on principles for effective peer review:
1) Be respectful to authors
2) Request reasonable revisions
3) Focus on whether data support the conclusions
4) Be transparent about expertise limits

thenode.biologists.com/peer-review-...

Method of the Year 2024: spatial proteomics - Nature Methods Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

Next month, Adam Bryce (University of Glasgow) and I will give an introductory workshop on #Spatial #Transcriptomics as part of the Festival of Genomics & Biodata. #FOG2025
Click here to reserve your space: hubs.la/Q02TptWZ0

Journals reward sexy stories, ignore rigor, there are easy to use tools, lack of knowledgeable analysts and reviewers. There is very low reward for deep investigation of noise in the data and statistical methods to fix it

Constructive Critics: Development's approach to peer review We're all familiar with complaints about peer review. Some think it's biased – editors (especially from ‘those’ journals) seem to have too much power to decide what gets published. It can be opaque – ...

New @dev-journal.bsky.social editorial

We know we have high standards - but we're committed to making publishing with us constructive

From clear revision guidance to limitations sections & transparent peer review, we're here to help you share your science

journals.biologists.com/dev/article/...

Only 3 days left to apply! Postdoc positions available in the Röper lab at the University of Cambridge!
@PDN_Cambridge
Discover the role that supracellular cytoskeletal assemblies and crosstalk play in sculpting organs in Drosophila or human organoids in culture!
Links below!

Hi 🦋 This is the saezlab (saezlab.org) bluesky account. We integrate #omics data with mechanistic molecular knowledge into statistical and machine learning #ML methods, and we share our tools as free #opensource packages (github.com/saezlab/) #systemsbiology #biology #compbio

Happy to share our new paper, which was just published in Nature Communications. In-context learning enables general-purpose vision language models to perform well on medical image analysis tasks. We don't need to train a neural network at all - just provide a handful of examples at inference time.