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...

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 ...

biorxiv.org

🚨 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

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...

biorxiv.org

👶🏼 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

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...

nature.com

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.

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...

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 ...

biorxiv.org

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'✍️

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

thenode.biologists.com

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

Supporting Scientific Research to Cure All Diseases

We’re investing in new technology and collaborative research to cure all disease by 2100

chanzuckerberg.com

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/

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 ...

science.org

"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...

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...

cell.com

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!

Katherine Brown@katherine-brown.bsky.social · last yr.

Big news - I'm going to be moving to a new position at The Company of Biologists, working across all our journals. This means my job is up for grabs! If you're an experienced editor with a love of developmental biology and its community, this could be the role for you. Full details in the link.

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

Sri Kosuri@srikosuri.bsky.social · last yr.

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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.

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...

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

which one do you want to be?

Martin Vögele@martinvoegele.bsky.social · 2y ago

There are two types of scientists. When I mention a new paper, the one type asks: “What is it about?” The other type asks: “In which journal?” #SciSky

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!

Bianca Habermann@biancah0406.bsky.social · 2y ago

New year, new version of mitoXplorer 3.0 (mitoxplorer3.ibdm.univ-amu.fr) : mine your single-cell RNA-seq data from a mitochondrial perspective by creating cell-type specific pseudo-bulks or by looking at mitochondrial variability on single-cell level. Check it out at doi: doi.org/10.1101/2024...

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!

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...

bihealth.org

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.

Department of Genetics, University of Cambridge@geneticscam.bsky.social · 2y ago

The Department is opening its doors to sponsor Early Career Researchers for external fellowships 👨‍🔬👩‍🔬 We will assist you with the development of your fellowship application and practice for interviews. Please share and get in touch! 📨💻 ➡️more info: jobs.cam.ac.uk/job/49356/

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-...

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...

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.

nature.com

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

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/...

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 – ...

journals.biologists.com

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.