Introducing openRxiv Labs! 🔬 Growing from the strong foundation of bioRxiv & medRxiv, Labs is an experimental space for working with collaborators to push the boundaries of open scientific communication. 👉 Check it out and learn more: openrxiv.org/openrxiv-lab... #OpenScience #Preprints #Scicomm

Launching openRxiv Labs - openRxiv

Over the last thirteen years, bioRxiv and medRxiv have grown into widely used infrastructure for rapid research sharing in biology and medicine. The reliability and researcher-first values that have d...

openrxiv.org

Come and start your group at @ki.se! ki.se/en/about-ki/...

Assistant Professor recruitment programme 2026

Karolinska Institutet continues to grow a global community of excellence. In summer 2026, KI is inviting applications for 21 Assistant Professor positions in medicine and health. We are once again loo...

ki.se

We built a joint experimental and computational platform for scalable multi-modal single-cell chemical screens — profiling RNA, protein (including phospho-signaling), and chromatin accessibility responses to thousands of small molecule perturbations in parallel. www.biorxiv.org/content/10.6...

Just analysed 48 single nuclei samples with scprocess and went from fastq files to cell-type annotation in a couple of weeks!! Really recommend this pipeline developed by @willmacnair.bsky.social and team, thank you for making it public!! github.com/marusakod/sc...

GitHub - marusakod/scprocess: Snakemake pipeline for processing single cell data

Snakemake pipeline for processing single cell data - marusakod/scprocess

github.com

A simple baseline for AI forecasting in machine learning. In a recent paper, SFI Complexity Postdoctoral Fellow Yuanzhao Zhang and co-author William Gilpin show that a deceptively simple forecasting strategy — context parroting — can outperform several leading machine-learning forecasting models.

A simple baseline for AI forecasting in machine learning

In a recent paper, SFI Complexity Postdoctoral Fellow Yuanzhao Zhang and co-author William Gilpin show that a deceptively simple forecasting strategy can outperform several leading machine learning forecasting models. Their method, called context parroting, relies on short stretches of time-series data (or context). As it moves through the time series, it scans for similar patterns or motifs that appeared earlier in the sequence, and uses those patterns to predict what might come next.

santafe.edu

1/ Apply for an inter-disciplinary postdoc position in Heidelberg with the Health & Life Science Alliance Deadline: **31 March** Project proposals can be self-designed or adapt one of the outlines on the website ("List of project outlines for download") www.health-life-sciences.de/opportunitie...

I saw this when it was a preprint? They have a unique version of the estimand-estimator-estimates workflow, will be useful for may biologists, not just ecologists. We need more case studies for ecologists to emulate and for norms to shift so "regression and storytelling" becomes unpublishable.

Laura Dee@lauradee.bsky.social · 6mo ago

Excited to share our new paper in @natcomms.nature.com We synthesize causal discovery & inference approaches across traditions (regression adjustment, quasi-expts, SEMs, Granger causality, convergent cross-mapping, and more) into a unified workflow for ecologists. www.nature.com/articles/s41...

RNAs outside of cells?! How did they get there? (Thread coming soon 👀) www.biorxiv.org/content/10.1...

Pseudouridine selects RNAs for extracellular transport

RNAs move through the extracellular space to transmit information between cells, including mammalian neurons, yet how specific RNAs are channeled into these extracellular routes is unknown. Using geno...

biorxiv.org

Britain is taking a novel approach to weighing up the risk of custom drugs for rare diseases and the almost inevitable suffering in their absence. Other countries should follow its lead

Britain’s good idea for custom genetic medicines

A way to tackle the tricky economics of drugs designed for one person

econ.st

Quick (20min) non-technical overview of genetic history of Europe by my colleague Johannes Krause @mpi-eva-leipzig.bsky.social. This talk is from Nov 2025. www.youtube.com/watch?v=Iyz_...

CARTA: The Genetic History of Europe with Johannes Krause

YouTube video by University of California Television (UCTV)

youtube.com

New online! Let the data speak — single-cell analysis with CellWhisperer

Let the data speak — single-cell analysis with CellWhisperer

Nature Reviews Genetics, Published online: 02 January 2026; doi:10.1038/s41576-025-00927-xIn this Tools of the Trade article, Moritz Schaefer introduces CellWhisperer, a multimodal machine learning model and software tool for the chat-based interrogation of single-cell RNA sequencing datasets.

nature.com

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance

Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

journals.plos.org

Finally some time off to catch up with some fun reading 📖📄

From “black British music” to “A Complicated Woman”, our selection has something for everyone

The best albums of 2025

Emerging stars and established acts alike released remarkable records this year

econ.st

Even as the prices of these text snippets fall, better, more verbose models mean more tokens must be generated to complete a task

AI tokens are surging, but are profits?

The tech world’s new favourite measure comes with several caveats

econ.st

Interesting finding on cancer lineage tracing for SCLC www.nature.com/articles/s41...

Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer - Nature

Basal cells, rather than neuroendocrine cells, have been identified as the probable origin of small cell lung cancer and other neuroendocrine–tuft cancers, explaining neuroendocrine–tuft heterogeneity and offering new perspectives for targeting lineage plasticity.

nature.com

Nature’s Careers team spoke to a group of researchers about why they love LinkedIn, and how other scientists can use it to their advantage to harness its career-boosting and collaboration potential. #Academicsky 🧪

‘LinkedIn is like air to me’: the scientists who’ve cracked professional networking

Fans of the global social-media platform explain how best to harness its career-boosting and collaboration potential.

go.nature.com

A pre-trained t-test transformer - www.nxn.se/p/a-pre-trai...

One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/

“SkinnyTok’s ruthless tone rings true to many women because they’re already being so ruthless toward themselves,” Annie Joy Williams writes:

When SkinnyTok Came for Me

The body positivity movement is over.

bit.ly

Ultraprocessed foods have "contributed to high rates of chronic disease in the United States" They need to be regulated. @nejm.org today, the ways they can be reined in. www.nejm.org/media/doi/fu...

Medical Media Center: New England Journal of Medicine

Much of the food consumed in the United States is ultraprocessed. Evidence indicates that ultraprocessed food, as a class, has contributed to high rates of chronic diseases.

nejm.org

Let’s give a big round of applause to Jakob Jung, who has successfully defended his dissertation! 👏 Congratulations, @jabster93.bsky.social‬! The #HIRI family is celebrating with you! 🥳 Read more: www.helmholtz-hiri.de/en/newsroom/...

liorpachter.wordpress.com/2025/06/03/e...

Epistemic failure of epistemic failure

Earlier this year I came across this interesting post by mathematician Daniel Litt, where he pondered how many intrinsically true results in mathematics have been published with erroneous proofs: D…

liorpachter.wordpress.com

The deadline for the VIB.AI group leader positions is approaching - send in your CV and short research plan before 14th June to start your BioML research lab in Leuven or Ghent

VIB.AI@vibai.bsky.social · last yr.

We want to connect: To link model builders with data generators. To bring together scientists asking why cells behave the way they do, and others figuring out how to model that behavior. If you're working on AI in biology, consider joining! https://tinyurl.com/y35m6khy

Experiments in infrared photography. 📷 Bronica S2 & Nikkor-P 75mm f/2.8 🎞️ Ilford SPX 200

Personal news: I have been appointed by the rector of @helsinki.fi to a tenure-track associate prof position in Clinical Microbiology and Immunology! My affiliations are with the Faculty of Medicine and HiLIFE, Institute of Life Sciences @helsinki.fi . Humbled and excited to start this new journey!

Excited to be back at #eshg2025! Come by my poster today to check out fresh results on how rare high impact variants influence gene expression across immune cells—analyzed in 5,000 UK Biobank participants

Gagneur lab@gagneurlab.bsky.social · last yr.

Eva Holtkamp @evaholtkamp.bsky.social shares insights on rare variant effects on cell type-specific gene expression in immune cells across 4,978 UK Biobank participants - catch poster P18.066.A (Sunday, 1pm)

A research team led from Stockholm University & @scilifelab.se has answered a long-standing question in cell biology, uncovering how the cell’s main energy currency, ATP, is transported into the endoplasmic reticulum (ER). The study is published in @nature.com.web.brid.gy www.su.se/department-o...

Scientists reveal how energy is delivered into the cells major “shipping port” - Department of Biochemistry and Biophysics

Scientists reveal how energy is delivered into the cells major “shipping port” - Department of Biochemistry and Biophysics

su.se