#NatureMethods
📝 "Engaging figures"

Master 7 principles for more impactful data visualization.

👤 Helena Jambor (@helenajambor.bsky.social)

🔗 https://helenajamborwrites.netlify.app/posts/26-10_Proximity/

#rladies#rstats#datavis#biovis#naturemethods
October 26, 2026 at 1:41 PM
2/3 We also apply CytoVI to routine clinical data to identify CLL cells and classify patient samples—a step toward reusing clinical cytometry archives for research and reference mapping.

Full walkthrough in our X tweetorial:
x.com/IdoAmitLab/s...
IdoAmitLab (@IdoAmitLab) on X
Different panels. Different technologies. Can we bring flow cytometry into biology’s AI revolution? Introducing CytoVI in @NatureMethods: linking cytometry & single-cell genomics to predict missing ma...
x.com
October 1, 2026 at 6:36 AM
Very happy about this months #PointsOfView in #NatureMethods - The Graphical Abstract.

Co-authored with @simonduerr.eu, with whom I share a long-time passion for #Icons #BioIcons and #CC0 figures - and fuelled by our joint workshop for the @sib.swiss at [BC]2!

Here is a 🎁 link lnkd.in/e5ew-E2R
September 10, 2026 at 4:04 PM
Great new @NatureMethods paper, "Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types," by our EIPM Drs. Lieke Michielsen and Iman Hajirasouliha!

www.nature.com/articles/s41...
Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types - Nature Methods
Spl-ISO-Seq2, Spl-IsoQuant-2 and Spl-IsoFind enable isoform sequencing, barcode calling of >450 million barcodes, and spatially variable isoform detection with high spatial resolution as demonstrat...
www.nature.com
September 9, 2026 at 5:56 PM
UC researchers bypassed the traditional low-MOI screening dogma by using medium-high MOI 5 to co-deliver multiple sgRNAs per cell, allowing robust genome-wide #CRISPRi screens to be successfully executed using only 500,000 sorted cells. 📊🤖 #HighThroughput #Genomics #ScreenCompression #NatureMethods
June 25, 2026 at 1:09 AM
Multiplexed perturbation in CRISPR screens boosts efficiency, co-delivering multip… PMID:42185540, Nat Methods 2026, @naturemethods @OTSociety @NAR_Open https://doi.org/10.1038/s41592-026-03095-w #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
Multiplexed perturbation enables scalable pooled screens | Nature Methods
CRISPR-based genetic perturbation screens have revolutionized the ability to link genes to cellular phenotypes with unprecedented precision and scale; however, conventional pooled CRISPR screens require large cell numbers to achieve adequate sgRNA representation, posing technical and financial challenges. Here, we investigate the impact of co-delivery of multiple guide RNAs via high multiplicity of infection (MOI) in pooled CRISPR interference screens as a strategy to enhance screening efficiency while reducing cell numbers. We systematically evaluate screen performance across varying MOIs, assessing the effects of multiplexing on knockdown efficiency, sgRNA representation and potential interference of multiple sgRNA phenotypes. Our data demonstrate that sgRNA multiplexing (MOI 2.5–10) can maintain screen performance while enabling significant reductions in cell number requirements. We further apply these optimized conditions to conduct a genome-wide CRISPR screen for regulators of the
doi.org
May 31, 2026 at 1:10 AM
It clearly explains common pitfalls with interpretability tools like SHAP, saliency maps, and feature attribution, and how to apply them more responsibly in real biological workflows.

#InterpretableML #ExplainableAI #AIinBiology #DataScience #MLinBiology #NatureMethods #Science
May 18, 2026 at 5:58 PM
May 17, 2026 at 6:01 PM
So happy to see our work with @guijacquemet, @LaineBioImaging and @HenriquesLab in @naturemethods out! I believe the topic is specially relevant for the #BioImageAnalysis community: "Avoiding a replication crisis in deep-learning-based bioimage analysis".
www.nature.com
www.nature.com
www.nature.com
May 7, 2026 at 9:26 AM
Your protein embedding looks fine. But is it biology—or noise?

From ESM-2 & ProtT5 to synthetic nearest-neighbors — a model-agnostic uncertainty score. 🧬📏

New NatureMethods: the Random Neighbor Score (RNS) tells you which to trust. 🧵 (1/3)
April 18, 2026 at 1:07 AM
Ab initio gene callers used to lag evidence-based pipelines. Not anymore.

From raw DNA → introns → gene structures across 566 species — one MoE language model. 🧬🔬

NatureMethods: ANNEVO jointly models distal + evolutionary signal 🧵 (1/3)
April 16, 2026 at 7:06 PM
Our heavily updated final version of ROCKET for experiment-guided structure modeling is out in @naturemethods!

New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH
Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...
rdcu.be
April 1, 2026 at 2:18 PM
Interested in neuromodulators, especially #norepinephrine / #noradrenaline? Check out this #Naturemethods paper hot off the press from the Patriarchi lab on next-generation NE sensors. It was a pleasure to contribute to this team effort. A genuinely 💡enlightening 💡 advance for monitoring NE in vivo.
February 26, 2026 at 1:26 PM
The most sensitive green and red #norepinephrine #sensors engineered to date are out in #naturemethods! Deeply grateful to all our funders and contributors who made this work possible. A true team effort. @erc.europa.eu @snsf.ch doi.org/10.1038/s415...
Next-generation multicolor indicators for in vivo imaging of norepinephrine - Nature Methods
Improved red and green indicators for norepinephrine and their characterization are reported. These indicators allow detection of norepinephrine release in awake behaving mice in dual-color fiber phot...
doi.org
February 26, 2026 at 10:20 AM
You don't want to miss out on this manuscript. For 𝑛𝑒𝑢𝑟𝑜𝑏𝑖𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, we have some very interesting findings 😉. For 𝑐𝑜𝑚𝑝𝑢𝑡𝑎𝑡𝑖𝑜𝑛𝑎𝑙 𝑚𝑒𝑡ℎ𝑜𝑑𝑜𝑙𝑜𝑔𝑖𝑠𝑡𝑠, the project has been a source of limitless creativity and innovation, including hashtag#SpotSweeper published in hashtag#NatureMethods.
February 20, 2026 at 8:18 PM
🎉 Our Spatial-Mux-seq got a shout-out in the @NatureMethods Year in Review 2025 as one of the team’s favorite methods!

Multi-omic spatial, all-in-one. That is the way to go!
doi.org/10.1038/s415...
Year in review 2025 - Nature Methods
We highlight some of the Nature Methods team’s favorite papers published in 2025, reflecting on some trends and new technology developments.
doi.org
January 15, 2026 at 1:31 PM
When conferences provide childcare, science doesn’t “accommodate parents”. It retains talent.

Thanks Vivien Marx for including my voice in your @NatureMethods piece on conference childcare, access, & why affordability is still the choke point.

www.nature.com/articles/s41...
#ParentsInSTEM
Conference daycare
Nature Methods - Not all conferences offer childcare, but when they do, these scientists, who are also mothers, rejoice. The toys are pretty good, too.
www.nature.com
January 6, 2026 at 7:32 PM
#ResultatScientifique🔎| Une nouvelle méthode permet de prédire comment les cellules évoluent et se différencient dans le temps et l’espace. 💻
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
www.insb.cnrs.fr
December 11, 2025 at 4:30 PM
The AIRR-ML-2025 challenge is LIVE on @kaggle.com!
We’re challenging the best in #MachineLearning & #DataScience to decode the immune system.

💰 $10,000 prize pool
📄 Co-author a NatureMethods paper
November 15, 2025 at 3:31 PM
The AIRR-ML-2025 challenge is LIVE on
@Kaggle, but the real question is… are you up for it?
We’re challenging the best in #MachineLearning & #DataScience to decode the immune system. Think you have the skills? Prove it.
💰 $10,000 prize pool 📄 Co-author a @NatureMethods
paper
November 14, 2025 at 7:11 PM
Congratulations to first author Gangadhar Eluru, co-authors Steven De Gieter, Stephan Schenck, Annelore Stroobants, Binesh Shrestha, Paul Erbel and Ruslan Efremov.
#MISO #CryoEM #StructuralBiology #MembraneProteins #VIB-VUB Center for Structural Biology #NatureMethods #DrugDiscovery #BioRender
November 14, 2025 at 6:43 PM
📢 Announcing the Adaptive Immune Profiling Challenge 2025!
Can you predict immune state labels from adaptive immune receptor repertoires?
💰 $10,000 prize pool!
📄 Top 10 teams co-author a @NatureMethods paper!
🗓️ Launches Nov 5 on @Kaggle
More Info: uio-bmi.github.io/adaptive_imm...
October 23, 2025 at 9:23 PM
👏 Phys.org has featured the work of our colleagues at IOCB Prague.

The team led by @pluskal-lab.org created the world’s largest database of small-molecule #massspec. See more ► doi.org/10.1038/s41592-025-02813-0

#IOCBPrague #massspec #metabolomics #drugdiscovery #NatureMethods
September 22, 2025 at 3:07 PM