Nature Methods

A paper from the JUMP Cell Painting Consortium presents image-based phenotypic profiles for 75% of the protein coding genome of human U-2 OS cells, offering a valuable resource for exploring gene relationships. @shantanu-singh.cc @drannecarpenter.bsky.social

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Unravelling cellular interactions using flow cytometry - Nature Methods We present a cost-effective ultra-high-throughput cytometry-based framework for the detection of physical interactions between cells, along with the characterization of complex cellular landscapes. Ap...

For a quick summary, read the Research Briefing here:

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Interact-omics is a high-throughput cytometry-based framework for cellular interaction mapping. @simonhaas.bsky.social

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Our August issue is live! 🎉
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On the cover, a cost-effective and scalable DNA sequencing approach by roll-to-roll fluidics.
Paper: www.nature.com/articles/s41...

PANCS-Binders (phage-assisted noncontinuous selection of protein binders) screens multiple high-diversity protein libraries against a panel of dozens of targets for high-throughput binder discovery. @chembiobryan.bsky.social @mstyles-chembiol.bsky.social

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Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social

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The Platinum Pedigree offers a pedigree-derived benchmark for SNVs, indels, structural variants and tandem repeats. The resulting variant map will help validate sequencing workflows and support development of new variant callers.

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Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social

Machine learning-trained protein domain insertion for the design of switchable proteins - Nature Methods ProDomino is a machine-learning model that efficiently predicts domain insertion sites in host proteins on the basis of amino acid sequence alone. The model enables the greatly accelerated design of f...

Check out the News & Views highlighting this work here:

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ProDomino is a machine learning-based method that predicts domain insertion sites and helps guide the engineering of functional multi-domain proteins.

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Those of you who are eagle-eyed may realize that this is the reason we are hiring a new editor with imaging/microscopy expertise! The job ad closes in 2 days, get your applications in! (The position is advertised for NYC/JC or Shanghai/Beijing.)

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Big news for one our editors... @ritastrack.bsky.social is moving to become the new Chief Editor of Nature Biomedical Engineering! We will miss her terribly but are so proud of her for this achievement and wish her all the best. 💕

Read the Research Briefing on SWING, here!

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a yellow sign that says we 're hiring ALT: a yellow sign that says we 're hiring

Job alert for Nature Methods, ad closing soon!

We are seeking a new editor with expertise in microscopy, imaging technology, and/or cell biology. The position is available in NYC/Jersey City or Shanghai/Beijing on a hybrid working model.

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From 2D to 3D and beyond: the evolution and impact of in vitro tumor models in cancer research - Nature Methods This Perspective discusses recent progresses in development of in vitro tumor models and the current challenges in this field.

A new Perspective discusses recent progress and challenges in the development of in vitro tumor models.

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Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions - Nature Methods SWING is a versatile interaction language model that can learn the language of peptide and protein interactions.

Introducing SWING, a versatile interaction language model that predicts peptide and protein interactions.

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GeneAgent: self-verification language agent for gene-set analysis using domain databases - Nature Methods GeneAgent is a language agent using large language models and self-verification to improve gene-set function annotation.

GeneAgent is a language agent using large language models and self-verification to improve gene set function annotation.

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Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes - Nature Methods Nature Methods - Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes

Surfice: www.nature.com/articles/s41...

MRIcroGL: voxel-based visualization for neuroimaging - Nature Methods Nature Methods - MRIcroGL: voxel-based visualization for neuroimaging

MRIcroGL and Surfice from Christopher Rorden are easy-to-use and open-source tools for viewing and interacting with voxel-based and surface-based human neuroimaging data, respectively.

MRIcroGL: www.nature.com/articles/s41...

DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research - Nature Methods Nature Methods - DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research

DSI Studio offers various analysis tools for human tractography. This latest version comes with the Fiber Data Hub, which contains more than 37,000 preprocessed fiber datasets derived from popular resources such as the HCP or ABCD projects. @fangchengyeh.bsky.social

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Our latest Points of Significance column discusses symmetric alternatives to the ordinary least squares regression. @martin-krzywinski.bsky.social ky.social‬ www.nature.com/articles/s41...-w

Research Highlight by Lin Tang: Sequencing DNA in the air

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Self-supervised learning of molecular representations - Nature Methods Nature Methods - Self-supervised learning of molecular representations

Research Highlight by @drarunimasingh.bsky.social: Self-supervised learning of molecular representations

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Research Highlight by @drleitang.bsky.social: Clone selection in retrospect

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Bat organoids at bat - Nature Methods Nature Methods - Bat organoids at bat

Research Highlight by Nina Vogt: Bat organoids at bat

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Escape rooms for proteins - Nature Methods Nature Methods - Escape rooms for proteins

Research Highlight by @ritastrack.bsky.social: Escape rooms for proteins

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Nature Methods Senior Editor @drarunimasingh.bsky.social is currently attending the #ISMB2025 conference. If you'd like to meet her, send her an email!

hCRAFi-CCR2 is a genetically encoded sensor that detects chemokine binding to the CCR2 receptor, demonstrated in cell culture and in mice. @piatkevich.bsky.social

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Associate Editor or Senior Editor, Nature Methods Job Title: Associate or Senior Editor, Nature Methods Locations: New York, Jersey City, Shanghai or Beijing Deadline: August 3, 2025    About Springer Nature Group Springer Nature opens the doors to d...

Nature Methods is hiring!

We are seeking a new editor with expertise in microscopy, imaging technology, and/or cell biology. The position is available in NYC/Jersey City or Shanghai/Beijing on a hybrid working model.

Apply by August 3!

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Roll-to-roll fluidics enhances reagent efficiency and reduces turnaround time in next-generation DNA sequencing, while maintaining high precision and sensitivity.

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