FlexConsensus: a tool for merging heterogeneous cryo-EM conformational landscapes into a common latent space to compare similarities and differences. www.nature.com/articles/s41...

Read the Research Briefing highlighting this work, here: www.nature.com/articles/s41...

scEpi2-seq: a method for simultaneous single-cell profiling of DNA methylation and histone modifications. @jervdberg.bsky.social @hubrechtinstitute.bsky.social www.nature.com/articles/s41...

EpiAgent: a foundation model for analyzing scATAC-seq data. www.nature.com/articles/s41...

Squeezed light field microscopy (SLIM) combines concepts from tomography and compressed sensing with light field microscopy for volumetric imaging at kilohertz rates. www.nature.com/articles/s41...

Tilt-corrected bright-field scanning transmission electron microscopy (tcBF-STEM) offers enhanced contrast and dose efficiency for cryo-EM in thick biological specimens. www.nature.com/articles/s41...

CORAL infers the occurrence of rare species based on common species, using DNA metabarcoding data and biodiversity data. www.nature.com/articles/s41...

Destabilized variants of MS2 and PP7 coat proteins offer improved live-cell imaging of tagged RNAs in mammalian cells. @johntngo.bsky.social www.nature.com/articles/s41...

We are thrilled to present a special September issue highlighting recent methods in the field of cancer biology. www.nature.com/articles/s41...

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

A new Perspective discusses the challenges of sharing annotated image datasets and offers advice for improving bioimage annotation and reuse, particularly for AI applications. www.nature.com/articles/s41...

In our latest Creature Column, @scottjuntti.bsky.social discusses why cichlids, well-known as popular ornamental aquarium fish, are also useful model organisms particularly for evolutionary studies. www.nature.com/articles/s41...

MSnLib: a large-scale, open multi-stage fragmentation mass spectral library for 30,000 unique small molecules. @robinschmid.bsky.social @pluskal-lab.org www.nature.com/articles/s41...

GRASP: a model for protein complex structure prediction that integrates data from crosslinking, covalent labeling, chemical shift perturbation, and deep mutational scanning experiments. www.nature.com/articles/s41...

Clonalscope: a method for cancer subclone detection leveraging copy number profiles estimated from spatial and single cell sequencing data. www.nature.com/articles/s41...

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

GHIST: a deep learning-based method to predict spatial gene expression at high resolution using histology data. www.nature.com/articles/s41...

Mutational effect transfer learning (METL) is a biophysics-based protein language model that excels in challenging protein engineering tasks. www.nature.com/articles/s41...

TDAC-seq is a method for targeted chromatin accessibility profiling that uses cytidine deaminases and long-read sequencing to resolve the effects of CRISPR edits on single chromatin fibers. www.nature.com/articles/s41...

Research Highlight by Nina Vogt: Neuropixels for nonhuman primates www.nature.com/articles/s41...

Research Highlight by @drarunimasingh.bsky.social: Spatiotemporal lipidomics in living tissue www.nature.com/articles/s41...

Research Highlight by Madhura Mukhopadhyay: Capturing host-microbe interactions www.nature.com/articles/s41...

Research Highlight by Lin Tang: Combating hallucination in digital pathology www.nature.com/articles/s41...

Research Highlight by @drleitang.bsky.social: Enhancing CRISPR DNA imaging www.nature.com/articles/s41...

CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data. www.nature.com/articles/s41...

Introducing WISDEM, a hybrid detector for making simultaneous EEG and fMRI recordings, enabling access to neural activity at high temporal and spatial resolution in rats. www.nature.com/articles/s41...

Scvi-hub is a versatile and efficient platform for model-based analysis of single-cell sequencing studies with access to a diverse array of datasets and downstream analysis. @canergen.bsky.social www.nature.com/articles/s41...

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes. www.nature.com/articles/s41...

Introducing inTRACKtive: a web-based tool for interactive cell tracking visualization. www.nature.com/articles/s41...

uMAIA offers an analytical framework designed to enable construction of high-resolution metabolic atlases using mass spec imaging data. @gioelelamanno.bsky.social www.nature.com/articles/s41...

Introducing TCAT, a pipeline to simultaneously capture gene expression programs related to T cell subsets and activation states. www.nature.com/articles/s41...

SDR-seq is a droplet-based single-cell DNA-RNA sequencing platform for studying gene expression profiles linked to both noncoding and coding variants. www.nature.com/articles/s41...

A laser flash melting procedure, followed by rapid revitrification, provides a simple approach to help mitigate the preferred orientation problem that plagues cryo-EM analysis. www.nature.com/articles/s41...

A standardized, realistic phantom dataset consisting of ground-truth annotations for 6 diverse complexes serves as a community resource for benchmarking cryo-ET algorithms. www.nature.com/articles/s41...

DeepMVP is a deep learning framework to predict PTM sites and variant-induced alterations across 6 common PTMs. www.nature.com/articles/s41...

This Resource paper introduces an approach to build connectomes from light microscopy-based reconstructions of mouse neurons and inferred synaptic connections. www.nature.com/articles/s41...

Ultrack is a tool for robust and long-term 3D segmentation in challenging samples such as zebrafish, fruit fly, and nematode embryos. www.nature.com/articles/s41...

FHIRM-TPM 3.0 is a miniature microscopy for multicolor 2-photon imaging in freely moving mice. www.nature.com/articles/s41...

Starting a new lab after a postdoctoral fellowship can involve a roadtrip to home turf. In Lab & life, @kallikappel.bsky.social and Anna Maurer share with @vivienm.bsky.social how moving away and coming home has shaped them scientifically and personally. www.nature.com/articles/s41...

Chemical-induced gene signatures (CIGS) is a high-resolution dataset of 319,045,108 gene expression events induced by chemical perturbation. www.nature.com/articles/s41...

A journey in science takes initiative, and also an ability to face headwinds. These PhD students aren’t scared away, @vivienm.bsky.social reports. www.nature.com/articles/s41... rdcu.be/eAUk2

Instruments and approaches are emerging for single-molecule protein analysis. In this Technology Feature by @vivienm.bsky.social some developers and early users talk about their first impressions. www.nature.com/articles/s41... rdcu.be/eAUlX

This month's Creature Column features the tubeworm Hydroides elegans - much maligned as a shipyard biofouling pest, but also a useful model organism for studying development, biomineralization and marine microbiology. www.nature.com/articles/s41...

In this month's Editorial, we discuss how automation and outsourcing are changing how scientific research is performed. www.nature.com/articles/s41...

MAPIT-seq is an antibody-guided RNA editing method for co-profiling RBP-RNA interactions and gene expression in single cells and tissue. www.nature.com/articles/s41...

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

Interact-omics is a high-throughput cytometry-based framework for cellular interaction mapping. @simonhaas.bsky.social www.nature.com/articles/s41...

Our August issue is live! 🎉 nature.com/nmeth/volume... 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 www.nature.com/articles/s41...

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