Nature Methods is pleased to publish several papers presenting methods developed by members of the Telomere-to-Telomere (T2T) Consortium, which facilitated the generation and analysis of the first complete human genome.

Tangram, gimVI and SpaGE outperformed other integration methods for predicting the spatial distributions of RNA transcripts, while Cell2location, SpatialDWLS and RCTD were the top-performing methods for the cell type deconvolution of spots in histological sections.

Repository-scale analysis of hundreds of millions to billions of mass spectra is a challenging endeavor due to the complexity and volume of associated data. A deep neural network embedding method is presented that enables large-scale investigation of repeatedly observed yet consistently unidentified mass spectra.

Determining the functional properties of a protein from its structure is challenging. This study presents an interpretable deep learning model that directly learns function-bearing structural motifs from raw data, allowing accurate mapping of protein binding sites and antibody epitopes onto a protein structure.

This article reports the cyclic immonium ion as a diagnostic fragment ion for lysine lactylation. The approach was used for identifying lactylation in various enriched and unenriched proteome databases, demonstrating prevalence of lactylation beyond histones.

The combination of engineered probes and spectral phasor analysis overcomes long-standing challenges associated with bioluminescence detection at the microscale, enabling multiplexed, real-time imaging of cellular features without the need for excitation light.

Extensive analyses of mammalian phosphoproteomics datasets show that protein histidine phosphorylation in human cells may not be as prevalent as previously thought.

A comparison of nine computational methods for identification of reprogramming factors for cell differentiation.

A method for high-content 3D imaging of organoids.

This work combines nanopore native RNA sequencing with machine learning models for identifying inosine-containing sites in transcriptomes.

Cameras are a crucial part of microscopes and are also built into many kinds of instruments. To make their output comparable takes standards.

Imaging and microscopy technology advances in leaps and bounds. To address accumulated pain points, academics and companies are making headway on standards.

A newly described fluorescent protein, StayGold, is bright and extremely photostable, enabling extended time-lapse imaging.

TALE-fused deaminases enable C-to-T or A-to-G base editing in human mitochondria.

A coarse-grained model enables simulating droplet formation with low-complexity RNA sequences.

To recapitulate some of the complexities of the human physiology, engineered tissues can be linked by vascular flow in a multi-organ chip.