Protein language models capture single proteins but struggle with interactions. Here, authors present MINT, trained on large PPI datasets, which outperforms existing PLMs in predicting binding, mutati...

Riboswitches are allosteric RNA molecules that change conformation upon ligand binding to regulate downstream genes. Here, the authors use Restricted Boltzmann machines trained on natural sequences to...

What is an Article in Press? How is the Article in Press different to the VoR?  Is the Article in Press citable?  How does indexing work with an Article in Press?  Can corrections/ amendments be m...

RNA nanotechnology creates structural and functional RNA architectures for biomedicine, synthetic biology and beyond. Here, the authors introduce pyFuRNAce, an intuitive browser-based RNA design tool....

Single-molecule localisation microscopy enables nanoscale mapping of molecular organisation, but clustering stochastic data remains challenging. Here, authors present a graph neural network method tha...

Embedding is a key step in single-cell Hi-C analysis to identify cell states. Here, the authors benchmark 13 embedding methods in 10 scHi-C datasets. They find that data representation, preprocessing ...

Cis regulatory elements endow genomes with sequence-encoded logic to drive cellular differentiation. Here, the authors introduce a biophysically principled sequence model that characterises complex TF...

The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...

Cells rely on limited numbers of transmembrane receptors to process signals from dynamic microenvironments. Using microfluidics and endogenous reporters, the authors track single cells to reveal how t...

Single-cell isoform quantification using Nanopore long reads remains limited by sequencing errors. Here, authors present Longcell, a computational framework that corrects these errors and uncovers spl...

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

Activity recognition in live-cell imaging is laborious. Here, authors present, IVEA, a fully automated AI ImageJ plugin, that efficiently detects and classifies exocytosis events, from synaptic transm...

Multi-species acute systemic toxicity assessment is fundamental for chemical classification, labelling and risk management. Here, the authors propose a machine learning paradigm, Adjoint Correlation L...

Individual data types in a single cell multi-omic assay are often processed and clustered independently before combined for further analysis. Here, authors showed that binarized gene expression d...

Single-cell CRISPR screens enable high-throughput analysis of how genetic changes affect individual cells. Here, authors present GPerturb, a method that accurately detects and quantifies gene-level ef...

To develop virtual cells, mathematical models must account for the heterogeneity of single cells. Here, authors develop virtual single cell NFκB signalling networks that recapitulate heterogenous expe...

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Histopathology is essential for diagnosing cancer, but cell annotation remains unreliable and inefficient. Here, authors develop a method using deep learning and immune-fluorescence-guided cell labell...

Accurate cell type annotation is a major challenge in single-cell and spatial omics. Here, authors present a user-friendly platform providing robust automatic annotation and enhanced biological interp...

Optimising operational conditions for biological systems is a complex task. Here, authors present a Bayesian optimisation-based iterative experimental design framework that integrates data generation,...

The cell nucleus coordinates diverse functions. Here, the authors utilise multiplexed super-resolution imaging to study how nuclear proteins are distributed relative to each other from the micro to th...

Job title: Associate or Senior Editor, Nature Reviews Electrical Engineering Location: Shanghai or New York – hybrid working model Closing date: 1st July 2025 About Springer Nature Group Springer Natu...

Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...

Mitophagy is crucial for mitochondrial function and is implicated in Alzheimer’s disease. Here, the authors introduce an AI-assisted fluorescence microscopy system to track mitophagic intermediates in...

Single-cell sequencing reveals cellular heterogeneity but is challenged by technical noise and batch effects. Here, authors present CellFM, an 800-million-parameter foundation model trained on 100 mil...

Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...

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Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....

Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot ability in various tasks.

Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...

Immunotherapy is transforming cancer treatment, with immune cell distribution in the tumour microenvironment key to predicting outcomes. Here, authors provide a robust framework to analyse spatial pat...

Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...

This cross-journal Collection shines a spotlight on research exploring DNA as a scalable and sustainable medium for computing and data storage.

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Fusion oncoproteins drive paediatric cancers but are challenging to target due to their intrinsic disorder and lack of druggable pockets. Here, authors present FusOn-pLM, trained on FusOn-DB, which us...

Overview of #January2025 #Computational_Biology Methods papers published in Nature Communications Nature Portfolio. (https://lnkd.in/ejMPmR-A) Jingyi Jessica…

Identifying and characterizing secreted virulence proteins are fundamental for deciphering microbial pathogenicity. Here, the authors introduce a practical training framework to improve protein langua...

Existing cell type deconvolution methods, crucial for studying tumour environments, overlook some critical issues. Here, authors analyse how these issues impact on deconvolution and develop methods to...

Existing tools face limitations in integrating spatial data with single-cell multi-omics datasets. Here, authors introduce a computational tool that maps diverse single-cell modalities, including RNA,...

Large-scale single-cell sequencing data brings computational barriers for downstream analysis. Here, the authors propose MetaQ, a metacell algorithm that reduces cell number while preserving biologica...

The authors develop Celina to detect cell type-specific spatially variable genes (ct-SVGs) in spatial transcriptomics. These ct-SVGs exhibit distinct spatial expression patterns within specific cell t...

#Code_Availability_Statement! The importance of licensing code when you publishing your computational biology papers Recently, we have seen an increasing…

Tools to determine the spatial distribution of components and their networks inside cells are not well developed. Here, authors provide the open-source 3D-cell-image analysis platform Cell Detection a...

Generative deep learning models can generate novel proteins, but these are often not functional due to thermodynamic instability. Here, authors present a method to learn both the sequence and thermody...

A key question in single-cell biology is how cells communicate and exchange information with neighboring cells in tissues. Here, the authors introduce NiCo to predict the downstream effect of cell-cel...