Computational biology and bioinformatics articles from across Nature Portfolio

Computational biology and bioinformatics is an interdisciplinary field that develops and applies computational methods to analyse large collections of biological data, such as genetic sequences, cell populations or protein samples, to make new predictions or discover new biology. The computational methods used include analytical methods, mathematical modelling and simulation.

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Expansion of artificial intelligence for genome editing

Artificial intelligence (AI) is advancing genome editing, from predictive modeling to generative design. Emerging generative AI tools such as RFdiffusion, AlphaFold 3 and ESM now facilitate the de novo design of linkers, inhibitors and enzymes. We highlight work where AI-driven design is used to enhance the precision of mitochondrial cytosine base editors.
- Heesoo Uhm
- Sangsu Bae
News & Views20 Nov 2025 Nature Structural & Molecular Biology
P: 1-3
New algorithm enables fast ‘gold-standard’ search of the world’s largest microbial DNA archives

Scientists have now sequenced more than two million bacterial and archaeal genomes, outstripping the ability to perform gold-standard searches for genes. LexicMap is a new tool that can scan millions of genomes for a gene in minutes, precisely locating mutations. This approach will enable many applications in epidemiology, ecology and evolution.

News & Views17 Nov 2025 Nature Biotechnology
P: 1-2
Mathematicians put AI model AlphaProof to the test

Mathematicians use computational tools to prove theorems. An AI model that is trained to use these tools might accelerate mathematical discovery.
- Talia Ringer
News & Views12 Nov 2025 Nature

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Latest Research and Reviews

DCS-NET: a multi-task model for uterine ROI detection and automatic staging of early endometrial cancer in MRI
- Lin Wang
- Longxiang Feng
- Fang Huang
ResearchOpen Access20 Nov 2025 Scientific Reports
Volume: 15, P: 41024
Cell line-matched reference enables high-precision functional genomics

Here the authors report that using an “isogenomic” reference genome (fully matched to the experimental cell line) improves the accuracy of genomic, epigenomic and transcriptomic analyses, as well as genome editing, compared to a non-matched generic reference.
- Luca Corda
- Emilia Volpe
- Simona Giunta
ResearchOpen Access20 Nov 2025 Nature Communications
P:
Inferring differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data with MultiVeloVAE

Understanding how cells differentiate to their final fates is a fundamental biological problem. Here, authors introduce MultiVeloVAE, a probabilistic framework that models gene expression and chromatin accessibility mechanistically, integrates multiple samples, accounts for bifurcations, and enables statistical testing over time.
- Chen Li
- Yichen Gu
- Joshua D. Welch
ResearchOpen Access20 Nov 2025 Nature Communications
P:
Automated tumor stroma ratio assessment in colorectal cancer using hybrid deep learning approach
- Tagne Poupi Theodore Armand
- Subrata Bhattacharjee
- Hee-Cheol Kim
ResearchOpen Access20 Nov 2025 Scientific Reports
Volume: 15, P: 40927
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization

A recent study presents BiRNA-BERT, utilizing adaptive dual-tokenization for improved RNA sequence processing and structural prediction accuracy.
- Md Toki Tahmid
- Haz Sameen Shahgir
- Md Shamsuzzoha Bayzid
ResearchOpen Access20 Nov 2025 Communications Biology
Volume: 8, P: 1621
Uncovering the molecular details of the 14-3-3 recruitment by mutant Sod1 species
- Lorenzo Di Rienzo
- Ilaria Genovese
- Ersilia Fornetti
ResearchOpen Access20 Nov 2025 Scientific Reports
Volume: 15, P: 41091

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News and Comment

NimbusImage: a cloud-computing platform for image analysis
- Zijian Niu
- Thibault Bruyère
- Arjun Raj
Correspondence20 Nov 2025 Nature Methods
P: 1-3
Expansion of artificial intelligence for genome editing

Artificial intelligence (AI) is advancing genome editing, from predictive modeling to generative design. Emerging generative AI tools such as RFdiffusion, AlphaFold 3 and ESM now facilitate the de novo design of linkers, inhibitors and enzymes. We highlight work where AI-driven design is used to enhance the precision of mitochondrial cytosine base editors.
- Heesoo Uhm
- Sangsu Bae
News & Views20 Nov 2025 Nature Structural & Molecular Biology
P: 1-3
If the AI bubble bursts, what will it mean for research?

The rise in artificial-intelligence technologies is unprecedented, but some predict a stock-market crash that could have knock-on effects for funding and jobs.
- Fred Schwaller
News19 Nov 2025 Nature
Mind-reading devices can now predict preconscious thoughts: is it time to worry?

Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use neurotechnology.
- Liam Drew
News19 Nov 2025 Nature
Volume: 647, P: 575-577
Panels of peers are needed to gauge AI’s trustworthiness — experts are not enough
- Cong Cheng
- Jian Dai
- Chengliang Wang
Correspondence18 Nov 2025 Nature
Volume: 647, P: 592
Google DeepMind won a Nobel prize for AI: can it produce the next big breakthrough?

The company was created to use AI for world- changing science — and achieved that with AlphaFold. But the advent of large language models raises deep questions about the future of DeepMind.
- Elizabeth Gibney
News18 Nov 2025 Nature
Volume: 647, P: 572-574