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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Timing and mechanisms of immune evasion in colorectal cancers

Evading elimination by the immune system is a hallmark of cancer, but the exact timing and pathways of immune evasion are still to be explored. Colorectal cancers were found to engage a combination of epigenetic, genetic and microenvironmental mechanisms, and establish immune evasion prior to their outgrowth.

News & Views07 Nov 2025 Nature Genetics
P: 1-2
Predicting cellular responses with conditional diffusion models

Modeling cellular responses to developmental and chemical cues is essential for understanding disease progression and informing therapeutic strategies, yet it often demands extensive experimental screening. We have developed a conditional diffusion model called Squidiff, which enables the in silico prediction of single-cell transcriptomic responses to both developmental signals and perturbations.

News & Views03 Nov 2025 Nature Methods
P: 1-2
Deep learning speeds the search for new antibiotic scaffolds

A deep learning model trained on experimental data from high-throughput screening identifies structurally novel antimicrobial compounds.
- Yumeng Zhang
- Jiangning Song
- Cesar de la Fuente-Nunez
News & Views24 Oct 2025 Nature Biotechnology
P: 1-3

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Latest Research and Reviews

Machine learning-based virtual screening and density functional theory characterisation of natural inhibitors targeting mutant PBP2x in Streptococcus pneumoniae
- Avani Panickar
- Anand Manoharan
- Sudha Ramaiah
ResearchOpen Access07 Nov 2025 Scientific Reports
Volume: 15, P: 39164
A generalizable 3D framework and model for self-supervised learning in medical imaging
- Tony Xu
- Sepehr Hosseini
- Maged Goubran
ResearchOpen Access07 Nov 2025 npj Digital Medicine
Volume: 8, P: 639
Exploring the inhibition mechanisms of momordin Ic on S. aureus serine/threonine phosphatase (Stp1) using theoretical and experimental approaches
- Yanan Yang
- Xuenan Li
- Na Wei
ResearchOpen Access07 Nov 2025 Scientific Reports
Volume: 15, P: 39054
Developmental and environmental stability of candidate reference genes in the wild bee ceratina calcarata
- Zixiao Zhao
- Rameshwor Pudasaini
- Hongmei Li-Byarlay
ResearchOpen Access07 Nov 2025 Scientific Reports
Volume: 15, P: 39046
Integrative human intervention study for mycotoxin biomarker discovery and toxicokinetic characterization
- Lia Visintin
- Eugenio Alladio
- Marthe De Boevre
ResearchOpen Access07 Nov 2025 Scientific Reports
Volume: 15, P: 39096
deepBreaks identifies and prioritizes genotype–phenotype associations using machine learning
- Mahdi Baghbanzadeh
- Tyson Dawson
- Ali Rahnavard
ResearchOpen Access07 Nov 2025 Scientific Reports
Volume: 15, P: 39095

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News and Comment

Scaling up sequence searching
- Lin Tang
Research Highlights07 Nov 2025 Nature Methods
P: 1
Reporting guidelines for studies involving generative artificial intelligence applications: what do I use, and when?

With a growing number of studies applying generative artificial intelligence (GAI) models for health purposes, reporting standards are being developed to guide authors in this space. We describe the currently available reporting guidelines that apply to GAI models and provide an overview of upcoming reporting standards. Investigators must remain up-to-date with the most applicable tools to guide the comprehensive reporting of their research as we integrate GAI in healthcare.
- Bright Huo
- Gary S. Collins
- Gordon Guyatt
Comments & OpinionOpen Access07 Nov 2025 npj Digital Medicine
Volume: 8, P: 646
Timing and mechanisms of immune evasion in colorectal cancers

Evading elimination by the immune system is a hallmark of cancer, but the exact timing and pathways of immune evasion are still to be explored. Colorectal cancers were found to engage a combination of epigenetic, genetic and microenvironmental mechanisms, and establish immune evasion prior to their outgrowth.

News & Views07 Nov 2025 Nature Genetics
P: 1-2
BioContextAI is a community hub for agentic biomedical systems
- Malte Kuehl
- Darius P. Schaub
- Victor G. Puelles
Correspondence06 Nov 2025 Nature Biotechnology
P: 1-3
Images for AI use can be sourced responsibly

A high-quality image data set shows that tech companies can obtain informed consent and avoid data bias without breaking the bank.

Editorial05 Nov 2025 Nature
Volume: 647, P: 8
Improving dataset transparency in dermatologic Artificial Intelligence using a dataset nutrition label

Biased and poorly documented dermatology datasets pose risks to the development of safe and generalizable artificial intelligence (AI) tools. We created a Dataset Nutrition Label (DNL) for multiple dermatology datasets to support transparent and responsible data use. The DNL offers a structured, digestible summary of key attributes, including metadata, limitations, and risks, enabling data users to better assess suitability and proactively address potential sources of bias in datasets.
- Yingjoy Li
- Matthew Taylor
- Veronica Rotemberg
Comments & OpinionOpen Access05 Nov 2025 npj Digital Medicine
Volume: 8, P: 641