npj Systems Biology and Applications

Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces

Nature·

Determining parameter impact in systems biology models via sensitivity analysis: a comparative approach

Nature·

Spatial analysis of malignant-immune cell interactions in the tumor microenvironment using topological data analysis

Nature·

A powerful representation learning method for enhanced analysis of incomplete multi-omics data

Nature·

Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns

Nature·

Integrating imaging and mathematical modeling to predict and optimize patient outcomes in oncology

Nature·

Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding

Nature·

Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations

Nature·

Prediction variability in physiologically based pharmacokinetic modeling of tissue disposition under deep uncertainty

Nature·

Optimizing genomics-aware clinical agents in precision oncology

Nature·

A fundamental trade-off among noise suppression, response sensitivity and speed in biological feedback networks

Nature·

Systematic proteomic analysis of neuroimaging metrics identifies therapeutic targets for pituitary neuroendocrine

Nature·

Multiscale hyperbolic embedding reveals hierarchical structure in complex biological systems

Nature·

Improvement in model flexibility reveals signaling pathway in T cell responses to pulsatile stimuli

Nature·

Comparing kinetic versus stoichiometric priorities in hybrid models of CHO metabolism

Nature·

GraphTME: graph-based framework for predicting immunotherapy response by interpreting tumour microenvironment interactions using spatial transcriptomics

Nature·

Molecular noise modulates transitions in the cell-fate differentiation landscape

Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data

Growth rate-dependent mutations and phenotypic switching facilitate rapid adaptation

Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces

Determining parameter impact in systems biology models via sensitivity analysis: a comparative approach

Spatial analysis of malignant-immune cell interactions in the tumor microenvironment using topological data analysis

A powerful representation learning method for enhanced analysis of incomplete multi-omics data

Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns

Integrating imaging and mathematical modeling to predict and optimize patient outcomes in oncology

Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding

Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations

Prediction variability in physiologically based pharmacokinetic modeling of tissue disposition under deep uncertainty

Optimizing genomics-aware clinical agents in precision oncology

A fundamental trade-off among noise suppression, response sensitivity and speed in biological feedback networks

Systematic proteomic analysis of neuroimaging metrics identifies therapeutic targets for pituitary neuroendocrine

Multiscale hyperbolic embedding reveals hierarchical structure in complex biological systems

Improvement in model flexibility reveals signaling pathway in T cell responses to pulsatile stimuli

Comparing kinetic versus stoichiometric priorities in hybrid models of CHO metabolism

GraphTME: graph-based framework for predicting immunotherapy response by interpreting tumour microenvironment interactions using spatial transcriptomics

Mapping gene expression dynamics to developmental phenotypes with information entropy analysis