npj Systems Biology and Applications

Article	Citations
Measuring criticality in control of complex biological networks	105
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	84
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	83
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	64
Leveraging public AI tools to explore systems biology resources in mathematical modeling	62
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	56
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	54
Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations	49
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data	44
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	41
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	40
Drug-tolerant persisters to TRAIL emerge from a dose-dependent surface in a cell-state continuum of sensitivity	39
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	35
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	34
Data-driven universal insights into tumorigenesis via hallmark networks	34
Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications	33
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	32
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	31
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	30
Revisiting the evolution of bow-tie architecture in signaling networks	30
Modelling HIV-1 control and remission	28
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	27
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	27
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	26
Data-driven synthetic microbes for sustainable future	25

Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	25
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	25
Spatiotemporal instability of influenza seasonality during viral co-circulation	24
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	23
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	23
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	23
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	22
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	22
A mechanism for the emergence of low-dimensional structures in brain dynamics	22
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	21
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	21
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	21
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	20
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression	20
Prediction variability in physiologically based pharmacokinetic modeling of tissue disposition under deep uncertainty	20
Matters of life and death in computational cell biology	20
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	20
Enhancing yeast cell tracking with a time-symmetric deep learning approach	20
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	19
Region-specific mean field models enhance simulations of local and global brain dynamics	19
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	19
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	18
Manifold-based learning for high-throughput single-peanut phenotyping	18
SIMBA-GNN: mechanistic graph learning for microbiome prediction	18
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	18
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	17
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	17
A Python toolbox for neural circuit parameter inference	17
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	17
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	17
LumbriCyc: towards metabolic modelling of earthworms	16
Design principles of improving the dose-response alignment in coupled GTPase switches	16
Learning patient-specific spatial biomarker dynamics via operator learning for Alzheimer’s disease progression	16
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	16
Integrating AI, mechanistic modelling and network approaches in systems biology for translational research	16
Genetic basis of temporal variation in phenology in a woody perennial plant	16
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	16
A robust ultrasensitive transcriptional switch in noisy cellular environments	16
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	16
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	16
An architecture for collaboration in systems biology at the age of the Metaverse	15
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	15
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	15
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	15
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	15
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	15
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	14
Oncostatin M orchestrates collective epithelial migration via HIF1A activation	14
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	14
PYEAST – A Computational Toolkit for Saccharomyces cerevisiae Genetic Engineering	14

Determining parameter impact in systems biology models via sensitivity analysis: a comparative approach	14
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	14
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	14
Characterizing open-ended evolution through undecidability mechanisms in random Boolean networks	14
Development of a severe rat refeeding syndrome model and mathematical modeling of the associated hypophosphatemia	14
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	14
Computational gastronomy: capturing culinary creativity by making food computable	14
The modular biochemical reaction network structure of cellular translation	13
Decoding cellular population dynamics through mechanistic modelling and statistical data analysis	13
Expanding the role of metabolism in whole plant models	13
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	13
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	13
A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors	13
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	13
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	13
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	12
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	12
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	12
Design principles for robust multistability in coupled feedforward-feedback regulatory circuits	12
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	12
TrackRefiner a tool for refinement of bacillus cell tracking data	12
A statistical framework for detecting therapy-induced resistance from drug screens	12
Genetic risk in Alzheimer’s disease	12
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	12
Publisher Correction: Mammalian synthetic gene circuits for biopharmaceutical development & manufacture	11
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	11
Systematic proteomic analysis of neuroimaging metrics identifies therapeutic targets for pituitary neuroendocrine	11
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	11
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	11
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	11
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	10
Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data	10
Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells	10
Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype	10
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	10
Machine learning estimation of FVIII pharmacokinetic parameters in Chinese children with severe Hemophilia A	10
A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations	10
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	10
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	10
Cross-platform metabolomics imputation using importance-weighted autoencoders	10
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	10
Representation and quantification of module activity from omics data with rROMA	10
A machine learning framework reveals key drivers of cytokine responses in a healthy human cohort	10
Spatial analysis of malignant-immune cell interactions in the tumor microenvironment using topological data analysis	10
Flexible modeling of regulatory networks improves transcription factor activity estimation	10
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	10
Integrating imaging and mathematical modeling to predict and optimize patient outcomes in oncology	9
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	9
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	9
Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells	9
Multi-omics integration reveals ANXA6-high γδ T cell–endothelial communication as a potential link between periodontitis and MASLD	9
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	9
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	9
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	9
Sometimes extracellular recordings fail for good reasons	8
Quantitative systems-based prediction of antimicrobial resistance evolution	8
Data-driven energy landscape reveals critical genes in cancer progression	8
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	8
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	8
Publisher Correction: Rethinking medical education through systems biology to address complexity	8
Nucleus pulposus cell network modelling in the intervertebral disc	8
Author Correction: Enhancing randomized clinical trials with digital twins	8
Decoupling the chemical and physical origins of the seed spectral manifold in sorghum	8
Liver progenitor cells perform wound healing in a scratch assay by concerted bistable circuits	8
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	8
Optimal control theory as a method for designing multidrug adaptive therapy regimens	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
Inferring relationships among major psychiatric disorders in a resting-state functional connectivity-informed embedding space	8
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	8
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	8
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	8
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Immune digital twins for complex human pathologies: applications, limitations, and challenges	8
GO2Sum: generating human-readable functional summary of proteins from GO terms	8
Metabolic gene expression-based stratification and prognostic risk predictive model of head and neck squamous cell carcinoma	8
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	8
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	8
Reliable interpretability of biology-inspired deep neural networks	8
Next generation lineage tracing and its applications to unravel development	8

Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases	8
Modeling single nucleus microglia across species identifies immune pathways and therapeutic candidates in Alzheimer’s disease	8
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	7
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	7
Revealing novel subtypes of synovial sarcoma through single cell transcriptomics	7
MMP9 shapes cell mechanics to enable collective invasion in cancer	7
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	7
Open problems in synthetic multicellularity	7
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	7
Molecular noise modulates transitions in the cell-fate differentiation landscape	7
Asthma-mediated control of optic glioma growth via T cell-microglia interactions: A mathematical model	7
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	7
Exploring CHO cell stability during prolonged passaging via eXplainable AI driven flux balance analysis	7
Forum on immune digital twins: a meeting report	7
Emergence of multiple collective motility modes in a physical model of cell chains	7
Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces	7
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	7
Global loss of metabolic responsiveness and elevated enzyme in leptin deficient obese mice during starvation	7
Single-trajectory Bayesian modeling reveals multi-state diffusion of the MSH sliding clamp	6
Data-driven modeling of amyloid-β targeted antibodies for Alzheimer’s disease	6
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	6
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data	6
Supervised machine learning identifies impaired mitochondrial quality control in β-cells with development of type 2 diabetes	6
Neuronal and glial networks interact with traumatic brain injury to modulate cognition in ABCD study	6
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	6
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	6
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	6
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	6
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	6
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	6
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	6
Deterministic patterns in single-cell transcriptomic data	6
Minimally sufficient experimental design using identifiability analysis	6
Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC	6
Multiscale hyperbolic embedding reveals hierarchical structure in complex biological systems	6
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	6
Designing function-specific minimal microbiomes from large microbial communities	6
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models	6
Effective dose window for containing tumor burden under tolerable level	6
From FAIR to CURE: guidelines for computational models of biological systems	6
Simulation-based inference of cell migration dynamics in complex spatial environments	6
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	6
Loss of long-range co-expression is a common feature in cancer	6
Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data	6
Multiscale modeling reveals synergy between CCL19 and PD-1 blockade in reshaping the TNBC microenvironment	5
Virtual twins and the future of human developmental biology	5
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	5
Metabolic set theory: a generalized model of microbial interactions	5
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	5
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	5
Asking the right questions for mutagenicity prediction from BioMedical text	5
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5
GraphTME: graph-based framework for predicting immunotherapy response by interpreting tumour microenvironment interactions using spatial transcriptomics	5
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	5
Th2 bias and T-cell exhaustion characterize the immunopathology of non-tuberculous mycobacterial pulmonary disease	5
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	5
Inferring absolute counts from proportions by constraining multivariate normal distributions	5
Current state and open problems in universal differential equations for systems biology	5
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Computer experimentation reveals mechanisms for signaling and coupled transport that trade efficiency for robust growth	5
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	5
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	5
Untargeted metabolomics reveals organism specific biomarkers of carbapenem resistance in Klebsiella pneumoniae and Escherichia coli	5
When normalization induces correlation: shared and unstable references can create hidden dependencies	5
The p21 resilience network: a conceptual framework linking senescence to ferroptosis and cuproptosis resistance	5
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	5
Path-based quantification of activation and repression in Boolean models using BooLEVARD	5
A computational approach for perturbation-induced EMT transitions	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	5
Improvement in model flexibility reveals signaling pathway in T cell responses to pulsatile stimuli	5
On the mechanisms of epidermal stemness and differentiation	5
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	5
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	5
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	4
Model-guided discovery of MTOR-oriented synergistic drug combinations in colorectal cancer	4
Generative design of synthetic gene circuits for functional and evolutionary properties	4
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	4
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	4
Flexible modulation of hybrid feedback loops in competitive biological oscillators	4
Interpreting MALDI imaging data for rare types of ampullary cancer using machine learning	4
The art of modeling gene regulatory circuits	4
A proteome optimal allocation model for elucidating effects of temperature on bacterial growth	4
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	4
Bistability in type I toxin-antitoxin systems may lead to stress-induced persister formation	4
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	4
Network hypermotifs in biological systems: structure, dynamics, and functional implications	4
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	4
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	4
Gene regulatory network inference during cell fate decisions by perturbation strategies	4
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	4
Computational systems biology in disease modeling and control, review and perspectives	4