npj Systems Biology and Applications

Article	Citations
Measuring criticality in control of complex biological networks	99
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	76
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	73
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	58
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	54
Leveraging public AI tools to explore systems biology resources in mathematical modeling	51
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	50
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	45
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	44
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	39
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data	39
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	36
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	34
Revisiting the evolution of bow-tie architecture in signaling networks	34
Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications	30
Data-driven universal insights into tumorigenesis via hallmark networks	30
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	29
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	29
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	27
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	27
Modelling HIV-1 control and remission	26
Data-driven synthetic microbes for sustainable future	25
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	25
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	25
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	25

Region-specific mean field models enhance simulations of local and global brain dynamics	24
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	23
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	23
Matters of life and death in computational cell biology	22
Enhancing yeast cell tracking with a time-symmetric deep learning approach	22
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression	22
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	21
Adaptive coding for DNA storage with high storage density and low coverage	20
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	20
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	20
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	20
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	19
A mechanism for the emergence of low-dimensional structures in brain dynamics	19
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	19
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	19
Spatiotemporal instability of influenza seasonality during viral co-circulation	19
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	19
SIMBA-GNN: mechanistic graph learning for microbiome prediction	18
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	18
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	18
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	18
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	17
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	17
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	17
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	16
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	16
LumbriCyc: towards metabolic modelling of earthworms	16
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	16
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	16
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	16
Manifold-based learning for high-throughput single-peanut phenotyping	15
A robust ultrasensitive transcriptional switch in noisy cellular environments	15
An architecture for collaboration in systems biology at the age of the Metaverse	15
Design principles of improving the dose-response alignment in coupled GTPase switches	15
Genetic basis of temporal variation in phenology in a woody perennial plant	15
Integrating AI, mechanistic modelling and network approaches in systems biology for translational research	15
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	15
A Python toolbox for neural circuit parameter inference	15
Learning patient-specific spatial biomarker dynamics via operator learning for Alzheimer’s disease progression	15
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	14
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	14
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	14
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	14
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	14
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	14
PYEAST – A Computational Toolkit for Saccharomyces cerevisiae Genetic Engineering	14
Development of a severe rat refeeding syndrome model and mathematical modeling of the associated hypophosphatemia	13
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	13
A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors	13
The modular biochemical reaction network structure of cellular translation	13

Computational gastronomy: capturing culinary creativity by making food computable	13
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	13
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	13
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	13
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	13
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	13
Design principles for robust multistability in coupled feedforward-feedback regulatory circuits	13
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	12
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	12
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	12
Decoding cellular population dynamics through mechanistic modelling and statistical data analysis	12
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	12
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	12
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	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	12
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	11
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	11
TrackRefiner a tool for refinement of bacillus cell tracking data	11
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	11
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	11
Genetic risk in Alzheimer’s disease	11
A statistical framework for detecting therapy-induced resistance from drug screens	11
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	10
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	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
Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype	10
Flexible modeling of regulatory networks improves transcription factor activity estimation	10
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
GO2Sum: generating human-readable functional summary of proteins from GO terms	9
Cross-platform metabolomics imputation using importance-weighted autoencoders	9
NETISCE: a network-based tool for cell fate reprogramming	9
A machine learning framework reveals key drivers of cytokine responses in a healthy human cohort	9
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	9
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	9
Machine learning estimation of FVIII pharmacokinetic parameters in Chinese children with severe Hemophilia A	9
Representation and quantification of module activity from omics data with rROMA	9
Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells	9
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	9
A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations	9
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	9
Optimal control theory as a method for designing multidrug adaptive therapy regimens	9
Metabolic gene expression-based stratification and prognostic risk predictive model of head and neck squamous cell carcinoma	8
Decoupling the chemical and physical origins of the seed spectral manifold in sorghum	8
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	8
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	8
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	8
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	8
Next generation lineage tracing and its applications to unravel development	8
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	8
Multi-omics integration reveals ANXA6-high γδ T cell–endothelial communication as a potential link between periodontitis and MASLD	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
Immune digital twins for complex human pathologies: applications, limitations, and challenges	8
Inferring relationships among major psychiatric disorders in a resting-state functional connectivity-informed embedding space	8
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	8
Publisher Correction: Rethinking medical education through systems biology to address complexity	8
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
Sometimes extracellular recordings fail for good reasons	8
Quantitative systems-based prediction of antimicrobial resistance evolution	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Author Correction: Enhancing randomized clinical trials with digital twins	8
Data-driven energy landscape reveals critical genes in cancer progression	8
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	7
Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases	7
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	7
Reliable interpretability of biology-inspired deep neural networks	7
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	7
Exploring CHO cell stability during prolonged passaging via eXplainable AI driven flux balance analysis	7
Open problems in synthetic multicellularity	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	7
Nucleus pulposus cell network modelling in the intervertebral disc	7
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	7
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	7
Revealing novel subtypes of synovial sarcoma through single cell transcriptomics	7
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	7

The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	7
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	7
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	7
Asthma-mediated control of optic glioma growth via T cell-microglia interactions: A mathematical model	7
Emergence of multiple collective motility modes in a physical model of cell chains	7
Global loss of metabolic responsiveness and elevated enzyme in leptin deficient obese mice during starvation	7
Supervised machine learning identifies impaired mitochondrial quality control in β-cells with development of type 2 diabetes	6
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	6
GraphTME: graph-based framework for predicting immunotherapy response by interpreting tumour microenvironment interactions using spatial transcriptomics	6
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	6
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	6
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	6
Minimally sufficient experimental design using identifiability analysis	6
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	6
MMP9 shapes cell mechanics to enable collective invasion in cancer	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
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	6
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data	6
Deterministic patterns in single-cell transcriptomic data	6
Single-trajectory Bayesian modeling reveals multi-state diffusion of the MSH sliding clamp	6
Simulation-based inference of cell migration dynamics in complex spatial environments	6
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	6
Data-driven modeling of amyloid-β targeted antibodies for Alzheimer’s disease	6
Loss of long-range co-expression is a common feature in cancer	6
Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC	6
Asking the right questions for mutagenicity prediction from BioMedical text	6
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	6
Effective dose window for containing tumor burden under tolerable level	6
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	6
From FAIR to CURE: guidelines for computational models of biological systems	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
Forum on immune digital twins: a meeting report	6
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	6
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	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
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	5
Multiscale modeling reveals synergy between CCL19 and PD-1 blockade in reshaping the TNBC microenvironment	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
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	5
When normalization induces correlation: shared and unstable references can create hidden dependencies	5
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
The p21 resilience network: a conceptual framework linking senescence to ferroptosis and cuproptosis resistance	5
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	5
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	5
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	5
Untargeted metabolomics reveals organism specific biomarkers of carbapenem resistance in Klebsiella pneumoniae and Escherichia coli	5
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	5
Path-based quantification of activation and repression in Boolean models using BooLEVARD	5
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
On the mechanisms of epidermal stemness and differentiation	5
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	4
Morphological entropy encodes cellular migration strategies on multiple length scales	4
Network hypermotifs in biological systems: structure, dynamics, and functional implications	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	4
Association-sensory spatiotemporal hierarchy and functional gradient-regularised recurrent neural network with implications for schizophrenia	4
Bistability in type I toxin-antitoxin systems may lead to stress-induced persister formation	4
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	4
Rethinking medical education through systems biology to address complexity	4
Author Correction: Amplitude response and singularity behavior of circadian clock to external stimuli	4
Gene regulatory network inference during cell fate decisions by perturbation strategies	4
A computational approach for perturbation-induced EMT transitions	4
GLUT1 production in cancer cells: a tragedy of the commons	4
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	4
Optimal dosing of anti-cancer treatment under drug-induced plasticity	4
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	4
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	4
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	4
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	4
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	4
Bringing evolutionary cancer therapy to the clinic: a systems approach	4
Interpreting MALDI imaging data for rare types of ampullary cancer using machine learning	4
Computational systems biology in disease modeling and control, review and perspectives	4
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	4
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	4
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	4
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	4
The art of modeling gene regulatory circuits	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
Multi-omics peripheral and core regions of cancer	4
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	3
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	3
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	3
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	3
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	3
Transomic analysis reveals DNA methylation and transcription factor roles in obese liver protein expression	3
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	3
Biomarker identification of triple negative breast cancer subtypes using machine learning	3
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	3