npj Systems Biology and Applications

Article	Citations
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	95
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	75
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	64
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data	57
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	53
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	49
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	48
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	45
Measuring criticality in control of complex biological networks	42
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	38
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	37
Leveraging public AI tools to explore systems biology resources in mathematical modeling	34
Revisiting the evolution of bow-tie architecture in signaling networks	33
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	31
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	29
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	28
Data-driven universal insights into tumorigenesis via hallmark networks	28
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	27
Data-driven synthetic microbes for sustainable future	27
Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications	26
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	26
Modelling HIV-1 control and remission	25
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	25
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	25
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	24

Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	23
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	22
Region-specific mean field models enhance simulations of local and global brain dynamics	22
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	21
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	20
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	20
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	20
Adaptive coding for DNA storage with high storage density and low coverage	19
SIMBA-GNN: mechanistic graph learning for microbiome prediction	19
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	19
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	19
Enhancing yeast cell tracking with a time-symmetric deep learning approach	18
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression	18
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	18
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	17
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
Matters of life and death in computational cell biology	17
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	17
A mechanism for the emergence of low-dimensional structures in brain dynamics	16
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	16
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	16
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	16
A Python toolbox for neural circuit parameter inference	16
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	16
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	16
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	15
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	15
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	15
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	15
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	15
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	15
Design principles of improving the dose-response alignment in coupled GTPase switches	15
LumbriCyc: towards metabolic modelling of earthworms	15
A robust ultrasensitive transcriptional switch in noisy cellular environments	15
Manifold-based learning for high-throughput single-peanut phenotyping	14
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	14
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	14
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	14
Integrating AI, mechanistic modelling and network approaches in systems biology for translational research	14
An architecture for collaboration in systems biology at the age of the Metaverse	14
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	14
Computational gastronomy: capturing culinary creativity by making food computable	13
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	13
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	13
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	13
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	13
PYEAST – A Computational Toolkit for Saccharomyces cerevisiae Genetic Engineering	13
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	13
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	12
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	12

Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	12
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	12
A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors	12
Development of a severe rat refeeding syndrome model and mathematical modeling of the associated hypophosphatemia	12
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	12
The modular biochemical reaction network structure of cellular translation	12
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	11
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	11
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	11
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	11
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	11
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	11
Publisher Correction: Mammalian synthetic gene circuits for biopharmaceutical development & manufacture	11
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	11
Genetic risk in Alzheimer’s disease	10
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	10
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	10
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	10
TrackRefiner a tool for refinement of bacillus cell tracking data	10
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	10
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	10
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	10
A statistical framework for detecting therapy-induced resistance from drug screens	10
Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data	10
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	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
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	9
Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells	9
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	9
Representation and quantification of module activity from omics data with rROMA	9
Machine learning estimation of FVIII pharmacokinetic parameters in Chinese children with severe Hemophilia A	9
Flexible modeling of regulatory networks improves transcription factor activity estimation	9
Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype	9
Cross-platform metabolomics imputation using importance-weighted autoencoders	9
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	9
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	9
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	9
Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells	9
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	9
Liver progenitor cells perform wound healing in a scratch assay by concerted bistable circuits	8
GO2Sum: generating human-readable functional summary of proteins from GO terms	8
Immune digital twins for complex human pathologies: applications, limitations, and challenges	8
Quantitative systems-based prediction of antimicrobial resistance evolution	8
Nucleus pulposus cell network modelling in the intervertebral disc	8
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	8
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	8
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	8
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	8
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	8
Inferring relationships among major psychiatric disorders in a resting-state functional connectivity-informed embedding space	8
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	8
Multi-omics integration reveals ANXA6-high γδ T cell–endothelial communication as a potential link between periodontitis and MASLD	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	8
Publisher Correction: Rethinking medical education through systems biology to address complexity	8
Author Correction: Enhancing randomized clinical trials with digital twins	8
Data-driven energy landscape reveals critical genes in cancer progression	7
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	7
Reliable interpretability of biology-inspired deep neural networks	7
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	7
Emergence of multiple collective motility modes in a physical model of cell chains	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
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	7
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	7
Next generation lineage tracing and its applications to unravel development	7
Forum on immune digital twins: a meeting report	7
Exploring CHO cell stability during prolonged passaging via eXplainable AI driven flux balance analysis	7
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	7
Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases	7
Asthma-mediated control of optic glioma growth via T cell-microglia interactions: A mathematical model	7
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	7
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	7
Global loss of metabolic responsiveness and elevated enzyme in leptin deficient obese mice during starvation	7

Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	6
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	6
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	6
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	6
Open problems in synthetic multicellularity	6
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	6
Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC	6
Loss of long-range co-expression is a common feature in cancer	6
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	6
Deterministic patterns in single-cell transcriptomic data	6
Designing function-specific minimal microbiomes from large microbial communities	6
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	6
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	6
From FAIR to CURE: guidelines for computational models of biological systems	6
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	6
Neuronal and glial networks interact with traumatic brain injury to modulate cognition in ABCD study	6
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	6
Effective dose window for containing tumor burden under tolerable level	6
SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data	6
Data-driven modeling of amyloid-β targeted antibodies for Alzheimer’s disease	6
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models	6
Revealing novel subtypes of synovial sarcoma through single cell transcriptomics	6
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	6
Simulation-based inference of cell migration dynamics in complex spatial environments	6
Minimally sufficient experimental design using identifiability analysis	6
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	5
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	5
A computational approach for perturbation-induced EMT transitions	5
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	5
On the mechanisms of epidermal stemness and differentiation	5
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	5
Single-trajectory Bayesian modeling reveals multi-state diffusion of the MSH sliding clamp	5
Asking the right questions for mutagenicity prediction from BioMedical text	5
Multiscale modeling reveals synergy between CCL19 and PD-1 blockade in reshaping the TNBC microenvironment	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
Computational systems biology in disease modeling and control, review and perspectives	5
GLUT1 production in cancer cells: a tragedy of the commons	5
When normalization induces correlation: shared and unstable references can create hidden dependencies	5
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	5
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	5
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	5
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Path-based quantification of activation and repression in Boolean models using BooLEVARD	5
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	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
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	5
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	5
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	5
Multi-omics peripheral and core regions of cancer	4
Morphological entropy encodes cellular migration strategies on multiple length scales	4
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	4
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	4
A proteome optimal allocation model for elucidating effects of temperature on bacterial growth	4
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	4
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	4
Network hypermotifs in biological systems: structure, dynamics, and functional implications	4
The art of modeling gene regulatory circuits	4
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	4
The p21 resilience network: a conceptual framework linking senescence to ferroptosis and cuproptosis resistance	4
Bringing evolutionary cancer therapy to the clinic: a systems approach	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
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	4
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	4
Optimal dosing of anti-cancer treatment under drug-induced plasticity	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
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	4
Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming	4
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	4
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	4
Flexible modulation of hybrid feedback loops in competitive biological oscillators	4
Rethinking medical education through systems biology to address complexity	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
An Allee-based distributed algorithm for microbial whole-cell sensors	3
A supervised machine learning approach with feature selection for sex-specific biomarker prediction	3
Biomarker identification of triple negative breast cancer subtypes using machine learning	3
Understanding and leveraging phenotypic plasticity during metastasis formation	3
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	3
Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing	3
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	3
Dynamical analysis of a model of BCL-2-dependent cellular decision making	3
Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks	3
Delaying cancer progression by integrating toxicity constraints in a model of adaptive therapy	3
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	3
Recovering biomolecular network dynamics from single-cell omics data requires three time points	3
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	3
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	3
The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease	3
Transomic analysis reveals DNA methylation and transcription factor roles in obese liver protein expression	3
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	3