npj Systems Biology and Applications

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	57
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	56
Measuring criticality in control of complex biological networks	44
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	40
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	40
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	34
Olfactory receptors contribute to progression of kidney fibrosis	31
Leveraging public AI tools to explore systems biology resources in mathematical modeling	30
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	30
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	29
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	29
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	28
Revisiting the evolution of bow-tie architecture in signaling networks	26
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	24
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	24
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	23
Modelling HIV-1 control and remission	21
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	21
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	19
Data-driven synthetic microbes for sustainable future	18
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	18
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	17
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	17
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	17
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17

Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	16
Enhancing yeast cell tracking with a time-symmetric deep learning approach	16
A mechanism for the emergence of low-dimensional structures in brain dynamics	16
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	15
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	15
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	15
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	14
Region-specific mean field models enhance simulations of local and global brain dynamics	14
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	14
Adaptive coding for DNA storage with high storage density and low coverage	14
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	14
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	13
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	13
A Python toolbox for neural circuit parameter inference	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
A robust ultrasensitive transcriptional switch in noisy cellular environments	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	12
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	12
Design principles of improving the dose-response alignment in coupled GTPase switches	12
An architecture for collaboration in systems biology at the age of the Metaverse	12
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	11
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	11
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	11
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	10
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	10
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Computational gastronomy: capturing culinary creativity by making food computable	10
An integrated network representation of multiple cancer-specific data for graph-based machine learning	9
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	9
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	9
The modular biochemical reaction network structure of cellular translation	9
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	9
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	9
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	9
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	8
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	8
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	8
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	8
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8

A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	8
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	7
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	7
NETISCE: a network-based tool for cell fate reprogramming	7
Representation and quantification of module activity from omics data with rROMA	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	7
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	7
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	7
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
GO2Sum: generating human-readable functional summary of proteins from GO terms	6
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Nucleus pulposus cell network modelling in the intervertebral disc	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	6
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	6
Quantitative systems-based prediction of antimicrobial resistance evolution	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
Next generation lineage tracing and its applications to unravel development	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	6
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	6
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	6
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	6
Reliable interpretability of biology-inspired deep neural networks	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Deterministic patterns in single-cell transcriptomic data	5
Effective dose window for containing tumor burden under tolerable level	5
Open problems in synthetic multicellularity	5
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	5
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	5
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	5
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	5
Minimally sufficient experimental design using identifiability analysis	5
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	5
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	5
Forum on immune digital twins: a meeting report	5
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	5
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	5
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	5
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	5
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	5
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	5
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	5
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	5
Emergence of multiple collective motility modes in a physical model of cell chains	5
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	5
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	5
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	5
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	5
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway	4
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	4
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	4
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	4
Tipping-point transition from transient to persistent inflammation in pancreatic islets	4
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	4
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	4
Asking the right questions for mutagenicity prediction from BioMedical text	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
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	4
Morphological entropy encodes cellular migration strategies on multiple length scales	4
Computational systems biology in disease modeling and control, review and perspectives	4
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	4
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	4
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	4
Designing function-specific minimal microbiomes from large microbial communities	4
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	4
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	4
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	4

GLUT1 production in cancer cells: a tragedy of the commons	4
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	4
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	4
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	4
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	4
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	4
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	3
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	3
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	3
The art of modeling gene regulatory circuits	3
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	3
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	3
Network topology and interaction logic determine states it supports	3
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	3
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	3
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	3
Multi-omics peripheral and core regions of cancer	3
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	3
A robust method for designing multistable systems by embedding bistable subsystems	3
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	3
Bringing evolutionary cancer therapy to the clinic: a systems approach	3
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	3
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	3
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	3
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	3
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	3
Robust parameter estimation and identifiability analysis with hybrid neural ordinary differential equations in computational biology	2
Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing	2
Constructing gene regulatory networks using epigenetic data	2
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	2
Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer	2
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	2
Single cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures	2
An Allee-based distributed algorithm for microbial whole-cell sensors	2
Loss formulations for assumption-free neural inference of SDE coefficient functions	2
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	2
Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response	2
Calibrating tumor growth and invasion parameters with spectral spatial analysis of cancer biopsy tissues	2
Neutral evolution of rare cancer mutations in the computer and the clinic	2
Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines	2
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	2
A supervised machine learning approach with feature selection for sex-specific biomarker prediction	2
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	2
Frequency-preference response in covalent modification cycles under substrate sequestration conditions	2
Recovering biomolecular network dynamics from single-cell omics data requires three time points	2
The Virtual Parkinsonian patient	2
Deep exploration of logical models of cell differentiation in human preimplantation embryos	2
Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks	2
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	2
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	2
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks	2
A web portal for exploring kinase-substrate interactions	2
Understanding and leveraging phenotypic plasticity during metastasis formation	2
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	2
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	2
Dysregulated autoantibodies targeting AGTR1 are associated with the accumulation of COVID-19 symptoms	2
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	2
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	2
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	2
Evaluating PSA dynamics for predicting androgen deprivation failure with a patient specific prostate cancer model	2
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	2
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	2
Integrated-omics analysis with explainable deep networks on pathobiology of infant bronchiolitis	2
Identifying biomarkers for treatment of uveal melanoma by T cell engager using a QSP model	2