npj Systems Biology and Applications

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	70
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	61
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	50
Measuring criticality in control of complex biological networks	41
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	39
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	38
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	36
Leveraging public AI tools to explore systems biology resources in mathematical modeling	34
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	34
Olfactory receptors contribute to progression of kidney fibrosis	32
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	30
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	28
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	27
Revisiting the evolution of bow-tie architecture in signaling networks	27
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	23
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	22
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	22
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	22
Modelling HIV-1 control and remission	21
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	21
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	20
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	20
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	17
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	17
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	15

Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	15
Adaptive coding for DNA storage with high storage density and low coverage	15
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	15
A mechanism for the emergence of low-dimensional structures in brain dynamics	15
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	15
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	15
Enhancing yeast cell tracking with a time-symmetric deep learning approach	14
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	13
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	12
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	12
An architecture for collaboration in systems biology at the age of the Metaverse	12
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	11
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	11
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	11
Computational gastronomy: capturing culinary creativity by making food computable	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	11
Design principles of improving the dose-response alignment in coupled GTPase switches	11
The modular biochemical reaction network structure of cellular translation	10
An integrated network representation of multiple cancer-specific data for graph-based machine learning	10
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	10
Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape	10
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	10
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	10
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	10
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	10
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	10
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	9
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	9
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	9
Cell morphology-based machine learning models for human cell state classification	8
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	8
Representation and quantification of module activity from omics data with rROMA	8
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	8
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	8
NETISCE: a network-based tool for cell fate reprogramming	8
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	7
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	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
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	7
Quantitative systems-based prediction of antimicrobial resistance evolution	7
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	6
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	5
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective	5
Reliable interpretability of biology-inspired deep neural networks	5
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	5
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	5
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	5
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	5
Nucleus pulposus cell network modelling in the intervertebral disc	5
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	5
Open problems in synthetic multicellularity	5
Forum on immune digital twins: a meeting report	5
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	5
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	5
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	5
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	5
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	5
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	5
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	5
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	5
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	4
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	4
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	4
Minimally sufficient experimental design using identifiability analysis	4
Tipping-point transition from transient to persistent inflammation in pancreatic islets	4
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	4
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	4
Asking the right questions for mutagenicity prediction from BioMedical text	4
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	4
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	4
Effective dose window for containing tumor burden under tolerable level	4
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection	4
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	4
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	4
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	4
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	4
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	4
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	4
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	4
Deterministic patterns in single-cell transcriptomic data	4
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	4
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	4
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	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
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
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	3
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	3
Author Correction: Amplitude response and singularity behavior of circadian clock to external stimuli	3
Gene regulatory network inference during cell fate decisions by perturbation strategies	3
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	3
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	3
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	3
The art of modeling gene regulatory circuits	3
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	3
The in vitro micronucleus assay using imaging flow cytometry and deep learning	3
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	3
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	3
Bifurcations in coupled amyloid-β aggregation-inflammation systems	3
Computational systems biology in disease modeling and control, review and perspectives	3
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	3
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	3
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	3
A robust method for designing multistable systems by embedding bistable subsystems	3

Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	3
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	3
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	3
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	3
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway	3
Multi-omics peripheral and core regions of cancer	3
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	3
Morphological entropy encodes cellular migration strategies on multiple length scales	3
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	3
GLUT1 production in cancer cells: a tragedy of the commons	3
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	3
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	3
An Allee-based distributed algorithm for microbial whole-cell sensors	3
Frequency-preference response in covalent modification cycles under substrate sequestration conditions	2
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	2
Recovering biomolecular network dynamics from single-cell omics data requires three time points	2
The Virtual Parkinsonian patient	2
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	2
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	2
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	2
Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines	2
Understanding and leveraging phenotypic plasticity during metastasis formation	2
Calibrating tumor growth and invasion parameters with spectral spatial analysis of cancer biopsy tissues	2
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	2
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	2
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	2
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	2
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	2
Loss formulations for assumption-free neural inference of SDE coefficient functions	2
Single cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures	2
Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer	2
A web portal for exploring kinase-substrate interactions	2
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	2
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	2
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	2
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	2
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	2
Network topology and interaction logic determine states it supports	2
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	2
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	2
Neutral evolution of rare cancer mutations in the computer and the clinic	2
Constructing gene regulatory networks using epigenetic data	2