npj Systems Biology and Applications

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	60
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	58
Measuring criticality in control of complex biological networks	47
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	42
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	40
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	35
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	32
Leveraging public AI tools to explore systems biology resources in mathematical modeling	32
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	31
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	30
Olfactory receptors contribute to progression of kidney fibrosis	29
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	29
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	29
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	26
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	24
Modelling HIV-1 control and remission	23
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	21
Revisiting the evolution of bow-tie architecture in signaling networks	21
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	19
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	18
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	18
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	18
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	18
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	17
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	17

Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
Data-driven synthetic microbes for sustainable future	17
A mechanism for the emergence of low-dimensional structures in brain dynamics	17
Enhancing yeast cell tracking with a time-symmetric deep learning approach	16
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	16
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
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	15
Region-specific mean field models enhance simulations of local and global brain dynamics	15
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	14
Adaptive coding for DNA storage with high storage density and low coverage	14
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	14
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	14
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
A Python toolbox for neural circuit parameter inference	13
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	12
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	12
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	12
An architecture for collaboration in systems biology at the age of the Metaverse	11
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	11
Design principles of improving the dose-response alignment in coupled GTPase switches	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	10
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	10
Computational gastronomy: capturing culinary creativity by making food computable	10
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	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
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	9
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	9
The modular biochemical reaction network structure of cellular translation	9
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	9
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	9
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	9
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	9
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	9
An integrated network representation of multiple cancer-specific data for graph-based machine learning	9
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	9
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	8
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	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
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	8

Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
A statistical framework for detecting therapy-induced resistance from drug screens	7
NETISCE: a network-based tool for cell fate reprogramming	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
Representation and quantification of module activity from omics data with rROMA	7
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	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
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	7
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	6
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	6
Nucleus pulposus cell network modelling in the intervertebral disc	6
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
Reliable interpretability of biology-inspired deep neural networks	6
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Quantitative systems-based prediction of antimicrobial resistance evolution	6
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	6
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	6
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
Next generation lineage tracing and its applications to unravel development	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	6
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	6
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	6
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	5
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	5
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	5
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	5
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	5
Designing function-specific minimal microbiomes from large microbial communities	5
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	5
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	5
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	5
Open problems in synthetic multicellularity	5
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	5
Minimally sufficient experimental design using identifiability analysis	5
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	5
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	5
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	5
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	5
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	5
Forum on immune digital twins: a meeting report	5
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	5
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	5
Deterministic patterns in single-cell transcriptomic data	5
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	5
Effective dose window for containing tumor burden under tolerable level	5
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	5
Emergence of multiple collective motility modes in a physical model of cell chains	5
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	4
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	4
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	4
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	4
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	4
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	4
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	4
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	4
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	4
Asking the right questions for mutagenicity prediction from BioMedical text	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

Gene regulatory network inference during cell fate decisions by perturbation strategies	4
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	4
Current state and open problems in universal differential equations for systems biology	4
Morphological entropy encodes cellular migration strategies on multiple length scales	4
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	4
Tipping-point transition from transient to persistent inflammation in pancreatic islets	4
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	4
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	4
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	4
Computational systems biology in disease modeling and control, review and perspectives	4
GLUT1 production in cancer cells: a tragedy of the commons	4
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	4
Author Correction: Amplitude response and singularity behavior of circadian clock to external stimuli	3
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	3
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	3
Optimal dosing of anti-cancer treatment under drug-induced plasticity	3
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	3
Multi-omics peripheral and core regions of cancer	3
Loss formulations for assumption-free neural inference of SDE coefficient functions	3
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	3
Bringing evolutionary cancer therapy to the clinic: a systems approach	3
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	3
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	3
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	3
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	3
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	3
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	3
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	3
A robust method for designing multistable systems by embedding bistable subsystems	3
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	3
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	3
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	3
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	3
The art of modeling gene regulatory circuits	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
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	3