npj Systems Biology and Applications

Article	Citations
Leveraging public AI tools to explore systems biology resources in mathematical modeling	75
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	68
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	48
Olfactory receptors contribute to progression of kidney fibrosis	47
Measuring criticality in control of complex biological networks	44
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	42
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	37
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	35
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	35
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	34
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	34
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	31
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	28
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	28
Modelling HIV-1 control and remission	27
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	26
Data-driven synthetic microbes for sustainable future	26
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	24
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	24
Revisiting the evolution of bow-tie architecture in signaling networks	23
Data-driven universal insights into tumorigenesis via hallmark networks	23
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	22
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	22
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	22
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	22

Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	21
Enhancing yeast cell tracking with a time-symmetric deep learning approach	21
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	20
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	19
A mechanism for the emergence of low-dimensional structures in brain dynamics	19
Adaptive coding for DNA storage with high storage density and low coverage	19
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	18
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	17
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	17
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	17
SIMBA-GNN: mechanistic graph learning for microbiome prediction	16
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	16
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	15
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	15
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	15
Region-specific mean field models enhance simulations of local and global brain dynamics	15
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	15
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	14
A Python toolbox for neural circuit parameter inference	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	13
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	13
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	13
Design principles of improving the dose-response alignment in coupled GTPase switches	13
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	13
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	12
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	12
An architecture for collaboration in systems biology at the age of the Metaverse	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	12
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	12
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	12
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	12
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	11
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	11
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	11
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	11
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	11
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	10
An integrated network representation of multiple cancer-specific data for graph-based machine learning	10
Computational gastronomy: capturing culinary creativity by making food computable	10
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	10
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	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
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	10
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	10
The modular biochemical reaction network structure of cellular translation	9
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	9

TrackRefiner a tool for refinement of bacillus cell tracking data	9
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	9
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	9
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	9
A statistical framework for detecting therapy-induced resistance from drug screens	9
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	9
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	9
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	8
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	8
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	8
Representation and quantification of module activity from omics data with rROMA	8
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	8
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	8
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
NETISCE: a network-based tool for cell fate reprogramming	8
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	8
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	8
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	8
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	8
Flexible modeling of regulatory networks improves transcription factor activity estimation	8
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	8
Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data	8
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	8
GO2Sum: generating human-readable functional summary of proteins from GO terms	8
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	7
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	7
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	7
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	7
Next generation lineage tracing and its applications to unravel development	7
Quantitative systems-based prediction of antimicrobial resistance evolution	7
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	7
Reliable interpretability of biology-inspired deep neural networks	7
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	7
Forum on immune digital twins: a meeting report	7
Emergence of multiple collective motility modes in a physical model of cell chains	7
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	7
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	7
Author Correction: Enhancing randomized clinical trials with digital twins	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	7
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	7
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	7
Nucleus pulposus cell network modelling in the intervertebral disc	7
Open problems in synthetic multicellularity	7
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	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
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	7
Data-driven energy landscape reveals critical genes in cancer progression	7
Immune digital twins for complex human pathologies: applications, limitations, and challenges	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
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	7
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	7
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	6
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	6
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	6
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	6
Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC	6
Deterministic patterns in single-cell transcriptomic data	6
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	6
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	6
Asking the right questions for mutagenicity prediction from BioMedical text	6
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	6
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	6
Minimally sufficient experimental design using identifiability analysis	6
Designing function-specific minimal microbiomes from large microbial communities	6
Data-driven modeling of amyloid-β targeted antibodies for Alzheimer’s disease	6
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	6
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	6
Effective dose window for containing tumor burden under tolerable level	6
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	6
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	6
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	6
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5

Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	5
On the mechanisms of epidermal stemness and differentiation	5
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	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
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	5
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	5
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	5
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	5
GLUT1 production in cancer cells: a tragedy of the commons	5
Bringing evolutionary cancer therapy to the clinic: a systems approach	5
Computational systems biology in disease modeling and control, review and perspectives	5
Path-based quantification of activation and repression in Boolean models using BooLEVARD	5
Current state and open problems in universal differential equations for systems biology	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	5
A computational approach for perturbation-induced EMT transitions	5
Multi-omics peripheral and core regions of cancer	5
Morphological entropy encodes cellular migration strategies on multiple length scales	5
The art of modeling gene regulatory circuits	4
A robust method for designing multistable systems by embedding bistable subsystems	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	4
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	4
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	4
Bistability in type I toxin-antitoxin systems may lead to stress-induced persister formation	4
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	4
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	4
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	4
Optimal dosing of anti-cancer treatment under drug-induced plasticity	4
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	4
Gene regulatory network inference during cell fate decisions by perturbation strategies	4
Flexible modulation of hybrid feedback loops in competitive biological oscillators	4
Evaluating PSA dynamics for predicting androgen deprivation failure with a patient specific prostate cancer model	4
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	4
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	4
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	4
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	4
Author Correction: Amplitude response and singularity behavior of circadian clock to external stimuli	4
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	4
Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming	4
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	4
Deep exploration of logical models of cell differentiation in human preimplantation embryos	4
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	4
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	3
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	3
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	3
Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing	3
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	3
Network topology and interaction logic determine states it supports	3
A strategic approach to multi-omics literature retrieval in next generation mammalian cell bioprocessing	3
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	3
Integrated-omics analysis with explainable deep networks on pathobiology of infant bronchiolitis	3
Dynamical analysis of a model of BCL-2-dependent cellular decision making	3
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	3
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	3
An Allee-based distributed algorithm for microbial whole-cell sensors	3
Understanding and leveraging phenotypic plasticity during metastasis formation	3
Transomic analysis reveals DNA methylation and transcription factor roles in obese liver protein expression	3
The Virtual Parkinsonian patient	3
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	3
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	3
Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks	3
Identifying biomarkers for treatment of uveal melanoma by T cell engager using a QSP model	3
Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines	3
A supervised machine learning approach with feature selection for sex-specific biomarker prediction	3
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	3
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	3
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	3
Recovering biomolecular network dynamics from single-cell omics data requires three time points	3
Loss formulations for assumption-free neural inference of SDE coefficient functions	3
Single cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures	3
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	3
Predicting treatment-free remission in chronic myeloid leukemia patients using an integrated model of tumor-immune dynamics	3
Dysregulated autoantibodies targeting AGTR1 are associated with the accumulation of COVID-19 symptoms	3
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	3
Neutral evolution of rare cancer mutations in the computer and the clinic	3