npj Systems Biology and Applications

Article	Citations
Measuring criticality in control of complex biological networks	63
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	60
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	51
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	44
Olfactory receptors contribute to progression of kidney fibrosis	43
Leveraging public AI tools to explore systems biology resources in mathematical modeling	41
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	38
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	34
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	33
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	33
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	32
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	31
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	31
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	29
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	29
Modelling HIV-1 control and remission	25
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	24
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	23
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	23
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	23
Revisiting the evolution of bow-tie architecture in signaling networks	22
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	22
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	21
A mechanism for the emergence of low-dimensional structures in brain dynamics	21
Data-driven synthetic microbes for sustainable future	21

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	21
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	21
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	20
Enhancing yeast cell tracking with a time-symmetric deep learning approach	18
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	17
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	17
Region-specific mean field models enhance simulations of local and global brain dynamics	17
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	17
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	17
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	16
Adaptive coding for DNA storage with high storage density and low coverage	16
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	15
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	15
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	15
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	15
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	15
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	14
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	14
An architecture for collaboration in systems biology at the age of the Metaverse	14
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	14
A Python toolbox for neural circuit parameter inference	14
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	13
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	13
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	12
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	12
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	12
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	12
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	12
Design principles of improving the dose-response alignment in coupled GTPase switches	12
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	12
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	11
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	11
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	11
Computational gastronomy: capturing culinary creativity by making food computable	11
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
The modular biochemical reaction network structure of cellular translation	10
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	10
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	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
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	9
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	9
A statistical framework for detecting therapy-induced resistance from drug screens	9
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	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	9

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	9
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	9
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	8
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	8
Representation and quantification of module activity from omics data with rROMA	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8
NETISCE: a network-based tool for cell fate reprogramming	8
Flexible modeling of regulatory networks improves transcription factor activity estimation	8
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	8
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	7
Next generation lineage tracing and its applications to unravel development	7
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	7
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	7
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	7
Immune digital twins for complex human pathologies: applications, limitations, and challenges	7
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	7
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	7
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	7
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	7
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	7
Quantitative systems-based prediction of antimicrobial resistance evolution	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	6
Minimally sufficient experimental design using identifiability analysis	6
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	6
Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer	6
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	6
Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series	6
Drug repositioning for immunotherapy in breast cancer using single-cell analysis	6
Reliable interpretability of biology-inspired deep neural networks	6
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	6
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data	6
Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC	6
Ecological disruptive selection acting on quantitative loci can drive sympatric speciation	6
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
Nucleus pulposus cell network modelling in the intervertebral disc	6
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	6
Emergence of multiple collective motility modes in a physical model of cell chains	6
Forum on immune digital twins: a meeting report	6
Author Correction: Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	6
Open problems in synthetic multicellularity	6
MMP9 shapes cell mechanics to enable collective invasion in cancer	6
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	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
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	5
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5
On the mechanisms of epidermal stemness and differentiation	5
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	5
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	5
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	5
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	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
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
Generalized linear modeling of flow cytometry data to analyze immune responses in tuberculosis vaccine research	5
Estimating treatment sensitivity in synthetic and in vitro tumors using a random differential equation model	5
Asking the right questions for mutagenicity prediction from BioMedical text	5
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	5
Designing function-specific minimal microbiomes from large microbial communities	5

Deterministic patterns in single-cell transcriptomic data	5
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	5
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	5
Current state and open problems in universal differential equations for systems biology	5
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	5
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	5
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	5
Computational systems biology in disease modeling and control, review and perspectives	4
Morphological entropy encodes cellular migration strategies on multiple length scales	4
Gene regulatory network inference during cell fate decisions by perturbation strategies	4
A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer	4
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	4
interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors	4
Multi-omics peripheral and core regions of cancer	4
GLUT1 production in cancer cells: a tragedy of the commons	4
Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida	4
Bifurcations in coupled amyloid-β aggregation-inflammation systems	4
A robust method for designing multistable systems by embedding bistable subsystems	4
Changes in epistatic green-beard alleles induce domain shift in hypostatic rock-paper-scissors-like green-beard competition	4
Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming	4
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	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
Optimal dosing of anti-cancer treatment under drug-induced plasticity	4
The art of modeling gene regulatory circuits	4
Self-consistent signal transduction analysis for modeling context-specific signaling cascades and perturbations	4
Author Correction: Amplitude response and singularity behavior of circadian clock to external stimuli	4
Bringing evolutionary cancer therapy to the clinic: a systems approach	4
Integration of single sample and population analysis for understanding immune evasion mechanisms of lung cancer	3
Breast cancer is detectable from peripheral blood using machine learning over T cell receptor repertoires	3
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	3
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	3
Constructing gene regulatory networks using epigenetic data	3
Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks	3
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	3
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	3
Predicting treatment-free remission in chronic myeloid leukemia patients using an integrated model of tumor-immune dynamics	3
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	3
Deep exploration of logical models of cell differentiation in human preimplantation embryos	3
Inertial effect of cell state velocity on the quiescence-proliferation fate decision	3
Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells	3
Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors	3
An Allee-based distributed algorithm for microbial whole-cell sensors	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
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	3
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	3
Single cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures	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
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	3
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	3
Understanding flux switching in metabolic networks through an analysis of synthetic lethals	3
Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming	3
Network topology and interaction logic determine states it supports	3
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	3
A supervised machine learning approach with feature selection for sex-specific biomarker prediction	3
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	3
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	3
Recovering biomolecular network dynamics from single-cell omics data requires three time points	3
The Virtual Parkinsonian patient	3
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	3
Loss formulations for assumption-free neural inference of SDE coefficient functions	3
Evaluating PSA dynamics for predicting androgen deprivation failure with a patient specific prostate cancer model	3