npj Systems Biology and Applications

Article	Citations
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	53
Network inference from perturbation time course data	49
An Allee-based distributed algorithm for microbial whole-cell sensors	35
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	32
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	31
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	30
Functional stratification of cancer drugs through integrated network similarity	25
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	24
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches	23
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	21
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	19
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding	19
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	19
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds	18
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	18
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	18
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	18
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	16
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	15
Executable models of immune signaling pathways in HIV-associated atherosclerosis	15
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis	15
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	15
Cell morphology-based machine learning models for human cell state classification	15
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	14
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	14

Network topology and interaction logic determine states it supports	13
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties	12
Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models	12
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	12
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	12
A possible path to persistent re-entry waves at the outlet of the left pulmonary vein	12
Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images	11
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	11
Designing function-specific minimal microbiomes from large microbial communities	10
Effective dose window for containing tumor burden under tolerable level	10
Operating principles of interconnected feedback loops driving cell fate transitions	9
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy	9
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	9
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	9
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	9
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	9
Measuring criticality in control of complex biological networks	9
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	8
A multiscale model of the regulation of aquaporin 2 recycling	8
Nobel Turing Challenge: creating the engine for scientific discovery	8
Olfactory receptors contribute to progression of kidney fibrosis	8
Deterministic patterns in single-cell transcriptomic data	8
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	8
Recovering biomolecular network dynamics from single-cell omics data requires three time points	7
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	7
Asking the right questions for mutagenicity prediction from BioMedical text	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	7
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	7
Predicting stress response and improved protein overproduction in Bacillus subtilis	7
An automated workflow for multi-omics screening of microbial model organisms	7
Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing	7
Publisher Correction: LimeMap: a comprehensive map of lipid mediator metabolic pathways	7
NETISCE: a network-based tool for cell fate reprogramming	6
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	6
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease	6
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control	6
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models	6
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	6
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	6
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	6
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	5
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	5
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	5
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	5
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment	5
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	5
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	5
Modelling HIV-1 control and remission	5
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	5

Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	5
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	5
Representation and quantification of module activity from omics data with rROMA	5
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	5
Revisiting the evolution of bow-tie architecture in signaling networks	5
Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs	5
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	5
Flexible modeling of regulatory networks improves transcription factor activity estimation	5
Computational modeling of DLBCL predicts response to BH3-mimetics	5
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	5
Adaptive coding for DNA storage with high storage density and low coverage	4
Tipping-point transition from transient to persistent inflammation in pancreatic islets	4
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	4
On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures	4
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	4
T-cell commitment inheritance—an agent-based multi-scale model	4
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	4
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	4
Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	4
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint	4
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	4
Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian	4
A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins	4
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	3
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	3
Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response	3
Predicted ‘wiring landscape’ of Ras-effector interactions in 29 human tissues	3
Frequency-preference response in covalent modification cycles under substrate sequestration conditions	3
Restoring circadian gene profiles in clock networks using synthetic feedback control	3
Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER	3
Crop-GPA: an integrated platform of crop gene-phenotype associations	3
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	3
GO2Sum: generating human-readable functional summary of proteins from GO terms	3
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	3
Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning	3
Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data	3
Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases	3
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	3
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	3
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	3
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	2
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	2
Peripheral gene interactions define interpretable clusters of core ASD genes in a network-based investigation of the omnigenic theory	2
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	2
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	2
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	2
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	2
Transient frequency preference responses in cell signaling systems	2
Assessing structural uncertainty of biochemical regulatory networks in metabolic pathways under varying data quality	2
Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD	2
Machine learning approach for discrimination of genotypes based on bright-field cellular images	2
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	2
Reverse engineering morphogenesis through Bayesian optimization of physics-based models	2
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	2
Immune digital twins for complex human pathologies: applications, limitations, and challenges	2
Understanding and leveraging phenotypic plasticity during metastasis formation	2
Canalization reduces the nonlinearity of regulation in biological networks	2
Quantitative systems-based prediction of antimicrobial resistance evolution	2
Optimal proteome allocation and the temperature dependence of microbial growth laws	2
Quantifying in vitro B. anthracis growth and PA production and decay: a mathematical modelling approach	2
Systems immunology approaches to study T cells in health and disease	2
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	2
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	2
Emergence of cyclic hypoxia and the impact of PARP inhibitors on tumor progression	2
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	2
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	2
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	2
High-throughput metabolomics for the design and validation of a diauxic shift model	2
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	1
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	1
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	1
Understanding repertoire sequencing data through a multiscale computational model of the germinal center	1
A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective	1
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	1
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	1
Enhancing mass spectrometry imaging accessibility using convolutional autoencoders for deriving hypoxia-associated peptides from tumors	1
Data-driven energy landscape reveals critical genes in cancer progression	1
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	1
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	1

Computational systems biology in disease modeling and control, review and perspectives	1
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway	1
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	1
Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer	1
Constructing gene regulatory networks using epigenetic data	1
Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model	1
An architecture for collaboration in systems biology at the age of the Metaverse	1
SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks	1
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	1
Integrated-omics analysis with explainable deep networks on pathobiology of infant bronchiolitis	1
Mitigating non-genetic resistance to checkpoint inhibition based on multiple states of immune exhaustion	1
Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines	1
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	1
Morphological entropy encodes cellular migration strategies on multiple length scales	1
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	1
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	1
Spatial interactions modulate tumor growth and immune infiltration	1
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	1
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	1
Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections	1
Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation	1
Design principles of improving the dose-response alignment in coupled GTPase switches	1
The small world coefficient 4.8 ± 1 optimizes information processing in 2D neuronal networks	1
Decoding the principle of cell-fate determination for its reverse control	1
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective	1
‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis	1
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	1