npj Systems Biology and Applications

Article	Citations
Loss formulations for assumption-free neural inference of SDE coefficient functions	68
Designing function-specific minimal microbiomes from large microbial communities	59
A possible path to persistent re-entry waves at the outlet of the left pulmonary vein	48
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis	39
Leveraging public AI tools to explore systems biology resources in mathematical modeling	38
Modeling critical dosing strategies for stromal-induced resistance to cancer therapy	38
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	35
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	33
Deterministic patterns in single-cell transcriptomic data	32
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	30
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	26
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	26
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	25
Effective dose window for containing tumor burden under tolerable level	24
Executable models of immune signaling pathways in HIV-associated atherosclerosis	23
Functional stratification of cancer drugs through integrated network similarity	21
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	21
Measuring criticality in control of complex biological networks	20
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	20
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	19
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	19
Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models	18
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties	17
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	17
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	15

An Allee-based distributed algorithm for microbial whole-cell sensors	15
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	15
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	15
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	14
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	13
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	13
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding	12
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	12
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	12
Network inference from perturbation time course data	11
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	11
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	11
Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images	10
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	10
Network topology and interaction logic determine states it supports	10
Operating principles of interconnected feedback loops driving cell fate transitions	10
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches	10
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	10
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	10
Olfactory receptors contribute to progression of kidney fibrosis	9
Cell morphology-based machine learning models for human cell state classification	9
A multiscale model of the regulation of aquaporin 2 recycling	9
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	9
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	9
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	9
An automated workflow for multi-omics screening of microbial model organisms	9
Nobel Turing Challenge: creating the engine for scientific discovery	9
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds	9
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	9
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	9
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	8
Flexible modeling of regulatory networks improves transcription factor activity estimation	8
NETISCE: a network-based tool for cell fate reprogramming	8
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	8
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	8
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	8
On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures	8
Predicting stress response and improved protein overproduction in Bacillus subtilis	8
Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian	7
Asking the right questions for mutagenicity prediction from BioMedical text	7
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	7
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	7
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	7
Representation and quantification of module activity from omics data with rROMA	7
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	7
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Recovering biomolecular network dynamics from single-cell omics data requires three time points	7
Revisiting the evolution of bow-tie architecture in signaling networks	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	6

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models	6
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	6
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	6
Modelling HIV-1 control and remission	6
Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	6
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	6
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	6
Computational modeling of DLBCL predicts response to BH3-mimetics	6
Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs	6
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	5
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment	5
Radiopharmaceutical transport in solid tumors via a 3-dimensional image-based spatiotemporal model	5
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control	5
Tipping-point transition from transient to persistent inflammation in pancreatic islets	5
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	5
A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins	5
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	5
T-cell commitment inheritance—an agent-based multi-scale model	5
Frequency-preference response in covalent modification cycles under substrate sequestration conditions	5
Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data	5
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	5
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	5
Quantitative systems-based prediction of antimicrobial resistance evolution	5
Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing	5
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	5
Cancer mutationscape: revealing the link between modular restructuring and intervention efficacy among mutations	5
Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations	4
Understanding and leveraging phenotypic plasticity during metastasis formation	4
Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling	4
Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model	4
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast	4
Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning	4
Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data	4
GO2Sum: generating human-readable functional summary of proteins from GO terms	4
Transient frequency preference responses in cell signaling systems	4
Quantifying in vitro B. anthracis growth and PA production and decay: a mathematical modelling approach	4
Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections	4
Assessing structural uncertainty of biochemical regulatory networks in metabolic pathways under varying data quality	4
Spatial interactions modulate tumor growth and immune infiltration	4
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	4
Machine learning approach for discrimination of genotypes based on bright-field cellular images	4
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	4
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	4
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	4
Characterizing heterogeneous single-cell dose responses computationally and experimentally using threshold inhibition surfaces and dose-titration assays	4
Systems immunology approaches to study T cells in health and disease	4
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	4
SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity	4
Immune digital twins for complex human pathologies: applications, limitations, and challenges	4
Reverse engineering morphogenesis through Bayesian optimization of physics-based models	4
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	4
Mitigating non-genetic resistance to checkpoint inhibition based on multiple states of immune exhaustion	3
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	3
Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer	3
Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER	3
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	3
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	3
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint	3
Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology	3
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	3
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	3
Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response	3
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	3
Peripheral gene interactions define interpretable clusters of core ASD genes in a network-based investigation of the omnigenic theory	3
Restoring circadian gene profiles in clock networks using synthetic feedback control	3
Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases	3
Constructing gene regulatory networks using epigenetic data	3
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	3
Canalization reduces the nonlinearity of regulation in biological networks	3
High-throughput metabolomics for the design and validation of a diauxic shift model	3
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	3
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	3
Adaptive coding for DNA storage with high storage density and low coverage	3
Enhancing yeast cell tracking with a time-symmetric deep learning approach	3
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	3
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	3
EpiScan: accurate high-throughput mapping of antibody-specific epitopes using sequence information	3
‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis	2
Data-driven energy landscape reveals critical genes in cancer progression	2

Automatic design of gene regulatory mechanisms for spatial pattern formation	2
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	2
An architecture for collaboration in systems biology at the age of the Metaverse	2
Dysregulated autoantibodies targeting AGTR1 are associated with the accumulation of COVID-19 symptoms	2
Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis	2
Optimal performance objectives in the highly conserved bone morphogenetic protein signaling pathway	2
Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source	2
Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections	2
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	2
A practically efficient algorithm for identifying critical control proteins in directed probabilistic biological networks	2
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	2
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	2
Emergence of cyclic hypoxia and the impact of PARP inhibitors on tumor progression	2
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	2
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	2
SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks	2
Nucleus pulposus cell network modelling in the intervertebral disc	2
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	2
Identifying biomarkers for treatment of uveal melanoma by T cell engager using a QSP model	2
Morphological entropy encodes cellular migration strategies on multiple length scales	2
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events	2
A deep learning framework for quantitative analysis of actin microridges	2
The small world coefficient 4.8 ± 1 optimizes information processing in 2D neuronal networks	2
Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD	2
MarkerMap: nonlinear marker selection for single-cell studies	2
Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy?	2
Integrated-omics analysis with explainable deep networks on pathobiology of infant bronchiolitis	2
Integrative systems biology framework discovers common gene regulatory signatures in mechanistically distinct inflammatory skin diseases	2
Crop-GPA: an integrated platform of crop gene-phenotype associations	2
Enhancing mass spectrometry imaging accessibility using convolutional autoencoders for deriving hypoxia-associated peptides from tumors	2