npj Systems Biology and Applications

Papers
(The TQCC of npj Systems Biology and Applications is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-12-01 to 2024-12-01.)
ArticleCitations
Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery69
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis53
Nobel Turing Challenge: creating the engine for scientific discovery49
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection35
Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining33
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis32
Adaptive coding for DNA storage with high storage density and low coverage31
High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures30
Cell morphology-based machine learning models for human cell state classification29
Computational systems biology in disease modeling and control, review and perspectives25
The in vitro micronucleus assay using imaging flow cytometry and deep learning24
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders23
Extending the landscape of omics technologies by pathomics23
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control21
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data19
Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape19
Predicted ‘wiring landscape’ of Ras-effector interactions in 29 human tissues19
Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism18
Constructing gene regulatory networks using epigenetic data18
Metabolic modeling of host–microbe interactions for therapeutics in colorectal cancer18
Optimal proteome allocation and the temperature dependence of microbial growth laws18
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling16
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects15
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy15
Leveraging network structure in nonlinear control15
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism15
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment15
The nonlinearity of regulation in biological networks14
Prediction of hemophilia A severity using a small-input machine-learning framework14
MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks13
Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box12
A dynamic multi-tissue model to study human metabolism12
Assessment of skin barrier function using skin images with topological data analysis12
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli12
GLUT1 production in cancer cells: a tragedy of the commons12
Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming12
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus12
Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods11
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network11
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps10
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy10
Employing active learning in the optimization of culture medium for mammalian cells9
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury9
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer9
LimeMap: a comprehensive map of lipid mediator metabolic pathways9
Automating parameter selection to avoid implausible biological pathway models9
NETISCE: a network-based tool for cell fate reprogramming9
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae9
Computational analysis of fused co-expression networks for the identification of candidate cancer gene biomarkers9
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study8
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease8
Mapping the dynamics of insulin-responsive pathways in the blood–brain barrier endothelium using time-series transcriptomics data8
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks8
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits8
Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells8
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway8
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds8
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells7
Network inference from perturbation time course data7
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 68037
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion7
Predicting stress response and improved protein overproduction in Bacillus subtilis7
A robust method for designing multistable systems by embedding bistable subsystems7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling7
Olfactory receptors contribute to progression of kidney fibrosis7
Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability7
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment6
Regulome-based characterization of drug activity across the human diseasome6
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective6
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders6
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment6
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures6
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding6
Efficient, cell-based simulations of cardiac electrophysiology; The Kirchhoff Network Model (KNM)5
The small world coefficient 4.8 ± 1 optimizes information processing in 2D neuronal networks5
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells5
Restoring circadian gene profiles in clock networks using synthetic feedback control5
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma5
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies5
Computational modeling of complex bioenergetic mechanisms that modulate CD4+ T cell effector and regulatory functions5
Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality5
Understanding repertoire sequencing data through a multiscale computational model of the germinal center5
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing5
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint5
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes5
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis5
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells5
Reliable interpretability of biology-inspired deep neural networks5
High-throughput metabolomics for the design and validation of a diauxic shift model5
Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE5
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy5
An integrated network representation of multiple cancer-specific data for graph-based machine learning5
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