OOIR: Observatory of International Research

Papers

(The median citation count of npj Systems Biology and Applications is 3. 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 2020-04-01 to 2024-04-01.)

Article	Citations
Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approach	68
Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery	64
Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modeling	61
ROS networks: designs, aging, Parkinson’s disease and precision therapies	53
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	45
Stratification and prediction of drug synergy based on target functional similarity	33
Nobel Turing Challenge: creating the engine for scientific discovery	32
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection	32
Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining	32
High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures	27
Adaptive coding for DNA storage with high storage density and low coverage	27
3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis	25
Cell morphology-based machine learning models for human cell state classification	25
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	23
Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data	22
Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts	19
Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer	19
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders	18
Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes	18
The in vitro micronucleus assay using imaging flow cytometry and deep learning	18
A global network for network medicine	18
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control	18
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media	17
Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape	17
Predicted ‘wiring landscape’ of Ras-effector interactions in 29 human tissues	17

Prostate cancer screening research can benefit from network medicine: an emerging awareness	16
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence	15
Metabolic modeling of host–microbe interactions for therapeutics in colorectal cancer	15
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	15
Optimal proteome allocation and the temperature dependence of microbial growth laws	14
Computational systems biology in disease modeling and control, review and perspectives	14
Application of physiologically based pharmacokinetic modeling for sertraline dosing recommendations in pregnancy	14
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy	13
Constructing gene regulatory networks using epigenetic data	13
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	12
Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data	12
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	11
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	11
Leveraging network structure in nonlinear control	10
A dynamic multi-tissue model to study human metabolism	10
GLUT1 production in cancer cells: a tragedy of the commons	10
Extending the landscape of omics technologies by pathomics	10
CODC: a Copula-based model to identify differential coexpression	10
Prediction of hemophilia A severity using a small-input machine-learning framework	10
MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks	10
Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box	9
Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming	9
Advice from a systems-biology model of the corona epidemics	9
The nonlinearity of regulation in biological networks	9
Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs	9
Temporal ordering of omics and multiomic events inferred from time-series data	9
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	9
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	9
Assessment of skin barrier function using skin images with topological data analysis	9
LimeMap: a comprehensive map of lipid mediator metabolic pathways	8
Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods	8
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	8
Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients	8
Automating parameter selection to avoid implausible biological pathway models	7
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	7
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	7
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	7
A robust method for designing multistable systems by embedding bistable subsystems	7
NETISCE: a network-based tool for cell fate reprogramming	7
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	7
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway	7
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment	7
Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism	6
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	6
Network inference from perturbation time course data	6
Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	6
Computational analysis of fused co-expression networks for the identification of candidate cancer gene biomarkers	6
Employing active learning in the optimization of culture medium for mammalian cells	6
Learning to encode cellular responses to systematic perturbations with deep generative models	6
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	6

Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability	5
Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER	5
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	5
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	5
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	5
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds	5
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study	5
SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	5
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease	5
Olfactory receptors contribute to progression of kidney fibrosis	4
Computational modeling of complex bioenergetic mechanisms that modulate CD4+ T cell effector and regulatory functions	4
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803	4
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective	4
Predicting stress response and improved protein overproduction in Bacillus subtilis	4
Genomic competition for noise reduction shaped evolutionary landscape of mir-4673	4
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	4
Regulome-based characterization of drug activity across the human diseasome	4
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	4
Restoring circadian gene profiles in clock networks using synthetic feedback control	4
Inferring clonal composition from multiple tumor biopsies	4
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	4
An integrated network representation of multiple cancer-specific data for graph-based machine learning	4
The small world coefficient 4.8 ± 1 optimizes information processing in 2D neuronal networks	4
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	4
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	3
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	3
A quantitative systems pharmacology model of the pathophysiology and treatment of COVID-19 predicts optimal timing of pharmacological interventions	3
Mapping the dynamics of insulin-responsive pathways in the blood–brain barrier endothelium using time-series transcriptomics data	3
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	3
Understanding repertoire sequencing data through a multiscale computational model of the germinal center	3
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	3
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	3
Executable models of immune signaling pathways in HIV-associated atherosclerosis	3
The economy of chromosomal distances in bacterial gene regulation	3
Growth exponents reflect evolutionary processes and treatment response in brain metastases	3
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	3
Design principles of improving the dose-response alignment in coupled GTPase switches	3
Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants	3
High-throughput metabolomics for the design and validation of a diauxic shift model	3
Functional stratification of cancer drugs through integrated network similarity	3
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding	3
Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis	3
Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells	3
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks	3
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	3
Multiomics data integration unveils core transcriptional regulatory networks governing cell-type identity	3