OOIR: Observatory of International Research

Papers

(The TQCC of npj Systems Biology and Applications is 8. 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
Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining	32
Nobel Turing Challenge: creating the engine for scientific discovery	32
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection	32
Adaptive coding for DNA storage with high storage density and low coverage	27
High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures	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
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	15
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
Application of physiologically based pharmacokinetic modeling for sertraline dosing recommendations in pregnancy	14
Optimal proteome allocation and the temperature dependence of microbial growth laws	14
Computational systems biology in disease modeling and control, review and perspectives	14
Constructing gene regulatory networks using epigenetic data	13
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy	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
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	11
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	11
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
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
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