OOIR: Observatory of International Research

Papers

(The median citation count of npj Systems Biology and Applications is 2. 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 2020-11-01 to 2024-11-01.)

Article	Citations
Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery	69
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	53
Nobel Turing Challenge: creating the engine for scientific discovery	47
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection	34
Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining	33
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	31
Adaptive coding for DNA storage with high storage density and low coverage	31
High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures	30
Cell morphology-based machine learning models for human cell state classification	29
Computational systems biology in disease modeling and control, review and perspectives	25
The in vitro micronucleus assay using imaging flow cytometry and deep learning	24
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders	23
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control	21
Application of physiologically based pharmacokinetic modeling for sertraline dosing recommendations in pregnancy	19
Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape	19
Predicted ‘wiring landscape’ of Ras-effector interactions in 29 human tissues	19
Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism	18
Constructing gene regulatory networks using epigenetic data	18
Metabolic modeling of host–microbe interactions for therapeutics in colorectal cancer	18
Optimal proteome allocation and the temperature dependence of microbial growth laws	18
Extending the landscape of omics technologies by pathomics	17
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling	16
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects	15
Mapping drug-target interactions and synergy in multi-molecular therapeutics for pressure-overload cardiac hypertrophy	15
Leveraging network structure in nonlinear control	15

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	15
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment	15
The nonlinearity of regulation in biological networks	14
Prediction of hemophilia A severity using a small-input machine-learning framework	14
Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data	13
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data	13
MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks	13
GLUT1 production in cancer cells: a tragedy of the commons	12
Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming	12
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus	12
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	12
A dynamic multi-tissue model to study human metabolism	12
Assessment of skin barrier function using skin images with topological data analysis	12
Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box	12
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	11
Prediction of degradation pathways of phenolic compounds in the human gut microbiota through enzyme promiscuity methods	11
Personalized modulation of coagulation factors using a thrombin dynamics model to treat trauma-induced coagulopathy	10
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps	10
Automating parameter selection to avoid implausible biological pathway models	9
Computational analysis of fused co-expression networks for the identification of candidate cancer gene biomarkers	9
Employing active learning in the optimization of culture medium for mammalian cells	9
Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae	9
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer	9
LimeMap: a comprehensive map of lipid mediator metabolic pathways	9
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	9
NETISCE: a network-based tool for cell fate reprogramming	9
Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells	8
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway	8
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds	8
Mapping the dynamics of insulin-responsive pathways in the blood–brain barrier endothelium using time-series transcriptomics data	8
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study	8
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease	8
Learning to encode cellular responses to systematic perturbations with deep generative models	8
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks	8
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	8
A robust method for designing multistable systems by embedding bistable subsystems	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
Network inference from perturbation time course data	7
Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability	7
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	7
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803	7
Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion	7
Predicting stress response and improved protein overproduction in Bacillus subtilis	7
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective	6
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures	6
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding	6
Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	6
Regulome-based characterization of drug activity across the human diseasome	6

SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment	6
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	6
Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality	5
Understanding repertoire sequencing data through a multiscale computational model of the germinal center	5
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint	5
Restoring circadian gene profiles in clock networks using synthetic feedback control	5
Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER	5
Olfactory receptors contribute to progression of kidney fibrosis	5
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	5
An integrated network representation of multiple cancer-specific data for graph-based machine learning	5
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 networks	5
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	5
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE	5
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	5
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	5
Reliable interpretability of biology-inspired deep neural networks	5
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	5
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	5
High-throughput metabolomics for the design and validation of a diauxic shift model	5
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	5
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	5
Computational modeling of complex bioenergetic mechanisms that modulate CD4+ T cell effector and regulatory functions	5
Diversity and molecular network patterns of symptom phenotypes	4
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME	4
Understanding and leveraging phenotypic plasticity during metastasis formation	4
Functional stratification of cancer drugs through integrated network similarity	4
The economy of chromosomal distances in bacterial gene regulation	4
A quantitative systems pharmacology model of the pathophysiology and treatment of COVID-19 predicts optimal timing of pharmacological interventions	4
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	4
Executable models of immune signaling pathways in HIV-associated atherosclerosis	4
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	4
Growth exponents reflect evolutionary processes and treatment response in brain metastases	4
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	4
Peripheral gene interactions define interpretable clusters of core ASD genes in a network-based investigation of the omnigenic theory	4
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	4
A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape	3
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	3
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	3
Reverse engineering morphogenesis through Bayesian optimization of physics-based models	3
Effective dose window for containing tumor burden under tolerable level	3
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	3
Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis	3
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	3
Design principles of improving the dose-response alignment in coupled GTPase switches	3
Computational modeling of DLBCL predicts response to BH3-mimetics	3
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	3
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm	3
A robust ultrasensitive transcriptional switch in noisy cellular environments	3
Argininosuccinate lyase is a metabolic vulnerability in breast development and cancer	3
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	3
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis	3
Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways	2
Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer	2
The Sherpa hypothesis: Phenotype-Preserving Disordered Proteins stabilize the phenotypes of neurons and oligodendrocytes	2
A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective	2
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	2
Frequency-preference response in covalent modification cycles under substrate sequestration conditions	2
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	2
Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	2
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	2
Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma	2
A multiscale chemical-mechanical model predicts impact of morphogen spreading on tissue growth	2
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	2
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	2
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	2
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	2
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	2
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models	2
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	2
Evaluation of single-sample network inference methods for precision oncology	2
Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder	2
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	2
‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis	2
Quantitative systems-based prediction of antimicrobial resistance evolution	2
Computational analysis of arrhythmogenesis in KCNH2 T618I mutation-associated short QT syndrome and the pharmacological effects of quinidine and sotalol	2
Machine learning approach for discrimination of genotypes based on bright-field cellular images	2
An automated workflow for multi-omics screening of microbial model organisms	2