OOIR: Observatory of International Research

Papers

(The TQCC of npj Systems Biology and Applications is 6. 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 2021-05-01 to 2025-05-01.)

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	70
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	61
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	50
Measuring criticality in control of complex biological networks	41
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	39
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	38
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	36
Leveraging public AI tools to explore systems biology resources in mathematical modeling	34
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	34
Olfactory receptors contribute to progression of kidney fibrosis	32
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	30
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	28
Revisiting the evolution of bow-tie architecture in signaling networks	27
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	27
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	23
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	22
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	22
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	22
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	21
Modelling HIV-1 control and remission	21
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	20
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	20
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	17
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	17
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	15

Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	15
Adaptive coding for DNA storage with high storage density and low coverage	15
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	15
A mechanism for the emergence of low-dimensional structures in brain dynamics	15
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	15
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	15
Enhancing yeast cell tracking with a time-symmetric deep learning approach	14
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	13
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	12
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	12
An architecture for collaboration in systems biology at the age of the Metaverse	12
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	11
Computational gastronomy: capturing culinary creativity by making food computable	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	11
Design principles of improving the dose-response alignment in coupled GTPase switches	11
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	11
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	11
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	10
Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape	10
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	10
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	10
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	10
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	10
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	10
The modular biochemical reaction network structure of cellular translation	10
An integrated network representation of multiple cancer-specific data for graph-based machine learning	10
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	9
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	9
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	9
Cell morphology-based machine learning models for human cell state classification	8
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	8
Representation and quantification of module activity from omics data with rROMA	8
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	8
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	8
NETISCE: a network-based tool for cell fate reprogramming	8
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	7

Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	7
Quantitative systems-based prediction of antimicrobial resistance evolution	7
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	7
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	6
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6