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 2021-08-01 to 2025-08-01.)

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	57
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	56
Measuring criticality in control of complex biological networks	44
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	40
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	40
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	34
Olfactory receptors contribute to progression of kidney fibrosis	31
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	30
Leveraging public AI tools to explore systems biology resources in mathematical modeling	30
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	29
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	29
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	28
Revisiting the evolution of bow-tie architecture in signaling networks	26
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	24
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	24
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	23
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	21
Modelling HIV-1 control and remission	21
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	19
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	18
Data-driven synthetic microbes for sustainable future	18
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	17
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	17
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	17

A mechanism for the emergence of low-dimensional structures in brain dynamics	16
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	16
Enhancing yeast cell tracking with a time-symmetric deep learning approach	16
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	15
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	15
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	15
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	14
Region-specific mean field models enhance simulations of local and global brain dynamics	14
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	14
Adaptive coding for DNA storage with high storage density and low coverage	14
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	14
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
A robust ultrasensitive transcriptional switch in noisy cellular environments	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	13
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	13
A Python toolbox for neural circuit parameter inference	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	13
An architecture for collaboration in systems biology at the age of the Metaverse	12
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	12
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	12
Design principles of improving the dose-response alignment in coupled GTPase switches	12
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	11
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	11
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	11
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Computational gastronomy: capturing culinary creativity by making food computable	10
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	10
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	10
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	10
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	9
An integrated network representation of multiple cancer-specific data for graph-based machine learning	9
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	9
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	9
The modular biochemical reaction network structure of cellular translation	9
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	9
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	9
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	8
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	8
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	8
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	8

Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	8
Representation and quantification of module activity from omics data with rROMA	7
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	7
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	7
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	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
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	7
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	7
NETISCE: a network-based tool for cell fate reprogramming	7
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	6
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	6
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	6
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	6
Reliable interpretability of biology-inspired deep neural networks	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
GO2Sum: generating human-readable functional summary of proteins from GO terms	6
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Nucleus pulposus cell network modelling in the intervertebral disc	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	6
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	6
Quantitative systems-based prediction of antimicrobial resistance evolution	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
Next generation lineage tracing and its applications to unravel development	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6