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 2021-09-01 to 2025-09-01.)

Article	Citations
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	60
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	58
Measuring criticality in control of complex biological networks	47
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	42
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	40
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	35
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	32
Leveraging public AI tools to explore systems biology resources in mathematical modeling	32
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	31
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	30
Olfactory receptors contribute to progression of kidney fibrosis	29
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	29
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	29
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	26
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	24
Modelling HIV-1 control and remission	23
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	21
Revisiting the evolution of bow-tie architecture in signaling networks	21
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	19
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	18
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	18
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	18
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	18
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	17
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	17

Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
Data-driven synthetic microbes for sustainable future	17
A mechanism for the emergence of low-dimensional structures in brain dynamics	17
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	16
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
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	15
Region-specific mean field models enhance simulations of local and global brain dynamics	15
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	14
Adaptive coding for DNA storage with high storage density and low coverage	14
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	14
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	14
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	13
A Python toolbox for neural circuit parameter inference	13
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	12
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	12
A robust ultrasensitive transcriptional switch in noisy cellular environments	12
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	12
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	12
An architecture for collaboration in systems biology at the age of the Metaverse	11
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	11
Design principles of improving the dose-response alignment in coupled GTPase switches	11
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	10
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	10
Computational gastronomy: capturing culinary creativity by making food computable	10
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	10
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	9
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	9
The modular biochemical reaction network structure of cellular translation	9
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	9
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	9
Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli	9
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	9
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	9
An integrated network representation of multiple cancer-specific data for graph-based machine learning	9
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	9
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	8
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism	8
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	8
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	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
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	8

Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
Representation and quantification of module activity from omics data with rROMA	7
NETISCE: a network-based tool for cell fate reprogramming	7
Flexible modeling of regulatory networks improves transcription factor activity estimation	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	7
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	7
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	7
A statistical framework for detecting therapy-induced resistance from drug screens	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
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	6
Quantitative systems-based prediction of antimicrobial resistance evolution	6
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	6
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	6
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	6
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	6
Next generation lineage tracing and its applications to unravel development	6
Data-driven energy landscape reveals critical genes in cancer progression	6
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	6
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	6
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	6
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	6
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	6
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	6
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	6
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	6
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	6
Immune digital twins for complex human pathologies: applications, limitations, and challenges	6
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	6
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	6
Nucleus pulposus cell network modelling in the intervertebral disc	6
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	6
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	6
Reliable interpretability of biology-inspired deep neural networks	6