OOIR: Observatory of International Research

Papers

(The TQCC of npj Systems Biology and Applications is 7. 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 2021-12-01 to 2025-12-01.)

Article	Citations
Measuring criticality in control of complex biological networks	70
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	64
Leveraging public AI tools to explore systems biology resources in mathematical modeling	53
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	46
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	45
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	41
Olfactory receptors contribute to progression of kidney fibrosis	41
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	36
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	35
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	34
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	34
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	31
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	31
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	31
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	29
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	26
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	26
Data-driven universal insights into tumorigenesis via hallmark networks	25
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	24
Revisiting the evolution of bow-tie architecture in signaling networks	24
Modelling HIV-1 control and remission	23
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	23
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	23
Data-driven synthetic microbes for sustainable future	23
Enhancing yeast cell tracking with a time-symmetric deep learning approach	22

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	22
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	21
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	21
A mechanism for the emergence of low-dimensional structures in brain dynamics	19
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	19
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	19
Adaptive coding for DNA storage with high storage density and low coverage	19
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	18
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	18
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	18
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	17
Region-specific mean field models enhance simulations of local and global brain dynamics	16
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	16
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	15
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	15
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	15
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	15
A Python toolbox for neural circuit parameter inference	15
A robust ultrasensitive transcriptional switch in noisy cellular environments	15
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	15
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	15
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	14
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	13
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	13
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	13
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	13
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	13
Design principles of improving the dose-response alignment in coupled GTPase switches	13
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	12
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	12
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	12
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	12
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	12
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	11
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	11
Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis	11
Computational gastronomy: capturing culinary creativity by making food computable	11
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	11
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	11
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	10
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	10
An integrated network representation of multiple cancer-specific data for graph-based machine learning	10
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	10
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	10
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	10
The modular biochemical reaction network structure of cellular translation	10
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	9
TrackRefiner a tool for refinement of bacillus cell tracking data	9

A statistical framework for detecting therapy-induced resistance from drug screens	9
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	9
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	9
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	9
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	9
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	8
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	8
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	8
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	8
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	8
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	8
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	8
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	8
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	8
Flexible modeling of regulatory networks improves transcription factor activity estimation	8
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	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
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Representation and quantification of module activity from omics data with rROMA	8
Nucleus pulposus cell network modelling in the intervertebral disc	7
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	7
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	7
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	7
GO2Sum: generating human-readable functional summary of proteins from GO terms	7
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	7
Data-driven energy landscape reveals critical genes in cancer progression	7
Unraveling the effect of intra- and intercellular processes on acetaminophen-induced liver injury	7
Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast	7
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	7
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	7
Quantitative systems-based prediction of antimicrobial resistance evolution	7
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	7
Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans	7
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	7
Emergence of multiple collective motility modes in a physical model of cell chains	7
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	7
Reliable interpretability of biology-inspired deep neural networks	7
Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery	7
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	7
Next generation lineage tracing and its applications to unravel development	7
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	7
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	7
Immune digital twins for complex human pathologies: applications, limitations, and challenges	7
Author Correction: Enhancing randomized clinical trials with digital twins	7
MMP9 shapes cell mechanics to enable collective invasion in cancer	7
Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans	7
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	7