OOIR: Observatory of International Research

Papers

(The TQCC of npj Systems Biology and Applications is 8. 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 2022-05-01 to 2026-05-01.)

Article	Citations
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	95
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	75
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	64
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data	57
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	53
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	49
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	48
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	45
Measuring criticality in control of complex biological networks	42
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	38
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	37
Leveraging public AI tools to explore systems biology resources in mathematical modeling	34
Revisiting the evolution of bow-tie architecture in signaling networks	33
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	31
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	29
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	28
Data-driven universal insights into tumorigenesis via hallmark networks	28
Data-driven synthetic microbes for sustainable future	27
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	27
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	26
Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications	26
Modelling HIV-1 control and remission	25
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	25
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	25
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	24

Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	23
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	22
Region-specific mean field models enhance simulations of local and global brain dynamics	22
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	21
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	20
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	20
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	20
SIMBA-GNN: mechanistic graph learning for microbiome prediction	19
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	19
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	19
Adaptive coding for DNA storage with high storage density and low coverage	19
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression	18
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	18
Enhancing yeast cell tracking with a time-symmetric deep learning approach	18
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	17
Matters of life and death in computational cell biology	17
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	17
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	17
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	16
A Python toolbox for neural circuit parameter inference	16
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	16
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	16
A mechanism for the emergence of low-dimensional structures in brain dynamics	16
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma	16
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	16
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	15
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	15
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	15
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	15
Design principles of improving the dose-response alignment in coupled GTPase switches	15
LumbriCyc: towards metabolic modelling of earthworms	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
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	15
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	14
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	14
Integrating AI, mechanistic modelling and network approaches in systems biology for translational research	14
An architecture for collaboration in systems biology at the age of the Metaverse	14
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	14
Manifold-based learning for high-throughput single-peanut phenotyping	14
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	14
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	13
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	13
PYEAST – A Computational Toolkit for Saccharomyces cerevisiae Genetic Engineering	13
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	13
Computational gastronomy: capturing culinary creativity by making food computable	13
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	13
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	13
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	12
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	12

A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors	12
Development of a severe rat refeeding syndrome model and mathematical modeling of the associated hypophosphatemia	12
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	12
The modular biochemical reaction network structure of cellular translation	12
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	12
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	12
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	11
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	11
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	11
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	11
Publisher Correction: Mammalian synthetic gene circuits for biopharmaceutical development & manufacture	11
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	11
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	11
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	11
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	10
TrackRefiner a tool for refinement of bacillus cell tracking data	10
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	10
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	10
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	10
A statistical framework for detecting therapy-induced resistance from drug screens	10
Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data	10
Genetic risk in Alzheimer’s disease	10
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	10
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	10
Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells	9
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	9
Representation and quantification of module activity from omics data with rROMA	9
Machine learning estimation of FVIII pharmacokinetic parameters in Chinese children with severe Hemophilia A	9
Flexible modeling of regulatory networks improves transcription factor activity estimation	9
Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype	9
Cross-platform metabolomics imputation using importance-weighted autoencoders	9
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	9
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	9
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	9
Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells	9
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	9
Optimal control theory as a method for designing multidrug adaptive therapy regimens	9
Metabolic gene expression-based stratification and prognostic risk predictive model of head and neck squamous cell carcinoma	9
NETISCE: a network-based tool for cell fate reprogramming	9
A machine learning framework reveals key drivers of cytokine responses in a healthy human cohort	9
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	9
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	8
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	8
GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases	8
Inferring relationships among major psychiatric disorders in a resting-state functional connectivity-informed embedding space	8
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways	8
Multi-omics integration reveals ANXA6-high γδ T cell–endothelial communication as a potential link between periodontitis and MASLD	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics	8
Publisher Correction: Rethinking medical education through systems biology to address complexity	8
Author Correction: Enhancing randomized clinical trials with digital twins	8
Liver progenitor cells perform wound healing in a scratch assay by concerted bistable circuits	8
GO2Sum: generating human-readable functional summary of proteins from GO terms	8
Immune digital twins for complex human pathologies: applications, limitations, and challenges	8
Quantitative systems-based prediction of antimicrobial resistance evolution	8
Nucleus pulposus cell network modelling in the intervertebral disc	8
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	8
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	8