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 2022-06-01 to 2026-06-01.)

Article	Citations
Measuring criticality in control of complex biological networks	99
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	76
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	73
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	58
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	54
Leveraging public AI tools to explore systems biology resources in mathematical modeling	51
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	50
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	45
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	44
Causality-aware graph neural networks for functional stratification and phenotype prediction at scale	39
Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data	39
Understanding the role of toggle genes in chronic lymphocytic leukemia proliferation	36
Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis	34
Revisiting the evolution of bow-tie architecture in signaling networks	34
Data-driven universal insights into tumorigenesis via hallmark networks	30
Extracellular matrix-driven patient stratification and network modeling reveal distinct molecular grades with potential clinical implications	30
Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer	29
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	29
Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods	27
Leveraging quantitative systems pharmacology modeling for elranatamab regimen optimization in relapsed or refractory multiple myeloma	27
Modelling HIV-1 control and remission	26
Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms	25
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	25
Data-driven synthetic microbes for sustainable future	25
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	25

Region-specific mean field models enhance simulations of local and global brain dynamics	24
An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells	23
Integrated omics of Saccharomyces cerevisiae CENPK2-1C reveals pleiotropic drug resistance and lipidomic adaptations to cannabidiol	23
Gene regulatory network transitions reveal the central transcription factors in lung adenocarcinoma progression	22
Matters of life and death in computational cell biology	22
Enhancing yeast cell tracking with a time-symmetric deep learning approach	22
Personalizing neoadjuvant chemotherapy regimens for triple-negative breast cancer using a biology-based digital twin	21
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis	20
Adaptive coding for DNA storage with high storage density and low coverage	20
Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers	20
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies	20
Spatiotemporal instability of influenza seasonality during viral co-circulation	19
YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico	19
Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer	19
A mechanism for the emergence of low-dimensional structures in brain dynamics	19
Alzheimer’s disease rewires gene coexpression networks coupling different brain regions	19
Systematic analysis of negative and positive feedback loops for robustness and temperature compensation in circadian rhythms	19
WEE1 inhibition delays resistance to CDK4/6 inhibitor and antiestrogen treatment in ER+ MCF7 cells	18
SIMBA-GNN: mechanistic graph learning for microbiome prediction	18
General relationship of local topologies, global dynamics, and bifurcation in cellular networks	18
A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers	18
Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production	17
Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates	17
Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy	17
LumbriCyc: towards metabolic modelling of earthworms	16
Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells	16
Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer	16
Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs	16
Globally invariant behavior of oncogenes and random genes at population but not at single cell level	16
Minimal gene signatures enable high-accuracy prediction of antibiotic resistance in Pseudomonas aeruginosa	16
Genetic basis of temporal variation in phenology in a woody perennial plant	15
Integrating AI, mechanistic modelling and network approaches in systems biology for translational research	15
Unraveling anti-inflammatory metabolic signatures of Glycyrrhiza uralensis and isoliquiritigenin through multiomics	15
A Python toolbox for neural circuit parameter inference	15
Learning patient-specific spatial biomarker dynamics via operator learning for Alzheimer’s disease progression	15
Manifold-based learning for high-throughput single-peanut phenotyping	15
A robust ultrasensitive transcriptional switch in noisy cellular environments	15
An architecture for collaboration in systems biology at the age of the Metaverse	15
Design principles of improving the dose-response alignment in coupled GTPase switches	15
An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1	14
PYEAST – A Computational Toolkit for Saccharomyces cerevisiae Genetic Engineering	14
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma	14
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles	14
A comprehensive mechanistic model of adipocyte signaling with layers of confidence	14
Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback	14
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota	14
Effects of resource packaging on the adaptative and pleiotropic consequences of evolution	13
Harnessing synthetic biology for advancing RNA therapeutics and vaccine design	13
QSP modeling of loncastuximab tesirine with T-cell-dependent bispecific antibodies guides dose-regimen strategy	13
Design principles for robust multistability in coupled feedforward-feedback regulatory circuits	13

Development of a severe rat refeeding syndrome model and mathematical modeling of the associated hypophosphatemia	13
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures	13
A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors	13
The modular biochemical reaction network structure of cellular translation	13
Computational gastronomy: capturing culinary creativity by making food computable	13
Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis	13
Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation	13
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	12
Assessing the impact of sampling bias on node centralities in synthetic and biological networks	12
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival	12
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	12
Publisher Correction: Mammalian synthetic gene circuits for biopharmaceutical development & manufacture	12
Fluxomics reveals cellular and molecular basis of increased renal ammoniagenesis	12
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	12
Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies	12
Decoding cellular population dynamics through mechanistic modelling and statistical data analysis	12
Genetic risk in Alzheimer’s disease	11
A statistical framework for detecting therapy-induced resistance from drug screens	11
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	11
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	11
TrackRefiner a tool for refinement of bacillus cell tracking data	11
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	11
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	11
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	10
Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data	10
Dual RAF inhibition outperforms RAF-MEK combinations for suppressing ERK signaling in KRAS mutant cells	10
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	10
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance	10
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations	10
DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	10
Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype	10
Flexible modeling of regulatory networks improves transcription factor activity estimation	10
Representation and quantification of module activity from omics data with rROMA	9
Mechanisms of rectified gap junctional coupling enhancing pacemaking activity of biologically engineered pacemaker cells	9
BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells	9
A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations	9
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	9
Optimal control theory as a method for designing multidrug adaptive therapy regimens	9
GO2Sum: generating human-readable functional summary of proteins from GO terms	9
Cross-platform metabolomics imputation using importance-weighted autoencoders	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
Author Correction: Mitochondria interaction networks show altered topological patterns in Parkinson’s disease	9
A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence	9
Machine learning estimation of FVIII pharmacokinetic parameters in Chinese children with severe Hemophilia A	9
Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy	8
Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing	8
Sometimes extracellular recordings fail for good reasons	8
Quantitative systems-based prediction of antimicrobial resistance evolution	8
Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development	8
Author Correction: Enhancing randomized clinical trials with digital twins	8
Data-driven energy landscape reveals critical genes in cancer progression	8
Metabolic gene expression-based stratification and prognostic risk predictive model of head and neck squamous cell carcinoma	8
Decoupling the chemical and physical origins of the seed spectral manifold in sorghum	8
Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients’ blood	8
Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma	8
Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection	8
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships	8
Next generation lineage tracing and its applications to unravel development	8
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment	8
Multi-omics integration reveals ANXA6-high γδ T cell–endothelial communication as a potential link between periodontitis and MASLD	8
Liver progenitor cells perform wound healing in a scratch assay by concerted bistable circuits	8
Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction	8
Immune digital twins for complex human pathologies: applications, limitations, and challenges	8
Inferring relationships among major psychiatric disorders in a resting-state functional connectivity-informed embedding space	8
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion	8
Publisher Correction: Rethinking medical education through systems biology to address complexity	8