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 2021-04-01 to 2025-04-01.)

Article	Citations
Loss formulations for assumption-free neural inference of SDE coefficient functions	68
Designing function-specific minimal microbiomes from large microbial communities	59
A possible path to persistent re-entry waves at the outlet of the left pulmonary vein	48
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis	39
Leveraging public AI tools to explore systems biology resources in mathematical modeling	38
Modeling critical dosing strategies for stromal-induced resistance to cancer therapy	38
Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control	35
Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer	33
Deterministic patterns in single-cell transcriptomic data	32
MorphoSim: an efficient and scalable phase-field framework for accurately simulating multicellular morphologies	30
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes	26
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model	26
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells	25
Effective dose window for containing tumor burden under tolerable level	24
Executable models of immune signaling pathways in HIV-associated atherosclerosis	23
Functional stratification of cancer drugs through integrated network similarity	21
Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma	21
Measuring criticality in control of complex biological networks	20
Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery	20
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks	19
Identification of Probucol as a candidate for combination therapy with Metformin for Type 2 diabetes	19
Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models	18
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties	17
Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML	17
A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants	15

An Allee-based distributed algorithm for microbial whole-cell sensors	15
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways	15
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies	15
Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis	14
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease	13
Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia	13
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits	12
NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding	12
Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli	12
Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space	11
Network inference from perturbation time course data	11
A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis	11
Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model	10
A multi-omics approach for biomarker discovery in neuroblastoma: a network-based framework	10
Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images	10
Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy	10
Network topology and interaction logic determine states it supports	10
Operating principles of interconnected feedback loops driving cell fate transitions	10
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches	10
Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer	9
Olfactory receptors contribute to progression of kidney fibrosis	9
Cell morphology-based machine learning models for human cell state classification	9
A multiscale model of the regulation of aquaporin 2 recycling	9
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks	9
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy	9
AutoTransOP: translating omics signatures without orthologue requirements using deep learning	9
An automated workflow for multi-omics screening of microbial model organisms	9
Nobel Turing Challenge: creating the engine for scientific discovery	9
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds	9
Author Correction: Computer modeling defines the system driving a constant current crucial for homeostasis in the mammalian cochlea by integrating unique ion transports	9
Predicting stress response and improved protein overproduction in Bacillus subtilis	8
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	8
Flexible modeling of regulatory networks improves transcription factor activity estimation	8
NETISCE: a network-based tool for cell fate reprogramming	8
A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation	8
Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling	8
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis	8
On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures	8
Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli	7
Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver	7
Recovering biomolecular network dynamics from single-cell omics data requires three time points	7
Revisiting the evolution of bow-tie architecture in signaling networks	7
Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian	7
Asking the right questions for mutagenicity prediction from BioMedical text	7
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation	7
Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum	7
Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data	7
Representation and quantification of module activity from omics data with rROMA	7
Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks	7
Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs	6

DeepARV: ensemble deep learning to predict drug-drug interaction of clinical relevance with antiretroviral therapy	6
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models	6
Tissue-wide cell-specific proteogenomic modeling reveals novel candidate risk genes in autism spectrum disorders	6
Codon usage and expression-based features significantly improve prediction of CRISPR efficiency	6
Modelling HIV-1 control and remission	6
Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells	6
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network	6
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system	6
Computational modeling of DLBCL predicts response to BH3-mimetics	6