| A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data |
31 |
| A landscape view on the interplay between EMT and cancer metastasis |
13 |
| Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms |
12 |
| Prevalence and patterns of higher-order drug interactions in Escherichia coli |
11 |
| A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis |
11 |
| iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery |
11 |
| From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease |
9 |
| From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL |
8 |
| The multiplex network of human diseases |
8 |
| A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection |
7 |
| Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types |
7 |
| Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes |
7 |
| A roadmap towards personalized immunology |
7 |
| Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition |
7 |
| The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches |
6 |
| Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation |
6 |
| Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects |
6 |
| Role of noise and parametric variation in the dynamics of gene regulatory circuits |
6 |
| Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer |
6 |
| Redefining environmental exposure for disease etiology |
6 |
| Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC which regulates Type 2 Diabetes associated genes |
5 |
| Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer |
5 |
| A yield-cost tradeoff governs Escherichia coli's decision between fermentation and respiration in carbon-limited growth |
5 |
| A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure |
5 |
| Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types |
4 |
| A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer |
4 |
| Defining subpopulations of differential drug response to reveal novel target populations |
4 |
| Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators |
4 |
| Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease |
4 |
| Mapping biological process relationships and disease perturbations within a pathway network |
4 |
| Large-scale computational drug repositioning to find treatments for rare diseases |
3 |
| Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae |
3 |
| Pathway crosstalk enables cells to interpret TGF-beta duration |
3 |
| Genetic signature related to heme-hemoglobin metabolism pathway in sepsis secondary to pneumonia |
3 |
| Regulatory feedback response mechanisms to phosphate starvation in rice |
3 |
| Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae |
3 |
| Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma |
3 |
| Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network |
3 |
| Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models |
3 |
| Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants |
3 |
| Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics |
3 |
| Flux sampling is a powerful tool to study metabolism under changing environmental conditions |
3 |
| PIMKL: Pathway-Induced Multiple Kernel Learning |
3 |
| Mapping the operational landscape of microRNAs in synthetic gene circuits |
3 |
| A network-based approach to uncover microRNA-mediated disease comorbidities and potential pathobiological implications |
3 |
| An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells |
3 |
| Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer |
2 |
| Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection |
2 |
| Regeneration in distantly related species: common strategies and pathways |
2 |
| Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease |
2 |
