| 1 | L1000CDS2: LINCS L1000 characteristic direction signatures search engine | Npj Systems Biology and Applications | 2016 | 255 |
| 2 | A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data | Npj Systems Biology and Applications | 2018 | 168 |
| 3 | Synthetic and systems biology for microbial production of commodity chemicals | Npj Systems Biology and Applications | 2016 | 161 |
| 4 | Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica | Npj Systems Biology and Applications | 2016 | 150 |
| 5 | Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypes | Npj Systems Biology and Applications | 2015 | 96 |
| 6 | Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach | Npj Systems Biology and Applications | 2017 | 96 |
| 7 | From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL | Npj Systems Biology and Applications | 2019 | 94 |
| 8 | Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modeling | Npj Systems Biology and Applications | 2020 | 92 |
| 9 | The multiplex network of human diseases | Npj Systems Biology and Applications | 2019 | 89 |
| 10 | Flux sampling is a powerful tool to study metabolism under changing environmental conditions | Npj Systems Biology and Applications | 2019 | 76 |
| 11 | The NAD World 2.0: the importance of the inter-tissue communication mediated by NAMPT/NAD+/SIRT1 in mammalian aging and longevity control | Npj Systems Biology and Applications | 2016 | 73 |
| 12 | MINERVA—a platform for visualization and curation of molecular interaction networks | Npj Systems Biology and Applications | 2016 | 71 |
| 13 | ROS networks: designs, aging, Parkinson’s disease and precision therapies | Npj Systems Biology and Applications | 2020 | 70 |
| 14 | Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis | Npj Systems Biology and Applications | 2021 | 69 |
| 15 | Prevalence and patterns of higher-order drug interactions in Escherichia coli | Npj Systems Biology and Applications | 2018 | 68 |
| 16 | Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery | Npj Systems Biology and Applications | 2021 | 67 |
| 17 | Food allergen detection by mass spectrometry: the role of systems biology | Npj Systems Biology and Applications | 2016 | 66 |
| 18 | VEGFR1 promotes cell migration and proliferation through PLCγ and PI3K pathways | Npj Systems Biology and Applications | 2017 | 63 |
| 19 | Multipartite viruses: adaptive trick or evolutionary treat? | Npj Systems Biology and Applications | 2017 | 61 |
| 20 | A landscape view on the interplay between EMT and cancer metastasis | Npj Systems Biology and Applications | 2018 | 61 |
| 21 | Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121) | Npj Systems Biology and Applications | 2017 | 58 |
| 22 | From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease | Npj Systems Biology and Applications | 2018 | 57 |
| 23 | Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data | Npj Systems Biology and Applications | 2023 | 57 |
| 24 | Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approach | Npj Systems Biology and Applications | 2020 | 55 |
| 25 | Computational systems biology in disease modeling and control, review and perspectives | Npj Systems Biology and Applications | 2022 | 55 |
| 26 | Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types | Npj Systems Biology and Applications | 2018 | 54 |
| 27 | Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models | Npj Systems Biology and Applications | 2020 | 51 |
| 28 | Crosstalk between Plk1, p53, cell cycle, and G2/M DNA damage checkpoint regulation in cancer: computational modeling and analysis | Npj Systems Biology and Applications | 2021 | 50 |
| 29 | Integrating personalized gene expression profiles into predictive disease-associated gene pools | Npj Systems Biology and Applications | 2017 | 49 |
| 30 | From START to FINISH: computational analysis of cell cycle control in budding yeast | Npj Systems Biology and Applications | 2015 | 46 |
| 31 | A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis | Npj Systems Biology and Applications | 2018 | 46 |
| 32 | A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth | Npj Systems Biology and Applications | 2019 | 45 |
| 33 | Stratification and prediction of drug synergy based on target functional similarity | Npj Systems Biology and Applications | 2020 | 45 |
| 34 | Improved prediction of PARP inhibitor response and identification of synergizing agents through use of a novel gene expression signature generation algorithm | Npj Systems Biology and Applications | 2017 | 44 |
| 35 | Clinical responses to ERK inhibition in BRAF
V600E-mutant colorectal cancer predicted using a computational model | Npj Systems Biology and Applications | 2017 | 43 |
| 36 | A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection | Npj Systems Biology and Applications | 2018 | 43 |
| 37 | Cell morphology-based machine learning models for human cell state classification | Npj Systems Biology and Applications | 2021 | 42 |
| 38 | A roadmap towards personalized immunology | Npj Systems Biology and Applications | 2018 | 41 |
| 39 | Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition | Npj Systems Biology and Applications | 2019 | 41 |
| 40 | Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism | Npj Systems Biology and Applications | 2023 | 41 |
| 41 | Meta-analysis of host response networks identifies a common core in tuberculosis | Npj Systems Biology and Applications | 2017 | 40 |
| 42 | Classification of gene signatures for their information value and functional redundancy | Npj Systems Biology and Applications | 2017 | 40 |
| 43 | Role of noise and parametric variation in the dynamics of gene regulatory circuits | Npj Systems Biology and Applications | 2018 | 40 |
| 44 | Adaptive coding for DNA storage with high storage density and low coverage | Npj Systems Biology and Applications | 2022 | 39 |
| 45 | Employing active learning in the optimization of culture medium for mammalian cells | Npj Systems Biology and Applications | 2023 | 39 |
| 46 | Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection | Npj Systems Biology and Applications | 2018 | 38 |
| 47 | Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes | Npj Systems Biology and Applications | 2019 | 38 |
| 48 | Pathways on demand: automated reconstruction of human signaling networks | Npj Systems Biology and Applications | 2016 | 37 |
| 49 | Performance of objective functions and optimisation procedures for parameter estimation in system biology models | Npj Systems Biology and Applications | 2017 | 37 |
| 50 | A multiscale model of early cell lineage specification including cell division | Npj Systems Biology and Applications | 2017 | 37 |
