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Top Articles

#TitleJournalYearCitations
1L1000CDS2: LINCS L1000 characteristic direction signatures search engineNpj Systems Biology and Applications2016250
2Synthetic and systems biology for microbial production of commodity chemicalsNpj Systems Biology and Applications2016187
3A machine learning approach to predict metabolic pathway dynamics from time-series multiomics dataNpj Systems Biology and Applications2018161
4Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolyticaNpj Systems Biology and Applications2016141
5Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypesNpj Systems Biology and Applications2015122
6Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approachNpj Systems Biology and Applications201796
7From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVALNpj Systems Biology and Applications201996
8Systems medicine disease maps: community-driven comprehensive representation of disease mechanismsNpj Systems Biology and Applications201884
9Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approachNpj Systems Biology and Applications202080
10iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discoveryNpj Systems Biology and Applications201979
11The multiplex network of human diseasesNpj Systems Biology and Applications201977
12Food allergen detection by mass spectrometry: the role of systems biologyNpj Systems Biology and Applications201672
13Prevalence and patterns of higher-order drug interactions in Escherichia coliNpj Systems Biology and Applications201871
14VEGFR1 promotes cell migration and proliferation through PLCγ and PI3K pathwaysNpj Systems Biology and Applications201869
15MINERVA—a platform for visualization and curation of molecular interaction networksNpj Systems Biology and Applications201668
16From START to FINISH: computational analysis of cell cycle control in budding yeastNpj Systems Biology and Applications201566
17The NAD World 2.0: the importance of the inter-tissue communication mediated by NAMPT/NAD+/SIRT1 in mammalian aging and longevity controlNpj Systems Biology and Applications201666
18Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfectionNpj Systems Biology and Applications201866
19A landscape view on the interplay between EMT and cancer metastasisNpj Systems Biology and Applications201866
20Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transitionNpj Systems Biology and Applications201965
21Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discoveryNpj Systems Biology and Applications202164
22Multipartite viruses: adaptive trick or evolutionary treat?Npj Systems Biology and Applications201762
23Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell typesNpj Systems Biology and Applications201862
24Flux sampling is a powerful tool to study metabolism under changing environmental conditionsNpj Systems Biology and Applications201962
25Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale modelsNpj Systems Biology and Applications202062
26Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121)Npj Systems Biology and Applications201761
27Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modelingNpj Systems Biology and Applications202061
28From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s diseaseNpj Systems Biology and Applications201859
29Performance of objective functions and optimisation procedures for parameter estimation in system biology modelsNpj Systems Biology and Applications201757
30Pathways on demand: automated reconstruction of human signaling networksNpj Systems Biology and Applications201655
31Meta-analysis of host response networks identifies a common core in tuberculosisNpj Systems Biology and Applications201755
32Improved prediction of PARP inhibitor response and identification of synergizing agents through use of a novel gene expression signature generation algorithmNpj Systems Biology and Applications201755
33Integrating personalized gene expression profiles into predictive disease-associated gene poolsNpj Systems Biology and Applications201754
34Sparsely-connected autoencoder (SCA) for single cell RNAseq data miningNpj Systems Biology and Applications202153
35On the performance of de novo pathway enrichmentNpj Systems Biology and Applications201751
36Classification of gene signatures for their information value and functional redundancyNpj Systems Biology and Applications201850
37ROS networks: designs, aging, Parkinson’s disease and precision therapiesNpj Systems Biology and Applications202050
38A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosisNpj Systems Biology and Applications201847
39Clinical responses to ERK inhibition in BRAF V600E-mutant colorectal cancer predicted using a computational modelNpj Systems Biology and Applications201745
40A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotectionNpj Systems Biology and Applications201845
41Role of noise and parametric variation in the dynamics of gene regulatory circuitsNpj Systems Biology and Applications201844
42Dynamic models of the complex microbial metapopulation of lake mendotaNpj Systems Biology and Applications201643
43A multiscale model of early cell lineage specification including cell divisionNpj Systems Biology and Applications201743
44A roadmap towards personalized immunologyNpj Systems Biology and Applications201843
45ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databasesNpj Systems Biology and Applications201843
46Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosisNpj Systems Biology and Applications202143
47A time-resolved molecular map of the macrophage response to VSV infectionNpj Systems Biology and Applications201642
48A method to identify and analyze biological programs through automated reasoningNpj Systems Biology and Applications201642
49Large-scale computational drug repositioning to find treatments for rare diseasesNpj Systems Biology and Applications201840
50Predicting ligand-dependent tumors from multi-dimensional signaling featuresNpj Systems Biology and Applications201739