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Top Articles

#TitleJournalYearCitations
1Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal OmegaMolecular Systems Biology201112,778
2Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collectionMolecular Systems Biology20066,537
3cytoHubba: identifying hub objects and sub-networks from complex interactomeBMC Systems Biology20143,371
4Coevolutionary games—A mini reviewBioSystems20101,630
5Ant colonies for the travelling salesman problemBioSystems19971,595
6Autopoiesis: The organization of living systems, its characterization and a modelBioSystems19741,459
7Current best practices in single‐cell RNA‐seq analysis: a tutorialMolecular Systems Biology20191,322
8Network‐based classification of breast cancer metastasisMolecular Systems Biology20071,320
9A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic informationMolecular Systems Biology20071,234
10Selected reaction monitoring for quantitative proteomics: a tutorialMolecular Systems Biology20081,215
11Deep learning for computational biologyMolecular Systems Biology20161,059
12Potential of fecal microbiota for early‐stage detection of colorectal cancerMolecular Systems Biology2014991
13COBRApy: COnstraints-Based Reconstruction and Analysis for PythonBMC Systems Biology2013973
14Network‐based prediction of protein functionMolecular Systems Biology2007918
15A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011Molecular Systems Biology2011917
16A comprehensive pathway map of epidermal growth factor receptor signalingMolecular Systems Biology2005902
17Deep proteome and transcriptome mapping of a human cancer cell lineMolecular Systems Biology2011878
18Large‐scale mapping of human protein–protein interactions by mass spectrometryMolecular Systems Biology2007850
19Ultrasensitive proteome analysis using paramagnetic bead technologyMolecular Systems Biology2014835
20Synthetic biology: new engineering rules for an emerging disciplineMolecular Systems Biology2006820
21Eigengene networks for studying the relationships between co-expression modulesBMC Systems Biology2007813
22CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networksBioSystems2015813
23The protein expression profile of ACE2 in human tissuesMolecular Systems Biology2020769
24Applications of genome‐scale metabolic reconstructionsMolecular Systems Biology2009759
25A side effect resource to capture phenotypic effects of drugsMolecular Systems Biology2010757
26Feedback between p21 and reactive oxygen production is necessary for cell senescenceMolecular Systems Biology2010754
27Signaling via the NFκB systemWiley Interdisciplinary Reviews: Systems Biology and Medicine2016724
28Data‐independent acquisition‐based SWATH ‐ MS for quantitative proteomics: a tutorialMolecular Systems Biology2018701
29The quantitative proteome of a human cell lineMolecular Systems Biology2011691
30Differential network biologyMolecular Systems Biology2012689
31Hematopoietic stem cell: self‐renewal versus differentiationWiley Interdisciplinary Reviews: Systems Biology and Medicine2010666
32Gene regulatory network inference: Data integration in dynamic models—A reviewBioSystems2009663
33Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data setsMolecular Systems Biology2018659
34PREDICT: a method for inferring novel drug indications with application to personalized medicineMolecular Systems Biology2011655
35Towards a theory of biological robustnessMolecular Systems Biology2007647
36The origin of land plants: A matter of mycotrophismBioSystems1975646
37Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coliMolecular Systems Biology2007623
38A uniform proteomics MS/MS analysis platform utilizing open XML file formatsMolecular Systems Biology2005620
39Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale modelsMolecular Systems Biology2010615
40Novel biomarkers for pre‐diabetes identified by metabolomicsMolecular Systems Biology2012605
41Revisiting biomarker discovery by plasma proteomicsMolecular Systems Biology2017597
42Remarks on feedforward circuits, adaptation, and pulse memoryIET Systems Biology2010588
43Network‐based global inference of human disease genesMolecular Systems Biology2008583
44Metabolic networks in motion: 13 C‐based flux analysisMolecular Systems Biology2006582
45A deep proteome and transcriptome abundance atlas of 29 healthy human tissuesMolecular Systems Biology2019576
46How to infer gene networks from expression profilesMolecular Systems Biology2007563
47The endocannabinoid system links gut microbiota to adipogenesisMolecular Systems Biology2010547
48Oscillations and variability in the p53 systemMolecular Systems Biology2006539
49Shifts in growth strategies reflect tradeoffs in cellular economicsMolecular Systems Biology2009535
50Sequence signatures and mRNA concentration can explain two‐thirds of protein abundance variation in a human cell lineMolecular Systems Biology2010526
51The auxin signalling network translates dynamic input into robust patterning at the shoot apexMolecular Systems Biology2011520
52Human disease classification in the postgenomic era: A complex systems approach to human pathobiologyMolecular Systems Biology2007489
53Phosphotyrosine interactome of the ErbB‐receptor kinase familyMolecular Systems Biology2005468
54BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic modelsBMC Systems Biology2010467
55Structural and functional analysis of cellular networks with CellNetAnalyzerBMC Systems Biology2007454
56Modular cell biology: retroactivity and insulationMolecular Systems Biology2008454
57Metabolomic and transcriptomic stress response of Escherichia coliMolecular Systems Biology2010451
58Re-evaluating genetic algorithm performance under coordinate rotation of benchmark functions. A survey of some theoretical and practical aspects of genetic algorithmsBioSystems1996447
59Metabolic modeling of a mutualistic microbial communityMolecular Systems Biology2007441
60Engineering microbial biofuel tolerance and export using efflux pumpsMolecular Systems Biology2011440
61A synthetic Escherichia coli predator–prey ecosystemMolecular Systems Biology2008425
62A top‐down systems biology view of microbiome‐mammalian metabolic interactions in a mouse modelMolecular Systems Biology2007420
63Predicting selective drug targets in cancer through metabolic networksMolecular Systems Biology2011418
64Genome‐scale models of metabolism and gene expression extend and refine growth phenotype predictionMolecular Systems Biology2013411
65Highly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110Molecular Systems Biology2006409
66Oncogenic K‐Ras decouples glucose and glutamine metabolism to support cancer cell growthMolecular Systems Biology2011404
67Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coliMolecular Systems Biology2007397
68Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse modelMolecular Systems Biology2008392
69Systems metabolic engineering of Escherichia coli for L ‐threonine productionMolecular Systems Biology2007391
70Connecting extracellular metabolomic measurements to intracellular flux states in yeastBMC Systems Biology2009391
71Determinants of translation efficiency and accuracyMolecular Systems Biology2011391
72Biogenic magnetite as a basis for magnetic field detection in animalsBioSystems1981388
73The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loopsMolecular Systems Biology2012386
74Understanding network concepts in modulesBMC Systems Biology2007385
75Experimental validation of a predicted feedback loop in the multi‐oscillator clock of Arabidopsis thalianaMolecular Systems Biology2006379
76Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cellsMolecular Systems Biology2012379
77Emergence of robust growth laws from optimal regulation of ribosome synthesisMolecular Systems Biology2014374
78Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraintsMolecular Systems Biology2017367
79HINT: High-quality protein interactomes and their applications in understanding human diseaseBMC Systems Biology2012366
80The Edinburgh human metabolic network reconstruction and its functional analysisMolecular Systems Biology2007364
81Eukaryote kingdoms: Seven or nine?BioSystems1981361
82Deciphering microbial interactions in synthetic human gut microbiome communitiesMolecular Systems Biology2018361
83Towards synthesis of a minimal cellMolecular Systems Biology2006360
84Cancer: A Systems Biology diseaseBioSystems2006359
85Flux balance analysis of primary metabolism in Chlamydomonas reinhardtiiBMC Systems Biology2009351
86Large‐scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in ArabidopsisMolecular Systems Biology2008347
87Gene‐specific correlation of RNA and protein levels in human cells and tissuesMolecular Systems Biology2016347
88Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivityMolecular Systems Biology2008346
89Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune networkIET Systems Biology2007345
90Hepatitis C virus infection protein networkMolecular Systems Biology2008340
91TIGRESS: Trustful Inference of Gene REgulation using Stability SelectionBMC Systems Biology2012338
92Glutamine‐driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxiaMolecular Systems Biology2013338
93A human B‐cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centersMolecular Systems Biology2010336
94Prioritization of disease microRNAs through a human phenome-microRNAome networkBMC Systems Biology2010335
95Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolismMolecular Systems Biology2010335
96An artificial immune system for data analysisBioSystems2000334
97Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeastMolecular Systems Biology2011333
98Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic dataMolecular Systems Biology2009332
99Identification of anticancer drugs for hepatocellular carcinoma through personalized genome‐scale metabolic modelingMolecular Systems Biology2014331
100InnateDB: facilitating systems‐level analyses of the mammalian innate immune responseMolecular Systems Biology2008330