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Top Articles

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2Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collectionMolecular Systems Biology20066,537
3Current best practices in single‐cell RNA‐seq analysis: a tutorialMolecular Systems Biology20191,322
4Network‐based classification of breast cancer metastasisMolecular Systems Biology20071,320
5A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic informationMolecular Systems Biology20071,234
6Selected reaction monitoring for quantitative proteomics: a tutorialMolecular Systems Biology20081,215
7Deep learning for computational biologyMolecular Systems Biology20161,059
8Potential of fecal microbiota for early‐stage detection of colorectal cancerMolecular Systems Biology2014991
9Network‐based prediction of protein functionMolecular Systems Biology2007918
10A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011Molecular Systems Biology2011917
11A comprehensive pathway map of epidermal growth factor receptor signalingMolecular Systems Biology2005902
12Deep proteome and transcriptome mapping of a human cancer cell lineMolecular Systems Biology2011878
13Large‐scale mapping of human protein–protein interactions by mass spectrometryMolecular Systems Biology2007850
14Ultrasensitive proteome analysis using paramagnetic bead technologyMolecular Systems Biology2014835
15Synthetic biology: new engineering rules for an emerging disciplineMolecular Systems Biology2006820
16The protein expression profile of ACE2 in human tissuesMolecular Systems Biology2020769
17Applications of genome‐scale metabolic reconstructionsMolecular Systems Biology2009759
18A side effect resource to capture phenotypic effects of drugsMolecular Systems Biology2010757
19Feedback between p21 and reactive oxygen production is necessary for cell senescenceMolecular Systems Biology2010754
20Data‐independent acquisition‐based SWATHMS for quantitative proteomics: a tutorialMolecular Systems Biology2018701
21The quantitative proteome of a human cell lineMolecular Systems Biology2011691
22Differential network biologyMolecular Systems Biology2012689
23Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data setsMolecular Systems Biology2018659
24PREDICT: a method for inferring novel drug indications with application to personalized medicineMolecular Systems Biology2011655
25Towards a theory of biological robustnessMolecular Systems Biology2007647
26Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coliMolecular Systems Biology2007623
27A uniform proteomics MS/MS analysis platform utilizing open XML file formatsMolecular Systems Biology2005620
28Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale modelsMolecular Systems Biology2010615
29Novel biomarkers for pre‐diabetes identified by metabolomicsMolecular Systems Biology2012605
30Revisiting biomarker discovery by plasma proteomicsMolecular Systems Biology2017597
31Network‐based global inference of human disease genesMolecular Systems Biology2008583
32Metabolic networks in motion: 13 C‐based flux analysisMolecular Systems Biology2006582
33A deep proteome and transcriptome abundance atlas of 29 healthy human tissuesMolecular Systems Biology2019576
34How to infer gene networks from expression profilesMolecular Systems Biology2007563
35The endocannabinoid system links gut microbiota to adipogenesisMolecular Systems Biology2010547
36Oscillations and variability in the p53 systemMolecular Systems Biology2006539
37Shifts in growth strategies reflect tradeoffs in cellular economicsMolecular Systems Biology2009535
38Sequence signatures and mRNA concentration can explain two‐thirds of protein abundance variation in a human cell lineMolecular Systems Biology2010526
39The auxin signalling network translates dynamic input into robust patterning at the shoot apexMolecular Systems Biology2011520
40Human disease classification in the postgenomic era: A complex systems approach to human pathobiologyMolecular Systems Biology2007489
41Phosphotyrosine interactome of the ErbB‐receptor kinase familyMolecular Systems Biology2005468
42Modular cell biology: retroactivity and insulationMolecular Systems Biology2008454
43Metabolomic and transcriptomic stress response of Escherichia coliMolecular Systems Biology2010451
44Metabolic modeling of a mutualistic microbial communityMolecular Systems Biology2007441
45Engineering microbial biofuel tolerance and export using efflux pumpsMolecular Systems Biology2011440
46A synthetic Escherichia coli predator–prey ecosystemMolecular Systems Biology2008425
47A top‐down systems biology view of microbiome‐mammalian metabolic interactions in a mouse modelMolecular Systems Biology2007420
48Predicting selective drug targets in cancer through metabolic networksMolecular Systems Biology2011418
49Genome‐scale models of metabolism and gene expression extend and refine growth phenotype predictionMolecular Systems Biology2013411
50Highly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110Molecular Systems Biology2006409