# | Title | Journal | Year | Citations |
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1 | Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega | Molecular Systems Biology | 2011 | 12,778 |
2 | Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection | Molecular Systems Biology | 2006 | 6,537 |
3 | cytoHubba: identifying hub objects and sub-networks from complex interactome | BMC Systems Biology | 2014 | 3,371 |
4 | Coevolutionary games—A mini review | BioSystems | 2010 | 1,630 |
5 | Ant colonies for the travelling salesman problem | BioSystems | 1997 | 1,595 |
6 | Autopoiesis: The organization of living systems, its characterization and a model | BioSystems | 1974 | 1,459 |
7 | Current best practices in single‐cell RNA‐seq analysis: a tutorial | Molecular Systems Biology | 2019 | 1,322 |
8 | Network‐based classification of breast cancer metastasis | Molecular Systems Biology | 2007 | 1,320 |
9 | A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information | Molecular Systems Biology | 2007 | 1,234 |
10 | Selected reaction monitoring for quantitative proteomics: a tutorial | Molecular Systems Biology | 2008 | 1,215 |
11 | Deep learning for computational biology | Molecular Systems Biology | 2016 | 1,059 |
12 | Potential of fecal microbiota for early‐stage detection of colorectal cancer | Molecular Systems Biology | 2014 | 991 |
13 | COBRApy: COnstraints-Based Reconstruction and Analysis for Python | BMC Systems Biology | 2013 | 973 |
14 | Network‐based prediction of protein function | Molecular Systems Biology | 2007 | 918 |
15 | A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011 | Molecular Systems Biology | 2011 | 917 |
16 | A comprehensive pathway map of epidermal growth factor receptor signaling | Molecular Systems Biology | 2005 | 902 |
17 | Deep proteome and transcriptome mapping of a human cancer cell line | Molecular Systems Biology | 2011 | 878 |
18 | Large‐scale mapping of human protein–protein interactions by mass spectrometry | Molecular Systems Biology | 2007 | 850 |
19 | Ultrasensitive proteome analysis using paramagnetic bead technology | Molecular Systems Biology | 2014 | 835 |
20 | Synthetic biology: new engineering rules for an emerging discipline | Molecular Systems Biology | 2006 | 820 |
21 | Eigengene networks for studying the relationships between co-expression modules | BMC Systems Biology | 2007 | 813 |
22 | CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks | BioSystems | 2015 | 813 |
23 | The protein expression profile of ACE2 in human tissues | Molecular Systems Biology | 2020 | 769 |
24 | Applications of genome‐scale metabolic reconstructions | Molecular Systems Biology | 2009 | 759 |
25 | A side effect resource to capture phenotypic effects of drugs | Molecular Systems Biology | 2010 | 757 |
26 | Feedback between p21 and reactive oxygen production is necessary for cell senescence | Molecular Systems Biology | 2010 | 754 |
27 | Signaling via the NFκB system | Wiley Interdisciplinary Reviews: Systems Biology and Medicine | 2016 | 724 |
28 | Data‐independent acquisition‐based SWATH ‐ MS for quantitative proteomics: a tutorial | Molecular Systems Biology | 2018 | 701 |
29 | The quantitative proteome of a human cell line | Molecular Systems Biology | 2011 | 691 |
30 | Differential network biology | Molecular Systems Biology | 2012 | 689 |
31 | Hematopoietic stem cell: self‐renewal versus differentiation | Wiley Interdisciplinary Reviews: Systems Biology and Medicine | 2010 | 666 |
32 | Gene regulatory network inference: Data integration in dynamic models—A review | BioSystems | 2009 | 663 |
33 | Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets | Molecular Systems Biology | 2018 | 659 |
34 | PREDICT: a method for inferring novel drug indications with application to personalized medicine | Molecular Systems Biology | 2011 | 655 |
35 | Towards a theory of biological robustness | Molecular Systems Biology | 2007 | 647 |
36 | The origin of land plants: A matter of mycotrophism | BioSystems | 1975 | 646 |
37 | Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli | Molecular Systems Biology | 2007 | 623 |
38 | A uniform proteomics MS/MS analysis platform utilizing open XML file formats | Molecular Systems Biology | 2005 | 620 |
39 | Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models | Molecular Systems Biology | 2010 | 615 |
40 | Novel biomarkers for pre‐diabetes identified by metabolomics | Molecular Systems Biology | 2012 | 605 |
41 | Revisiting biomarker discovery by plasma proteomics | Molecular Systems Biology | 2017 | 597 |
42 | Remarks on feedforward circuits, adaptation, and pulse memory | IET Systems Biology | 2010 | 588 |
43 | Network‐based global inference of human disease genes | Molecular Systems Biology | 2008 | 583 |
44 | Metabolic networks in motion: 13 C‐based flux analysis | Molecular Systems Biology | 2006 | 582 |
45 | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues | Molecular Systems Biology | 2019 | 576 |
46 | How to infer gene networks from expression profiles | Molecular Systems Biology | 2007 | 563 |
47 | The endocannabinoid system links gut microbiota to adipogenesis | Molecular Systems Biology | 2010 | 547 |
48 | Oscillations and variability in the p53 system | Molecular Systems Biology | 2006 | 539 |
49 | Shifts in growth strategies reflect tradeoffs in cellular economics | Molecular Systems Biology | 2009 | 535 |
50 | Sequence signatures and mRNA concentration can explain two‐thirds of protein abundance variation in a human cell line | Molecular Systems Biology | 2010 | 526 |
51 | The auxin signalling network translates dynamic input into robust patterning at the shoot apex | Molecular Systems Biology | 2011 | 520 |
52 | Human disease classification in the postgenomic era: A complex systems approach to human pathobiology | Molecular Systems Biology | 2007 | 489 |
53 | Phosphotyrosine interactome of the ErbB‐receptor kinase family | Molecular Systems Biology | 2005 | 468 |
54 | BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models | BMC Systems Biology | 2010 | 467 |
55 | Structural and functional analysis of cellular networks with CellNetAnalyzer | BMC Systems Biology | 2007 | 454 |
56 | Modular cell biology: retroactivity and insulation | Molecular Systems Biology | 2008 | 454 |
57 | Metabolomic and transcriptomic stress response of Escherichia coli | Molecular Systems Biology | 2010 | 451 |
58 | Re-evaluating genetic algorithm performance under coordinate rotation of benchmark functions. A survey of some theoretical and practical aspects of genetic algorithms | BioSystems | 1996 | 447 |
59 | Metabolic modeling of a mutualistic microbial community | Molecular Systems Biology | 2007 | 441 |
60 | Engineering microbial biofuel tolerance and export using efflux pumps | Molecular Systems Biology | 2011 | 440 |
61 | A synthetic Escherichia coli predator–prey ecosystem | Molecular Systems Biology | 2008 | 425 |
62 | A top‐down systems biology view of microbiome‐mammalian metabolic interactions in a mouse model | Molecular Systems Biology | 2007 | 420 |
63 | Predicting selective drug targets in cancer through metabolic networks | Molecular Systems Biology | 2011 | 418 |
64 | Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction | Molecular Systems Biology | 2013 | 411 |
65 | Highly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110 | Molecular Systems Biology | 2006 | 409 |
66 | Oncogenic K‐Ras decouples glucose and glutamine metabolism to support cancer cell growth | Molecular Systems Biology | 2011 | 404 |
67 | Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli | Molecular Systems Biology | 2007 | 397 |
68 | Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model | Molecular Systems Biology | 2008 | 392 |
69 | Systems metabolic engineering of Escherichia coli for L ‐threonine production | Molecular Systems Biology | 2007 | 391 |
70 | Connecting extracellular metabolomic measurements to intracellular flux states in yeast | BMC Systems Biology | 2009 | 391 |
71 | Determinants of translation efficiency and accuracy | Molecular Systems Biology | 2011 | 391 |
72 | Biogenic magnetite as a basis for magnetic field detection in animals | BioSystems | 1981 | 388 |
73 | The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops | Molecular Systems Biology | 2012 | 386 |
74 | Understanding network concepts in modules | BMC Systems Biology | 2007 | 385 |
75 | Experimental validation of a predicted feedback loop in the multi‐oscillator clock of Arabidopsis thaliana | Molecular Systems Biology | 2006 | 379 |
76 | Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells | Molecular Systems Biology | 2012 | 379 |
77 | Emergence of robust growth laws from optimal regulation of ribosome synthesis | Molecular Systems Biology | 2014 | 374 |
78 | Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints | Molecular Systems Biology | 2017 | 367 |
79 | HINT: High-quality protein interactomes and their applications in understanding human disease | BMC Systems Biology | 2012 | 366 |
80 | The Edinburgh human metabolic network reconstruction and its functional analysis | Molecular Systems Biology | 2007 | 364 |
81 | Eukaryote kingdoms: Seven or nine? | BioSystems | 1981 | 361 |
82 | Deciphering microbial interactions in synthetic human gut microbiome communities | Molecular Systems Biology | 2018 | 361 |
83 | Towards synthesis of a minimal cell | Molecular Systems Biology | 2006 | 360 |
84 | Cancer: A Systems Biology disease | BioSystems | 2006 | 359 |
85 | Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii | BMC Systems Biology | 2009 | 351 |
86 | Large‐scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis | Molecular Systems Biology | 2008 | 347 |
87 | Gene‐specific correlation of RNA and protein levels in human cells and tissues | Molecular Systems Biology | 2016 | 347 |
88 | Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity | Molecular Systems Biology | 2008 | 346 |
89 | Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network | IET Systems Biology | 2007 | 345 |
90 | Hepatitis C virus infection protein network | Molecular Systems Biology | 2008 | 340 |
91 | TIGRESS: Trustful Inference of Gene REgulation using Stability Selection | BMC Systems Biology | 2012 | 338 |
92 | Glutamine‐driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia | Molecular Systems Biology | 2013 | 338 |
93 | A human B‐cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers | Molecular Systems Biology | 2010 | 336 |
94 | Prioritization of disease microRNAs through a human phenome-microRNAome network | BMC Systems Biology | 2010 | 335 |
95 | Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism | Molecular Systems Biology | 2010 | 335 |
96 | An artificial immune system for data analysis | BioSystems | 2000 | 334 |
97 | Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast | Molecular Systems Biology | 2011 | 333 |
98 | Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data | Molecular Systems Biology | 2009 | 332 |
99 | Identification of anticancer drugs for hepatocellular carcinoma through personalized genome‐scale metabolic modeling | Molecular Systems Biology | 2014 | 331 |
100 | InnateDB: facilitating systems‐level analyses of the mammalian innate immune response | Molecular Systems Biology | 2008 | 330 |