| 1 | Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega | Molecular Systems Biology | 2011 | 11,616 |
| 2 | Current best practices in single‐cell RNA‐seq analysis: a tutorial | Molecular Systems Biology | 2019 | 1,286 |
| 3 | A genome‐scale metabolic reconstruction for
Escherichia coli
K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information | Molecular Systems Biology | 2007 | 952 |
| 4 | Network‐based classification of breast cancer metastasis | Molecular Systems Biology | 2007 | 908 |
| 5 | Deep learning for computational biology | Molecular Systems Biology | 2016 | 869 |
| 6 | Ultrasensitive proteome analysis using paramagnetic bead technology | Molecular Systems Biology | 2014 | 853 |
| 7 | Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets | Molecular Systems Biology | 2018 | 845 |
| 8 | A comprehensive genome‐scale reconstruction of
Escherichia coli
metabolism—2011 | Molecular Systems Biology | 2011 | 747 |
| 9 | Feedback between p21 and reactive oxygen production is necessary for cell senescence | Molecular Systems Biology | 2010 | 720 |
| 10 | The protein expression profile of ACE2 in human tissues | Molecular Systems Biology | 2020 | 710 |
| 11 | Large‐scale mapping of human protein–protein interactions by mass spectrometry | Molecular Systems Biology | 2007 | 688 |
| 12 | Revisiting biomarker discovery by plasma proteomics | Molecular Systems Biology | 2017 | 651 |
| 13 | Synthetic biology: new engineering rules for an emerging discipline | Molecular Systems Biology | 2006 | 597 |
| 14 | The quantitative proteome of a human cell line | Molecular Systems Biology | 2011 | 592 |
| 15 | PREDICT: a method for inferring novel drug indications with application to personalized medicine | Molecular Systems Biology | 2011 | 572 |
| 16 | Omic data from evolved
E. coli
are consistent with computed optimal growth from genome‐scale models | Molecular Systems Biology | 2010 | 546 |
| 17 | A side effect resource to capture phenotypic effects of drugs | Molecular Systems Biology | 2010 | 546 |
| 18 | The endocannabinoid system links gut microbiota to adipogenesis | Molecular Systems Biology | 2010 | 512 |
| 19 | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues | Molecular Systems Biology | 2019 | 504 |
| 20 | Differential network biology | Molecular Systems Biology | 2012 | 483 |
| 21 | A uniform proteomics MS/MS analysis platform utilizing open XML file formats | Molecular Systems Biology | 2005 | 473 |
| 22 | Systematic evaluation of objective functions for predicting intracellular fluxes in
Escherichia coli | Molecular Systems Biology | 2007 | 471 |
| 23 | Shifts in growth strategies reflect tradeoffs in cellular economics | Molecular Systems Biology | 2009 | 456 |
| 24 | Metabolic networks in motion:
13
C‐based flux analysis | Molecular Systems Biology | 2006 | 448 |
| 25 | The auxin signalling network translates dynamic input into robust patterning at the shoot apex | Molecular Systems Biology | 2011 | 441 |
| 26 | Oscillations and variability in the p53 system | Molecular Systems Biology | 2006 | 435 |
| 27 | How to infer gene networks from expression profiles | Molecular Systems Biology | 2007 | 411 |
| 28 | Network‐based global inference of human disease genes | Molecular Systems Biology | 2008 | 411 |
| 29 | Metabolomic and transcriptomic stress response of
Escherichia coli | Molecular Systems Biology | 2010 | 407 |
| 30 | Phosphotyrosine interactome of the ErbB‐receptor kinase family | Molecular Systems Biology | 2005 | 394 |
| 31 | Metabolic modeling of a mutualistic microbial community | Molecular Systems Biology | 2007 | 384 |
| 32 | Engineering microbial biofuel tolerance and export using efflux pumps | Molecular Systems Biology | 2011 | 384 |
| 33 | Oncogenic K‐Ras decouples glucose and glutamine metabolism to support cancer cell growth | Molecular Systems Biology | 2011 | 372 |
| 34 | Determinants of translation efficiency and accuracy | Molecular Systems Biology | 2011 | 366 |
| 35 | Systems metabolic engineering of
Escherichia coli
for
L
‐threonine production | Molecular Systems Biology | 2007 | 361 |
| 36 | Deciphering microbial interactions in synthetic human gut microbiome communities | Molecular Systems Biology | 2018 | 359 |
| 37 | Gyrase inhibitors induce an oxidative damage cellular death pathway in
Escherichia coli | Molecular Systems Biology | 2007 | 353 |
| 38 | Highly accurate genome sequences of
Escherichia coli
K‐12 strains MG1655 and W3110 | Molecular Systems Biology | 2006 | 352 |
| 39 | Gene‐specific correlation of
RNA
and protein levels in human cells and tissues | Molecular Systems Biology | 2016 | 348 |
| 40 | Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints | Molecular Systems Biology | 2017 | 345 |
| 41 | Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models | Molecular Systems Biology | 2021 | 337 |
| 42 | A synthetic
Escherichia coli
predator–prey ecosystem | Molecular Systems Biology | 2008 | 335 |
| 43 | Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation | Molecular Systems Biology | 2022 | 327 |
| 44 | Predicting selective drug targets in cancer through metabolic networks | Molecular Systems Biology | 2011 | 324 |
| 45 | Glutamine‐driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia | Molecular Systems Biology | 2013 | 322 |
| 46 | The clock gene circuit in
Arabidopsis
includes a repressilator with additional feedback loops | Molecular Systems Biology | 2012 | 314 |
| 47 | Emergence of robust growth laws from optimal regulation of ribosome synthesis | Molecular Systems Biology | 2014 | 314 |
| 48 | Experimental validation of a predicted feedback loop in the multi‐oscillator clock of
Arabidopsis thaliana | Molecular Systems Biology | 2006 | 312 |
| 49 | Modular cell biology: retroactivity and insulation | Molecular Systems Biology | 2008 | 312 |
| 50 | Evolution and functional cross‐talk of protein post‐translational modifications | Molecular Systems Biology | 2013 | 300 |