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papers
65.2K(top 5%)
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102(top 5%)
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Top Articles

#TitleJournalYearCitations
1cytoHubba: identifying hub objects and sub-networks from complex interactomeBMC Systems Biology20143,371
2COBRApy: COnstraints-Based Reconstruction and Analysis for PythonBMC Systems Biology2013973
3Eigengene networks for studying the relationships between co-expression modulesBMC Systems Biology2007813
4BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic modelsBMC Systems Biology2010467
5Structural and functional analysis of cellular networks with CellNetAnalyzerBMC Systems Biology2007454
6Connecting extracellular metabolomic measurements to intracellular flux states in yeastBMC Systems Biology2009391
7Understanding network concepts in modulesBMC Systems Biology2007385
8HINT: High-quality protein interactomes and their applications in understanding human diseaseBMC Systems Biology2012366
9Flux balance analysis of primary metabolism in Chlamydomonas reinhardtiiBMC Systems Biology2009351
10TIGRESS: Trustful Inference of Gene REgulation using Stability SelectionBMC Systems Biology2012338
11Prioritization of disease microRNAs through a human phenome-microRNAome networkBMC Systems Biology2010335
12OptFlux: an open-source software platform for in silico metabolic engineeringBMC Systems Biology2010321
13Network target for screening synergistic drug combinations with application to traditional Chinese medicineBMC Systems Biology2011309
14From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression dataBMC Systems Biology2007304
15Data integration in the era of omics: current and future challengesBMC Systems Biology2014300
16Semi-supervised drug-protein interaction prediction from heterogeneous biological spacesBMC Systems Biology2010290
17Identification of functional modules using network topology and high-throughput dataBMC Systems Biology2007267
18Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics dataBMC Systems Biology2011262
19Catabolic efficiency of aerobic glycolysis: The Warburg effect revisitedBMC Systems Biology2010255
20An additional k-means clustering step improves the biological features of WGCNA gene co-expression networksBMC Systems Biology2017253
21Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ 661 and proposing alternative drug targetsBMC Systems Biology2007246
22Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistanceBMC Systems Biology2009242
23Reconstruction of genome-scale metabolic models for 126 human tissues using mCADREBMC Systems Biology2012239
24A review of imaging techniques for systems biologyBMC Systems Biology2008235
25A systematic analysis of FDA-approved anticancer drugsBMC Systems Biology2017235
26Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosisBMC Systems Biology2007234
27Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancerBMC Systems Biology2014233
28Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genesBMC Systems Biology2013227
29A general co-expression network-based approach to gene expression analysis: comparison and applicationsBMC Systems Biology2010226
30Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell CarcinomaBMC Systems Biology2010223
31Extended local similarity analysis (eLSA) of microbial community and other time series data with replicatesBMC Systems Biology2011223
32targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysisBMC Systems Biology2008222
33A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factoryBMC Systems Biology2008222
34Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertilityBMC Systems Biology2008221
35Optimization in computational systems biologyBMC Systems Biology2008218
36Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approachBMC Systems Biology2011215
37Transforming Boolean models to continuous models: methodology and application to T-cell receptor signalingBMC Systems Biology2009212
38Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup LanguageBMC Systems Biology2011211
39A new essential protein discovery method based on the integration of protein-protein interaction and gene expression dataBMC Systems Biology2012211
40Global dynamic optimization approach to predict activation in metabolic pathwaysBMC Systems Biology2014211
41The Cell Collective: Toward an open and collaborative approach to systems biologyBMC Systems Biology2012199
42CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalismsBMC Systems Biology2012198
43OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strainsBMC Systems Biology2010188
44Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivoBMC Systems Biology2009187
45Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetaseBMC Systems Biology2010184
46Low-complexity regions within protein sequences have position-dependent rolesBMC Systems Biology2010181
47BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence featuresBMC Systems Biology2010177
48Snazer: the simulations and networks analyzerBMC Systems Biology2010175
49The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysisBMC Systems Biology2010175
50Metabolic effects of influenza virus infection in cultured animal cells: Intra- and extracellular metabolite profilingBMC Systems Biology2010174