| # | Title | Journal | Year | Citations |
|---|
| 1 | From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline | Current Protocols in Bioinformatics | 2013 | 4,796 |
| 2 | Comparative Protein Structure Modeling Using Modeller | Current Protocols in Bioinformatics | 2006 | 2,858 |
| 3 | The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses | Current Protocols in Bioinformatics | 2016 | 2,405 |
| 4 | Comparative Protein Structure Modeling Using MODELLER | Current Protocols in Bioinformatics | 2016 | 2,248 |
| 5 | Multiple Sequence Alignment Using ClustalW and ClustalX | Current Protocols in Bioinformatics | 2003 | 1,862 |
| 6 | BEDTools: The Swiss‐Army Tool for Genome Feature Analysis | Current Protocols in Bioinformatics | 2014 | 1,836 |
| 7 | Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis | Current Protocols in Bioinformatics | 2019 | 1,644 |
| 8 | Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences | Current Protocols in Bioinformatics | 2009 | 1,548 |
| 9 | Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis | Current Protocols in Bioinformatics | 2016 | 1,293 |
| 10 | Using SPAdes De Novo Assembler | Current Protocols in Bioinformatics | 2020 | 1,113 |
| 11 | Aligning Short Sequencing Reads with Bowtie | Current Protocols in Bioinformatics | 2010 | 1,027 |
| 12 | Comparative Protein Structure Modeling Using MODELLER | Current Protocols in Bioinformatics | 2014 | 860 |
| 13 | Mapping RNA‐seq Reads with STAR | Current Protocols in Bioinformatics | 2015 | 858 |
| 14 | Using ggtree to Visualize Data on Tree‐Like Structures | Current Protocols in Bioinformatics | 2020 | 810 |
| 15 | Biological Network Exploration with Cytoscape 3 | Current Protocols in Bioinformatics | 2014 | 780 |
| 16 | Using AutoDock for Ligand‐Receptor Docking | Current Protocols in Bioinformatics | 2008 | 573 |
| 17 | An Introduction to Sequence Similarity (“Homology”) Searching | Current Protocols in Bioinformatics | 2013 | 565 |
| 18 | Genome Annotation and Curation Using MAKER and MAKER‐P | Current Protocols in Bioinformatics | 2014 | 543 |
| 19 | Using Repeat Masker to Identify Repetitive Elements in Genomic Sequences | Current Protocols in Bioinformatics | 2004 | 517 |
| 20 | Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities | Current Protocols in Bioinformatics | 2011 | 507 |
| 21 | Using MUMmer to Identify Similar Regions in Large Sequence Sets | Current Protocols in Bioinformatics | 2003 | 505 |
| 22 | Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies | Current Protocols in Bioinformatics | 2010 | 482 |
| 23 | Byonic: Advanced Peptide and Protein Identification Software | Current Protocols in Bioinformatics | 2012 | 473 |
| 24 | Clustal Omega | Current Protocols in Bioinformatics | 2014 | 461 |
| 25 | Protein Sequence Analysis Using the MPI Bioinformatics Toolkit | Current Protocols in Bioinformatics | 2020 | 458 |
| 26 | LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine | Current Protocols in Bioinformatics | 2012 | 406 |
| 27 | Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups | Current Protocols in Bioinformatics | 2011 | 397 |
| 28 | mtDNA Variation and Analysis Using Mitomap and Mitomaster | Current Protocols in Bioinformatics | 2013 | 390 |
| 29 | Searching Online Mendelian Inheritance in Man (OMIM): A Knowledgebase of Human Genes and Genetic Phenotypes | Current Protocols in Bioinformatics | 2017 | 378 |
| 30 | Extracting Biological Meaning from Large Gene Lists with DAVID | Current Protocols in Bioinformatics | 2009 | 375 |
| 31 | Protein Structure and Function Prediction Using I‐TASSER | Current Protocols in Bioinformatics | 2015 | 367 |
| 32 | Inferring Evolutionary Trees with PAUP * | Current Protocols in Bioinformatics | 2003 | 334 |
| 33 | Biological Sequence Motif Discovery Using motif‐x | Current Protocols in Bioinformatics | 2011 | 330 |
| 34 | Non‐Coding RNA Analysis Using the Rfam Database | Current Protocols in Bioinformatics | 2018 | 309 |
| 35 | Analyzing Protein Disorder with IUPred2A | Current Protocols in Bioinformatics | 2020 | 233 |
| 36 | Using the KEGG Database Resource | Current Protocols in Bioinformatics | 2012 | 232 |
| 37 | Predicting Genes in Single Genomes with AUGUSTUS | Current Protocols in Bioinformatics | 2019 | 225 |
| 38 | Employing ProteoWizard to Convert Raw Mass Spectrometry Data | Current Protocols in Bioinformatics | 2014 | 215 |
| 39 | Using RAxML to Infer Phylogenies | Current Protocols in Bioinformatics | 2015 | 215 |
| 40 | QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data | Current Protocols in Bioinformatics | 2020 | 212 |
| 41 | Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence | Current Protocols in Bioinformatics | 2008 | 209 |
| 42 | Using MACS to Identify Peaks from ChIP‐Seq Data | Current Protocols in Bioinformatics | 2011 | 203 |
| 43 | Next Generation Sequence Assembly with AMOS | Current Protocols in Bioinformatics | 2011 | 200 |
| 44 | The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution | Current Protocols in Bioinformatics | 2012 | 198 |
| 45 | Using MODELTEST and PAUP * to Select a Model of Nucleotide Substitution | Current Protocols in Bioinformatics | 2003 | 196 |
| 46 | Metabolomic Data Processing, Analysis, and Interpretation Using MetaboAnalyst | Current Protocols in Bioinformatics | 2011 | 190 |
| 47 | Validation of Tandem Mass Spectrometry Database Search Results Using DTASelect | Current Protocols in Bioinformatics | 2006 | 187 |
| 48 | Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection | Current Protocols in Bioinformatics | 2013 | 174 |
| 49 | miRBase: microRNA Sequences and Annotation | Current Protocols in Bioinformatics | 2010 | 171 |
| 50 | Viewing and Editing Assembled Sequences Using Consed | Current Protocols in Bioinformatics | 2003 | 160 |
