| # | Title | Journal | Year | Citations |
|---|
| 1 | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs | Nucleic Acids Research | 1997 | 64,420 |
| 2 | CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | Nucleic Acids Research | 1994 | 59,168 |
| 3 | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 | Genome Biology | 2014 | 58,325 |
| 4 | A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures | Physiologia Plantarum | 1962 | 56,749 |
| 5 | The neighbor-joining method: a new method for reconstructing phylogenetic trees. | Molecular Biology and Evolution | 1987 | 49,040 |
| 6 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 | Molecular Biology and Evolution | 2013 | 37,728 |
| 7 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks | Genome Research | 2003 | 37,062 |
| 8 | MUSCLE: multiple sequence alignment with high accuracy and high throughput | Nucleic Acids Research | 2004 | 36,947 |
| 9 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets | Molecular Biology and Evolution | 2016 | 36,708 |
| 10 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods | Molecular Biology and Evolution | 2011 | 36,550 |
| 11 | CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP | Evolution; International Journal of Organic Evolution | 1985 | 35,356 |
| 12 | The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools | Nucleic Acids Research | 1997 | 34,934 |
| 13 | Gene Ontology: tool for the unification of biology | Nature Genetics | 2000 | 34,499 |
| 14 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability | Molecular Biology and Evolution | 2013 | 32,012 |
| 15 | The Protein Data Bank | Nucleic Acids Research | 2000 | 31,087 |
| 16 | A new mathematical model for relative quantification in real-time RT-PCR | Nucleic Acids Research | 2001 | 28,594 |
| 17 | Inference of Population Structure Using Multilocus Genotype Data | Genetics | 2000 | 28,015 |
| 18 | PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses | American Journal of Human Genetics | 2007 | 26,761 |
| 19 | limma powers differential expression analyses for RNA-sequencing and microarray studies | Nucleic Acids Research | 2015 | 26,032 |
| 20 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 | Molecular Biology and Evolution | 2007 | 25,988 |
| 21 | A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences | Journal of Molecular Evolution | 1980 | 25,715 |
| 22 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | Molecular Biology and Evolution | 2018 | 25,630 |
| 23 | KEGG: Kyoto Encyclopedia of Genes and Genomes | Nucleic Acids Research | 2000 | 25,375 |
| 24 | The SILVA ribosomal RNA gene database project: improved data processing and web-based tools | Nucleic Acids Research | 2012 | 21,425 |
| 25 | The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data | Genome Research | 2010 | 21,358 |
| 26 | clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters | OMICS A Journal of Integrative Biology | 2012 | 21,237 |
| 27 | MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space | Systematic Biology | 2012 | 20,458 |
| 28 | Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology | Genetics in Medicine | 2015 | 20,455 |
| 29 | SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing | Journal of Computational Biology | 2012 | 20,193 |
| 30 | Methods for Dietary Fiber, Neutral Detergent Fiber, and Nonstarch Polysaccharides in Relation to Animal Nutrition | Journal of Dairy Science | 1991 | 20,119 |
| 31 | COPPER ENZYMES IN ISOLATED CHLOROPLASTS. POLYPHENOLOXIDASE IN BETA VULGARIS | Plant Physiology | 1949 | 19,369 |
| 32 | Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana | Plant Journal | 1998 | 19,148 |
| 33 | Detecting the number of clusters of individuals using the software structure: a simulation study | Molecular Ecology | 2005 | 18,555 |
| 34 | A simple salting out procedure for extracting DNA from human nucleated cells | Nucleic Acids Research | 1988 | 17,239 |
| 35 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | Molecular Biology and Evolution | 2015 | 16,610 |
| 36 | Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors | Gene | 1985 | 16,607 |
| 37 | Confidence Limits on Phylogenies: An Approach Using the Bootstrap | Evolution; International Journal of Organic Evolution | 1985 | 16,574 |
| 38 | A comprehensive set of sequence analysis programs for the VAX | Nucleic Acids Research | 1984 | 15,665 |
| 39 | A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood | Systematic Biology | 2003 | 15,438 |
| 40 | A rapid alkaline extraction procedure for screening recombinant plasmid DNA | Nucleic Acids Research | 1979 | 15,424 |
| 41 | New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 | Systematic Biology | 2010 | 15,166 |
| 42 | GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism | Journal of Heredity | 1995 | 14,222 |
| 43 | THE GENETICS OF CAENORHABDITIS ELEGANS | Genetics | 1974 | 13,957 |
| 44 | Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement | Cytotherapy | 2006 | 13,839 |
| 45 | KEGG: Kyoto Encyclopedia of Genes and Genomes | Nucleic Acids Research | 1999 | 13,711 |
| 46 | Differential expression analysis for sequence count data | Genome Biology | 2010 | 13,707 |
| 47 | Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows | Molecular Ecology Resources | 2010 | 13,484 |
| 48 | Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists | Nucleic Acids Research | 2009 | 13,313 |
| 49 | ANALYZING TABLES OF STATISTICAL TESTS | Evolution; International Journal of Organic Evolution | 1989 | 13,049 |
| 50 | Evolutionary trees from DNA sequences: A maximum likelihood approach | Journal of Molecular Evolution | 1981 | 12,784 |
| 51 | MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform | Nucleic Acids Research | 2002 | 12,537 |
| 52 | genalex 6: genetic analysis in Excel. Population genetic software for teaching and research | Molecular Ecology Notes | 2006 | 12,505 |
| 53 | STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets | Nucleic Acids Research | 2019 | 12,237 |
| 54 | Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei | Nucleic Acids Research | 1983 | 12,076 |
| 55 | Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. | Genetics | 1989 | 11,867 |
| 56 | Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. | Genetics | 1992 | 11,818 |
| 57 | Mfold web server for nucleic acid folding and hybridization prediction | Nucleic Acids Research | 2003 | 11,479 |
| 58 | PAML 4: Phylogenetic Analysis by Maximum Likelihood | Molecular Biology and Evolution | 2007 | 11,130 |
| 59 | ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data | Nucleic Acids Research | 2010 | 10,960 |
| 60 | Gene Expression Omnibus: NCBI gene expression and hybridization array data repository | Nucleic Acids Research | 2002 | 10,953 |
| 61 | DNA polymorphisms amplified by arbitrary primers are useful as genetic markers | Nucleic Acids Research | 1990 | 10,873 |
| 62 | AFLP: a new technique for DNA fingerprinting | Nucleic Acids Research | 1995 | 10,873 |
| 63 | WebLogo: A Sequence Logo Generator | Genome Research | 2004 | 10,751 |
| 64 | RNA-Seq: a revolutionary tool for transcriptomics | Nature Reviews Genetics | 2009 | 10,529 |
| 65 | ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE | Evolution; International Journal of Organic Evolution | 1984 | 10,475 |
| 66 | Rapid isolation of high molecular weight plant DNA | Nucleic Acids Research | 1980 | 10,345 |
| 67 | STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method | Conservation Genetics Resources | 2012 | 10,115 |
| 68 | A framework for variation discovery and genotyping using next-generation DNA sequencing data | Nature Genetics | 2011 | 10,018 |
| 69 | Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments | Statistical Applications in Genetics and Molecular Biology | 2004 | 9,992 |
| 70 | The RAST Server: Rapid Annotations using Subsystems Technology | BMC Genomics | 2008 | 9,977 |
| 71 | Median-joining networks for inferring intraspecific phylogenies | Molecular Biology and Evolution | 1999 | 9,666 |
| 72 | tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence | Nucleic Acids Research | 1997 | 9,417 |
| 73 | ESTIMATION OF AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE FROM A SMALL NUMBER OF INDIVIDUALS | Genetics | 1978 | 9,389 |
| 74 | jModelTest: Phylogenetic Model Averaging | Molecular Biology and Evolution | 2008 | 9,343 |
| 75 | micro-checker: software for identifying and correcting genotyping errors in microsatellite data | Molecular Ecology Notes | 2004 | 9,051 |
| 76 | Bayesian Phylogenetics with BEAUti and the BEAST 1.7 | Molecular Biology and Evolution | 2012 | 9,040 |
| 77 | STRING v10: protein–protein interaction networks, integrated over the tree of life | Nucleic Acids Research | 2015 | 9,029 |
| 78 | Circos: An information aesthetic for comparative genomics | Genome Research | 2009 | 9,003 |
| 79 | Principal components analysis corrects for stratification in genome-wide association studies | Nature Genetics | 2006 | 8,889 |
| 80 | Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis | Molecular Biology and Evolution | 2000 | 8,843 |
| 81 | The Human Genome Browser at UCSC | Genome Research | 2002 | 8,776 |
| 82 | Velvet: Algorithms for de novo short read assembly using de Bruijn graphs | Genome Research | 2008 | 8,699 |
| 83 | A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. | Genetics | 1989 | 8,595 |
| 84 | TCS: a computer program to estimate gene genealogies | Molecular Ecology | 2000 | 8,515 |
| 85 | SWISS-MODEL: homology modelling of protein structures and complexes | Nucleic Acids Research | 2018 | 8,474 |
| 86 | Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. | Molecular Biology and Evolution | 1993 | 8,355 |
| 87 | ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts | Molecular Ecology | 1993 | 8,354 |
| 88 | Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants | Plant Physiology and Biochemistry | 2010 | 8,238 |
| 89 | PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes | Nature Genetics | 2003 | 8,185 |
| 90 | MEME SUITE: tools for motif discovery and searching | Nucleic Acids Research | 2009 | 8,180 |
| 91 | EMBOSS: The European Molecular Biology Open Software Suite | Trends in Genetics | 2000 | 8,136 |
| 92 | Site-directed mutagenesis by overlap extension using the polymerase chain reaction | Gene | 1989 | 7,939 |
| 93 | EVOLUTION IN MENDELIAN POPULATIONS | Genetics | 1931 | 7,737 |
| 94 | Dating of the human-ape splitting by a molecular clock of mitochondrial DNA | Journal of Molecular Evolution | 1985 | 7,690 |
| 95 | genepop’007: a complete re‐implementation of the genepop software for Windows and Linux | Molecular Ecology Resources | 2008 | 7,546 |
| 96 | CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes | Genome Research | 2015 | 7,539 |
| 97 | Primer3—new capabilities and interfaces | Nucleic Acids Research | 2012 | 7,501 |
| 98 | Application of Phylogenetic Networks in Evolutionary Studies | Molecular Biology and Evolution | 2006 | 7,402 |
| 99 | A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species | Planta | 1980 | 7,254 |
| 100 | Enrichr: a comprehensive gene set enrichment analysis web server 2016 update | Nucleic Acids Research | 2016 | 7,240 |
