| # | Title | Journal | Year | Citations |
|---|
|
| 1 | clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters | OMICS A Journal of Integrative Biology | 2012 | 23,430 |
| 2 | The RAST Server: Rapid Annotations using Subsystems Technology | BMC Genomics | 2008 | 10,338 |
| 3 | A plant DNA minipreparation: Version II | Plant Molecular Biology Reporter | 1983 | 6,137 |
| 4 | Assaying chimeric genes in plants: The GUS gene fusion system | Plant Molecular Biology Reporter | 1987 | 3,955 |
| 5 | Oxidative stress and some antioxidant systems in acid rain-treated bean plants | Plant Science | 2000 | 3,716 |
| 6 | A simple and efficient method for isolating RNA from pine trees | Plant Molecular Biology Reporter | 1993 | 3,124 |
| 7 | The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation | BMC Genomics | 2020 | 2,905 |
| 8 | BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons | BMC Genomics | 2011 | 2,840 |
| 9 | Nuclear DNA content of some important plant species | Plant Molecular Biology Reporter | 1991 | 2,807 |
| 10 | Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden | Genome Medicine | 2017 | 2,617 |
| 11 | Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions | DNA Research | 1996 | 2,559 |
| 12 | Repbase Update, a database of repetitive elements in eukaryotic genomes | Mobile DNA | 2015 | 2,398 |
| 13 | Centering, scaling, and transformations: improving the biological information content of metabolomics data | BMC Genomics | 2006 | 1,902 |
| 14 | Next-Generation DNA Sequencing Methods | Annual Review of Genomics and Human Genetics | 2008 | 1,828 |
| 15 | Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics | BMC Genomics | 2018 | 1,809 |
| 16 | Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components | Plant Molecular Biology Reporter | 1997 | 1,806 |
| 17 | PacBio Sequencing and its Applications | Genomics, Proteomics and Bioinformatics | 2015 | 1,758 |
| 18 | Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences | G3: Genes, Genomes, Genetics | 2011 | 1,717 |
| 19 | A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers | BMC Genomics | 2012 | 1,645 |
| 20 | Heavy metal hyperaccumulating plants: How and why do they do it? And what makes them so interesting? | Plant Science | 2011 | 1,569 |
| 21 | Exosome and Exosomal MicroRNA: Trafficking, Sorting, and Function | Genomics, Proteomics and Bioinformatics | 2015 | 1,565 |
| 22 | Antioxidant responses of rice seedlings to salinity stress | Plant Science | 1998 | 1,543 |
| 23 | Apolipoprotein E: Far More Than a Lipid Transport Protein | Annual Review of Genomics and Human Genetics | 2000 | 1,509 |
| 24 | Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison | Standards in Genomic Sciences | 2010 | 1,506 |
| 25 | Flavonoids as antioxidants in plants: Location and functional significance | Plant Science | 2012 | 1,494 |
| 26 | Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing | BMC Genomics | 2015 | 1,480 |
| 27 | A NEWAPPROACH TODECODINGLIFE: Systems Biology | Annual Review of Genomics and Human Genetics | 2001 | 1,474 |
| 28 | Potential biochemical indicators of salinity tolerance in plants | Plant Science | 2004 | 1,468 |
| 29 | BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams | BMC Genomics | 2008 | 1,434 |
| 30 | KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies | Genomics, Proteomics and Bioinformatics | 2010 | 1,405 |
| 31 | Mechanism of Salinity Tolerance in Plants: Physiological, Biochemical, and Molecular Characterization | International Journal of Genomics | 2014 | 1,339 |
| 32 | A genome-wide association study of seed protein and oil content in soybean | BMC Genomics | 2014 | 1,324 |
| 33 | The healthy human microbiome | Genome Medicine | 2016 | 1,296 |
| 34 | Nanoparticulate material delivery to plants | Plant Science | 2010 | 1,293 |
| 35 | Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research | DNA Research | 2006 | 1,237 |
| 36 | Doxorubicin pathways | Pharmacogenetics and Genomics | 2011 | 1,237 |
| 37 | Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.) | DNA Research | 2002 | 1,221 |
| 38 | Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12 | DNA Research | 2001 | 1,207 |
| 39 | The molecular portraits of breast tumors are conserved across microarray platforms | BMC Genomics | 2006 | 1,185 |
| 40 | BlobToolKit – Interactive Quality Assessment of Genome Assemblies | G3: Genes, Genomes, Genetics | 2020 | 1,138 |
| 41 | Sex-specific, male-line transgenerational responses in humans | European Journal of Human Genetics | 2006 | 1,084 |
| 42 | Polyamines and environmental challenges: recent development | Plant Science | 1999 | 1,082 |
| 43 | Impact of the gut microbiota on inflammation, obesity, and metabolic disease | Genome Medicine | 2016 | 1,062 |
| 44 | Copy Number Variation in Human Health, Disease, and Evolution | Annual Review of Genomics and Human Genetics | 2009 | 1,054 |
| 45 | Sequence Analysis of the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence Determination of the Entire Genome and Assignment of Potential Protein-coding Regions (Supplement) | DNA Research | 1996 | 1,005 |
| 46 | The Ciliopathies: An Emerging Class of Human Genetic Disorders | Annual Review of Genomics and Human Genetics | 2006 | 1,005 |
| 47 | SRST2: Rapid genomic surveillance for public health and hospital microbiology labs | Genome Medicine | 2014 | 1,002 |
| 48 | KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging | Genomics, Proteomics and Bioinformatics | 2006 | 988 |
| 49 | Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity | Pharmacogenomics Journal | 2005 | 975 |
| 50 | Lead toxicity induces lipid peroxidation and alters the activities of antioxidant enzymes in growing rice plants | Plant Science | 2003 | 959 |
| 51 | Comprehensive Analysis of NAC Family Genes in Oryza sativa and Arabidopsis thaliana | DNA Research | 2003 | 950 |
| 52 | Genotype Imputation | Annual Review of Genomics and Human Genetics | 2009 | 942 |
| 53 | The complex transcriptional landscape of the anucleate human platelet | BMC Genomics | 2013 | 935 |
| 54 | Antioxidative parameters in the seedlings of pigeonpea (Cajanus cajan (L.) Millspaugh) in response to Zn and Ni stresses | Plant Science | 2000 | 934 |
| 55 | Production of plant secondary metabolites: a historical perspective | Plant Science | 2001 | 931 |
| 56 | Differential response of wheat genotypes to long term salinity stress in relation to oxidative stress, antioxidant activity and osmolyte concentration | Plant Science | 2002 | 922 |
| 57 | Characterization of microRNA expression profiles in normal human tissues | BMC Genomics | 2007 | 916 |
| 58 | Characterization of human plasma-derived exosomal RNAs by deep sequencing | BMC Genomics | 2013 | 899 |
| 59 | Genotype Imputation with Thousands of Genomes | G3: Genes, Genomes, Genetics | 2011 | 892 |
| 60 | A data-driven approach to preprocessing Illumina 450K methylation array data | BMC Genomics | 2013 | 877 |
| 61 | A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains | BMC Genomics | 2007 | 864 |
| 62 | Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database | European Journal of Human Genetics | 2020 | 856 |
| 63 | LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana | BMC Genomics | 2008 | 854 |
| 64 | Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data | Genome Medicine | 2019 | 848 |
| 65 | MAMMALIAN CIRCADIAN BIOLOGY: Elucidating Genome-Wide Levels of Temporal Organization | Annual Review of Genomics and Human Genetics | 2004 | 843 |
| 66 | Stressful “memories” of plants: Evidence and possible mechanisms | Plant Science | 2007 | 841 |
| 67 | The Cytochrome P450 Homepage | Human Genomics | 2009 | 837 |
| 68 | A simple and efficient method for DNA extraction from grapevine cultivars andVitis species | Plant Molecular Biology Reporter | 1994 | 836 |
| 69 | Predicting the Effects of Amino Acid Substitutions on Protein Function | Annual Review of Genomics and Human Genetics | 2006 | 824 |
| 70 | Phytoremediation and rhizoremediation of organic soil contaminants: Potential and challenges | Plant Science | 2009 | 822 |
| 71 | Roles, Functions, and Mechanisms of Long Non-Coding RNAs in Cancer | Genomics, Proteomics and Bioinformatics | 2016 | 821 |
| 72 | PrognoScan: a new database for meta-analysis of the prognostic value of genes | BMC Medical Genomics | 2009 | 820 |
| 73 | Cardiovascular and diabetes mortality determined by nutrition during parents' and grandparents' slow growth period | European Journal of Human Genetics | 2002 | 802 |
| 74 | ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases | BMC Genomics | 2014 | 799 |
| 75 | Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes | BMC Genomics | 2012 | 794 |
| 76 | A new approach for efficient genotype imputation using information from relatives | BMC Genomics | 2014 | 791 |
| 77 | Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers | Plant Science | 2004 | 789 |
| 78 | BioMart – biological queries made easy | BMC Genomics | 2009 | 786 |
| 79 | The Human Gene Mutation Database: 2008 update | Genome Medicine | 2009 | 782 |
| 80 | A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications | Genome Medicine | 2017 | 782 |
| 81 | Microprep protocol for extraction of DNA from tomato and other herbaceous plants | Plant Molecular Biology Reporter | 1995 | 781 |
| 82 | Complete Genomic Sequence of Nitrogen-fixing Symbiotic Bacterium Bradyrhizobium japonicum USDA110 | DNA Research | 2002 | 778 |
| 83 | A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis | Plant Molecular Biology Reporter | 1993 | 777 |
| 84 | Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes | DNA Research | 2007 | 772 |
| 85 | Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile | BMC Genomics | 2018 | 771 |
| 86 | Locating rearrangement events in a phylogeny based on highly fragmented assemblies | BMC Genomics | 2016 | 767 |
| 87 | Polygenic risk scores: from research tools to clinical instruments | Genome Medicine | 2020 | 766 |
| 88 | Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks | Comparative and Functional Genomics | 2001 | 762 |
| 89 | Recent advances on the regulation of anthocyanin synthesis in reproductive organs | Plant Science | 2011 | 758 |
| 90 | A Brief Review on the Mechanisms of miRNA Regulation | Genomics, Proteomics and Bioinformatics | 2009 | 750 |
| 91 | Effect of cadmium on lipid peroxidation, superoxide anion generation and activities of antioxidant enzymes in growing rice seedlings | Plant Science | 2001 | 749 |
| 92 | Complete Genome Structure of the Nitrogen-fixing Symbiotic Bacterium Mesorhizobium loti | DNA Research | 2000 | 744 |
| 93 | Transcriptional Regulatory Elements in the Human Genome | Annual Review of Genomics and Human Genetics | 2006 | 734 |
| 94 | Silicon alleviates salt stress and increases antioxidant enzymes activity in leaves of salt-stressed cucumber (Cucumis sativus L.) | Plant Science | 2004 | 720 |
| 95 | Nomenclature update for the mammalian UDP glycosyltransferase (UGT) gene superfamily | Pharmacogenetics and Genomics | 2005 | 717 |
| 96 | The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms | Annual Review of Genomics and Human Genetics | 2009 | 716 |
| 97 | The RASopathies | Annual Review of Genomics and Human Genetics | 2013 | 711 |
| 98 | Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks | BMC Genomics | 2019 | 705 |
| 99 | Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing | BMC Genomics | 2017 | 700 |
| 100 | The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation | Genome Medicine | 2016 | 699 |
