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3A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye bindingAnalytical Biochemistry1976215,588
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9Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA StatementPLoS Medicine200950,671
10The Sequence Alignment/Map format and SAMtoolsBioinformatics200949,124
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12Fiji: an open-source platform for biological-image analysisNature Methods201247,818
13NIH Image to ImageJ: 25 years of image analysisNature Methods201246,756
14Trimmomatic: a flexible trimmer for Illumina sequence dataBioinformatics201446,646
15Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics200943,062
16Fast gapped-read alignment with Bowtie 2Nature Methods201242,357
17A simple method for the isolation and purification of total lipides from animal tissuesJournal of Biological Chemistry195741,692
18MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0Molecular Biology and Evolution201337,728
19MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger DatasetsMolecular Biology and Evolution201636,708
20MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsMolecular Biology and Evolution201136,550
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22STAR: ultrafast universal RNA-seq alignerBioinformatics201335,376
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24edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics201032,955
25MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution201332,012
26QIIME allows analysis of high-throughput community sequencing dataNature Methods201031,818
27Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform ExtractionAnalytical Biochemistry198727,111
28RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesBioinformatics201426,744
29MrBayes 3: Bayesian phylogenetic inference under mixed modelsBioinformatics200326,519
30MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0Molecular Biology and Evolution200725,988
31A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution198025,715
32MEGA X: Molecular Evolutionary Genetics Analysis across Computing PlatformsMolecular Biology and Evolution201825,630
33Clustal W and Clustal X version 2.0Bioinformatics200725,174
34A technique for radiolabeling DNA restriction endonuclease fragments to high specific activityAnalytical Biochemistry198324,572
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37A simple method for displaying the hydropathic character of a proteinJournal of Molecular Biology198222,171
38clusterProfiler: an R Package for Comparing Biological Themes Among Gene ClustersOMICS A Journal of Integrative Biology201221,237
39BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics201020,367
40SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology201220,193
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42MRBAYES: Bayesian inference of phylogenetic treesBioinformatics200120,154
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44Measurement of protein using bicinchoninic acidAnalytical Biochemistry198519,774
45The Reliability of Molecular Weight Determinations by Dodecyl Sulfate-Polyacrylamide Gel ElectrophoresisJournal of Biological Chemistry196919,178
46MODELTEST: testing the model of DNA substitution.Bioinformatics199818,761
47DADA2: High-resolution sample inference from Illumina amplicon dataNature Methods201618,691
48Search and clustering orders of magnitude faster than BLASTBioinformatics201018,572
49High resolution two-dimensional electrophoresis of proteins.Journal of Biological Chemistry197517,755
50THE COLORIMETRIC DETERMINATION OF PHOSPHORUSJournal of Biological Chemistry192517,551
51SciPy 1.0: fundamental algorithms for scientific computing in PythonNature Methods202017,539
52WGCNA: an R package for weighted correlation network analysisBMC Bioinformatics200817,294
53HTSeq—a Python framework to work with high-throughput sequencing dataBioinformatics201517,270
54featureCounts: an efficient general purpose program for assigning sequence reads to genomic featuresBioinformatics201416,839
55A new generation of Ca2+ indicators with greatly improved fluorescence propertiesJournal of Biological Chemistry198516,813
56IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood PhylogeniesMolecular Biology and Evolution201516,610
57Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectorsGene198516,607
58The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresisJournal of Biological Chemistry196916,592
59HISAT: a fast spliced aligner with low memory requirementsNature Methods201516,262
60Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataBioinformatics201216,096
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62The Ferric Reducing Ability of Plasma (FRAP) as a Measure of “Antioxidant Power”: The FRAP AssayAnalytical Biochemistry199616,000
63High resolution two-dimensional electrophoresis of proteinsJournal of Biological Chemistry197515,403
64BLAST+: architecture and applicationsBMC Bioinformatics200914,935
65RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics200614,675
66Glutathione S-TransferasesJournal of Biological Chemistry197414,618
67GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and EcumenicismJournal of Heredity199514,222
69The PRISMA Statement for Reporting Systematic Reviews and Meta-Analyses of Studies That Evaluate Health Care Interventions: Explanation and ElaborationPLoS Medicine200913,772
70DnaSP v5: a software for comprehensive analysis of DNA polymorphism dataBioinformatics200913,645
71jModelTest 2: more models, new heuristics and parallel computingNature Methods201213,416
72UCHIME improves sensitivity and speed of chimera detectionBioinformatics201113,241
73Haploview: analysis and visualization of LD and haplotype mapsBioinformatics200513,223
74UPARSE: highly accurate OTU sequences from microbial amplicon readsNature Methods201313,193
75Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase IJournal of Molecular Biology197713,093
76Prokka: rapid prokaryotic genome annotationBioinformatics201412,881
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78Phosphorus Assay in Column ChromatographyJournal of Biological Chemistry195912,077
79Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods200812,050
80Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology199311,892
81Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDaAnalytical Biochemistry198711,692
82FLASH: fast length adjustment of short reads to improve genome assembliesBioinformatics201111,573
83A procedure for the isolation of deoxyribonucleic acid from micro-organismsJournal of Molecular Biology196111,512
84A method and server for predicting damaging missense mutationsNature Methods201011,491
85Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. CohenJournal of Molecular Biology200111,404
86Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortalScience Signaling201311,344
87The variant call format and VCFtoolsBioinformatics201111,326
88TopHat: discovering splice junctions with RNA-SeqBioinformatics200911,265
89Basic Local Alignment Search ToolJournal of Molecular Biology199011,186
90PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution200711,130
91fastp: an ultra-fast all-in-one FASTQ preprocessorBioinformatics201811,005
92Superoxide DismutaseJournal of Biological Chemistry196910,959
93Glutathione S-transferases. The first enzymatic step in mercapturic acid formationJournal of Biological Chemistry197410,908
94Studies on transformation of Escherichia coli with plasmidsJournal of Molecular Biology198310,861
95Analysis of nitrate, nitrite, and [15N]nitrate in biological fluidsAnalytical Biochemistry198210,819
96GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an updateBioinformatics201210,741
97APE: Analyses of Phylogenetics and Evolution in R languageBioinformatics200410,601
98MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignmentBriefings in Bioinformatics200410,598
99Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchBioinformatics200510,566
100RNA-Seq: a revolutionary tool for transcriptomicsNature Reviews Genetics200910,529