# | Title | Journal | Year | Citations |
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1 | Basic local alignment search tool | Journal of Molecular Biology | 1990 | 82,180 |
2 | Detection of specific sequences among DNA fragments separated by gel electrophoresis | Journal of Molecular Biology | 1975 | 35,546 |
3 | A simple method for displaying the hydropathic character of a protein | Journal of Molecular Biology | 1982 | 22,171 |
4 | SHELXT– Integrated space-group and crystal-structure determination | Acta Crystallographica Section A: Foundations and Advances | 2015 | 18,933 |
5 | WGCNA: an R package for weighted correlation network analysis | BMC Bioinformatics | 2008 | 17,294 |
6 | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome | BMC Bioinformatics | 2011 | 16,042 |
7 | BLAST+: architecture and applications | BMC Bioinformatics | 2009 | 14,935 |
8 | Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I | Journal of Molecular Biology | 1977 | 13,093 |
9 | Comparative Protein Modelling by Satisfaction of Spatial Restraints | Journal of Molecular Biology | 1993 | 11,892 |
10 | A procedure for the isolation of deoxyribonucleic acid from micro-organisms | Journal of Molecular Biology | 1961 | 11,512 |
11 | Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen | Journal of Molecular Biology | 2001 | 11,404 |
12 | Studies on transformation of Escherichia coli with plasmids | Journal of Molecular Biology | 1983 | 10,861 |
13 | A general method applicable to the search for similarities in the amino acid sequence of two proteins | Journal of Molecular Biology | 1970 | 9,639 |
14 | The protein data bank: A computer-based archival file for macromolecular structures | Journal of Molecular Biology | 1977 | 8,738 |
15 | pROC: an open-source package for R and S+ to analyze and compare ROC curves | BMC Bioinformatics | 2011 | 8,498 |
16 | Inference of Macromolecular Assemblies from Crystalline State | Journal of Molecular Biology | 2007 | 8,484 |
17 | On the nature of allosteric transitions: A plausible model | Journal of Molecular Biology | 1965 | 8,467 |
18 | Identification of common molecular subsequences | Journal of Molecular Biology | 1981 | 8,440 |
19 | Prodigal: prokaryotic gene recognition and translation initiation site identification | BMC Bioinformatics | 2010 | 8,237 |
20 | Solvent content of protein crystals | Journal of Molecular Biology | 1968 | 8,228 |
21 | GSVA: gene set variation analysis for microarray and RNA-Seq data | BMC Bioinformatics | 2013 | 7,876 |
22 | MUSCLE: a multiple sequence alignment method with reduced time and space complexity | BMC Bioinformatics | 2004 | 7,508 |
23 | T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton | Journal of Molecular Biology | 2000 | 6,404 |
24 | Selective extraction of polyoma DNA from infected mouse cell cultures | Journal of Molecular Biology | 1967 | 6,287 |
25 | Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes | Journal of Molecular Biology | 1986 | 6,199 |
26 | Comparison of multiple Amber force fields and development of improved protein backbone parameters | Proteins: Structure, Function and Bioinformatics | 2006 | 6,049 |
27 | Improved Prediction of Signal Peptides: SignalP 3.0 | Journal of Molecular Biology | 2004 | 6,015 |
28 | Genetic regulatory mechanisms in the synthesis of proteins | Journal of Molecular Biology | 1961 | 6,014 |
29 | Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen | Journal of Molecular Biology | 1997 | 5,937 |
30 | An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database | Journal of the American Society for Mass Spectrometry | 1994 | 5,912 |
31 | The interpretation of protein structures: Estimation of static accessibility | Journal of Molecular Biology | 1971 | 5,785 |
32 | SCOP: a structural classification of proteins database for the investigation of sequences and structures | Journal of Molecular Biology | 1995 | 5,400 |
33 | Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons | Proteins: Structure, Function and Bioinformatics | 1991 | 5,360 |
34 | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool | BMC Bioinformatics | 2013 | 5,305 |
35 | Genome sequence-based species delimitation with confidence intervals and improved distance functions | BMC Bioinformatics | 2013 | 5,139 |
36 | Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne | Journal of Molecular Biology | 1999 | 5,026 |
37 | Computer Visualization of Three-Dimensional Image Data Using IMOD | Journal of Structural Biology | 1996 | 4,964 |
38 | From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline | Current Protocols in Bioinformatics | 2013 | 4,796 |
39 | An automated method for finding molecular complexes in large protein interaction networks | BMC Bioinformatics | 2003 | 4,773 |
40 | RELION: Implementation of a Bayesian approach to cryo-EM structure determination | Journal of Structural Biology | 2012 | 4,715 |
41 | Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins | Journal of Molecular Biology | 1978 | 4,696 |
42 | Improved side‐chain torsion potentials for the Amber ff99SB protein force field | Proteins: Structure, Function and Bioinformatics | 2010 | 4,694 |
43 | ImageJ2: ImageJ for the next generation of scientific image data | BMC Bioinformatics | 2017 | 4,464 |
44 | Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction | BMC Bioinformatics | 2012 | 4,446 |
45 | Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature | Journal of Molecular Biology | 1962 | 4,433 |
46 | I-TASSER server for protein 3D structure prediction | BMC Bioinformatics | 2008 | 4,415 |
47 | Automated electron microscope tomography using robust prediction of specimen movements | Journal of Structural Biology | 2005 | 4,320 |
48 | A complementation analysis of the restriction and modification of DNA in Escherichia coli | Journal of Molecular Biology | 1969 | 4,258 |
49 | Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence | Journal of Molecular Biology | 2000 | 4,166 |
50 | Structure validation by Cα geometry: ϕ,ψ and Cβ deviation | Proteins: Structure, Function and Bioinformatics | 2003 | 4,134 |
51 | Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix | Acta Crystallographica Section D: Structural Biology | 2019 | 4,060 |
52 | Maturation of the head of bacteriophage T4 | Journal of Molecular Biology | 1973 | 4,042 |
53 | Diffusion of univalent ions across the lamellae of swollen phospholipids | Journal of Molecular Biology | 1965 | 4,013 |
54 | Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme | Journal of Molecular Biology | 1976 | 3,971 |
55 | SCOP: A structural classification of proteins database for the investigation of sequences and structures | Journal of Molecular Biology | 1995 | 3,952 |
56 | The COG database: an updated version includes eukaryotes | BMC Bioinformatics | 2003 | 3,913 |
57 | CTFFIND4: Fast and accurate defocus estimation from electron micrographs | Journal of Structural Biology | 2015 | 3,894 |
58 | Protein Structure Comparison by Alignment of Distance Matrices | Journal of Molecular Biology | 1993 | 3,851 |
59 | Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing | Journal of Molecular Biology | 1980 | 3,786 |
60 | Prediction of complete gene structures in human genomic DNA | Journal of Molecular Biology | 1997 | 3,746 |
61 | ViennaRNA Package 2.0 | Algorithms for Molecular Biology | 2011 | 3,719 |
62 | Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure | Journal of Molecular Biology | 1999 | 3,486 |
63 | cytoHubba: identifying hub objects and sub-networks from complex interactome | BMC Systems Biology | 2014 | 3,371 |
64 | Gctf: Real-time CTF determination and correction | Journal of Structural Biology | 2016 | 3,244 |
65 | The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes | BMC Bioinformatics | 2008 | 3,200 |
66 | Stereochemistry of polypeptide chain configurations | Journal of Molecular Biology | 1963 | 3,147 |
67 | Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy | Journal of Molecular Biology | 1990 | 3,109 |
68 | CpG Islands in vertebrate genomes | Journal of Molecular Biology | 1987 | 3,038 |
69 | GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists | BMC Bioinformatics | 2009 | 3,032 |
70 | MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data | BMC Bioinformatics | 2010 | 3,031 |
71 | Essential dynamics of proteins | Proteins: Structure, Function and Bioinformatics | 1993 | 2,927 |
72 | Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice | Journal of Molecular Biology | 1974 | 2,895 |
73 | BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences | Journal of Molecular Biology | 2016 | 2,872 |
74 | Prediction of Protein Secondary Structure at Better than 70% Accuracy | Journal of Molecular Biology | 1993 | 2,860 |
75 | Comparative Protein Structure Modeling Using Modeller | Current Protocols in Bioinformatics | 2006 | 2,858 |
76 | The CCPN data model for NMR spectroscopy: Development of a software pipeline | Proteins: Structure, Function and Bioinformatics | 2005 | 2,805 |
77 | EMAN2: An extensible image processing suite for electron microscopy | Journal of Structural Biology | 2007 | 2,798 |
78 | Sequence and structure-based prediction of eukaryotic protein phosphorylation sites | Journal of Molecular Biology | 1999 | 2,767 |
79 | Calcium-dependent bacteriophage DNA infection | Journal of Molecular Biology | 1970 | 2,741 |
80 | Torsion angle dynamics for NMR structure calculation with the new program Dyana | Journal of Molecular Biology | 1997 | 2,731 |
81 | Reagent and laboratory contamination can critically impact sequence-based microbiome analyses | BMC Biology | 2014 | 2,677 |
82 | Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm | Journal of Molecular Biology | 1999 | 2,668 |
83 | Analysis of gene control signals by DNA fusion and cloning in Escherichia coli | Journal of Molecular Biology | 1980 | 2,655 |
84 | A Fast Flexible Docking Method using an Incremental Construction Algorithm | Journal of Molecular Biology | 1996 | 2,609 |
85 | DNA methylation arrays as surrogate measures of cell mixture distribution | BMC Bioinformatics | 2012 | 2,563 |
86 | Molecular dynamics simulations of biomolecules | Nature Structural Biology | 2002 | 2,473 |
87 | Gene finding in novel genomes | BMC Bioinformatics | 2004 | 2,443 |
88 | Improved protein-ligand docking using GOLD | Proteins: Structure, Function and Bioinformatics | 2003 | 2,417 |
89 | Funnels, pathways, and the energy landscape of protein folding: A synthesis | Proteins: Structure, Function and Bioinformatics | 1995 | 2,415 |
90 | The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses | Current Protocols in Bioinformatics | 2016 | 2,405 |
91 | Analysis of bacteriophage T7 early RNAs and proteins on slab gels | Journal of Molecular Biology | 1973 | 2,380 |
92 | ‘Green mice’ as a source of ubiquitous green cells | FEBS Letters | 1997 | 2,364 |
93 | Announcing the worldwide Protein Data Bank | Nature Structural and Molecular Biology | 2003 | 2,355 |
94 | CATH – a hierarchic classification of protein domain structures | Structure | 1997 | 2,347 |
95 | Exon-intron circular RNAs regulate transcription in the nucleus | Nature Structural and Molecular Biology | 2015 | 2,330 |
96 | Sedimentation studies of the size and shape of DNA | Journal of Molecular Biology | 1965 | 2,329 |
97 | Automated protein model building combined with iterative structure refinement | Nature Structural Biology | 1999 | 2,328 |
98 | Bias in random forest variable importance measures: Illustrations, sources and a solution | BMC Bioinformatics | 2007 | 2,328 |
99 | EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions | Journal of Structural Biology | 1999 | 2,320 |
100 | A fluorescent complex between ethidium bromide and nucleic acids | Journal of Molecular Biology | 1967 | 2,313 |