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Top Articles

#TitleJournalYearCitations
1Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis setComputational Materials Science199654,900
2The Sequence Alignment/Map format and SAMtoolsBioinformatics200949,124
3Trimmomatic: a flexible trimmer for Illumina sequence dataBioinformatics201446,646
4Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics200943,062
5UCSF Chimera?A visualization system for exploratory research and analysisJournal of Computational Chemistry200437,095
6STAR: ultrafast universal RNA-seq alignerBioinformatics201335,376
7Fast Parallel Algorithms for Short-Range Molecular DynamicsJournal of Computational Physics199535,279
8edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics201032,955
9RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogeniesBioinformatics201426,744
10MrBayes 3: Bayesian phylogenetic inference under mixed modelsBioinformatics200326,519
11Clustal W and Clustal X version 2.0Bioinformatics200725,174
12Semiempirical GGA-type density functional constructed with a long-range dispersion correctionJournal of Computational Chemistry200624,222
13Multiwfn: A multifunctional wavefunction analyzerJournal of Computational Chemistry201221,818
14AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreadingJournal of Computational Chemistry201021,573
15BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics201020,367
16SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell SequencingJournal of Computational Biology201220,193
17MRBAYES: Bayesian inference of phylogenetic treesBioinformatics200120,154
18General atomic and molecular electronic structure systemJournal of Computational Chemistry199319,020
19MODELTEST: testing the model of DNA substitutionBioinformatics199818,761
20Search and clustering orders of magnitude faster than BLASTBioinformatics201018,572
21Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesJournal of Computational Physics197718,418
22HTSeq—a Python framework to work with high-throughput sequencing dataBioinformatics201517,270
23AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibilityJournal of Computational Chemistry200916,850
24featureCounts: an efficient general purpose program for assigning sequence reads to genomic featuresBioinformatics201416,839
25Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataBioinformatics201216,096
26Effect of the damping function in dispersion corrected density functional theoryJournal of Computational Chemistry201115,980
27Scalable molecular dynamics with NAMDJournal of Computational Chemistry200515,208
28RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics200614,675
29Development and testing of a general amber force fieldJournal of Computational Chemistry200414,342
30The Structure and Function of Complex NetworksSIAM Review200314,326
31CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry198314,316
32GROMACS: Fast, flexible, and freeJournal of Computational Chemistry200513,676
33DnaSP v5: a software for comprehensive analysis of DNA polymorphism dataBioinformatics200913,645
34LINCS: A linear constraint solver for molecular simulationsJournal of Computational Chemistry199713,446
35UCHIME improves sensitivity and speed of chimera detectionBioinformatics201113,241
36Haploview: analysis and visualization of LD and haplotype mapsBioinformatics200513,223
37Prokka: rapid prokaryotic genome annotationBioinformatics201412,881
38Silhouettes: A graphical aid to the interpretation and validation of cluster analysisJournal of Computational and Applied Mathematics198712,746
39Volume of fluid (VOF) method for the dynamics of free boundariesJournal of Computational Physics198112,164
40Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulationsJournal of Computational Physics198811,578
41FLASH: fast length adjustment of short reads to improve genome assembliesBioinformatics201111,573
42The variant call format and VCFtoolsBioinformatics201111,326
43TopHat: discovering splice junctions with RNA-SeqBioinformatics200911,265
44fastp: an ultra-fast all-in-one FASTQ preprocessorBioinformatics201811,005
45GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an updateBioinformatics201210,741
46APE: Analyses of Phylogenetics and Evolution in R languageBioinformatics200410,601
47Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchBioinformatics200510,566
48Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics201010,002
49Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray ExperimentsStatistical Applications in Genetics and Molecular Biology20049,992
50BUSCO: assessing genome assembly and annotation completeness with single-copy orthologsBioinformatics20159,712
51The ORCA program systemWiley Interdisciplinary Reviews: Computational Molecular Science20129,098
52An algorithm for the machine calculation of complex Fourier seriesMathematics of Computation19658,978
53Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequencesBioinformatics20068,965
54Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy functionJournal of Computational Chemistry19988,897
55Chemistry with ADFJournal of Computational Chemistry20018,854
56Approximate Riemann solvers, parameter vectors, and difference schemesJournal of Computational Physics19818,613
57A perfectly matched layer for the absorption of electromagnetic wavesJournal of Computational Physics19948,574
58Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics20098,091
59trimAl: a tool for automated alignment trimming in large-scale phylogenetic analysesBioinformatics20097,974
60Minimap2: pairwise alignment for nucleotide sequencesBioinformatics20187,764
61The Amber biomolecular simulation programsJournal of Computational Chemistry20057,742
62A fast and robust algorithm for Bader decomposition of charge densityComputational Materials Science20067,727
63A continuum method for modeling surface tensionJournal of Computational Physics19927,608
64A comparison of normalization methods for high density oligonucleotide array data based on variance and biasBioinformatics20037,383
65Optimization of parameters for semiempirical methods I. MethodJournal of Computational Chemistry19897,369
66Tensor Decompositions and ApplicationsSIAM Review20097,108
67CHARMM: The biomolecular simulation programJournal of Computational Chemistry20097,077
68CD-HIT: accelerated for clustering the next-generation sequencing dataBioinformatics20127,030
69QUAST: quality assessment tool for genome assembliesBioinformatics20136,983
70Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation modelJournal of Computational Chemistry20036,758
71Power-Law Distributions in Empirical DataSIAM Review20096,595
72InterProScan 5: genome-scale protein function classificationBioinformatics20146,553
73The SWISS-MODEL workspace: a web-based environment for protein structure homology modellingBioinformatics20066,515
74TASSEL: software for association mapping of complex traits in diverse samplesBioinformatics20076,407
75Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-FJournal of Computational Chemistry19836,294
76Fractional Brownian Motions, Fractional Noises and ApplicationsSIAM Review19686,147
77Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water modelsJournal of Computational Chemistry19926,106
78GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitBioinformatics20136,072
79adegenet: a R package for the multivariate analysis of genetic markersBioinformatics20085,999
80Towards the ultimate conservative difference scheme. V. A second-order sequel to Godunov's methodJournal of Computational Physics19795,957
81Complex heatmaps reveal patterns and correlations in multidimensional genomic dataBioinformatics20165,891
82PACKMOL: A package for building initial configurations for molecular dynamics simulationsJournal of Computational Chemistry20095,831
83THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The methodJournal of Computational Chemistry19925,736
84DnaSP, DNA polymorphism analyses by the coalescent and other methodsBioinformatics20035,561
85Muiltiobjective Optimization Using Nondominated Sorting in Genetic AlgorithmsEvolutionary Computation19945,518
86A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing dataBioinformatics20115,467
87CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structureBioinformatics20075,408
88CHARMM‐GUI: A web‐based graphical user interface for CHARMMJournal of Computational Chemistry20085,402
89ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networksBioinformatics20095,348
90Tree View: An application to display phylogenetic trees on personal computersBioinformatics19965,235
91Compact finite difference schemes with spectral-like resolutionJournal of Computational Physics19925,222
92Efficient Implementation of Weighted ENO SchemesJournal of Computational Physics19965,195
93ape 5.0: an environment for modern phylogenetics and evolutionary analyses in RBioinformatics20195,128
94MEGA2: molecular evolutionary genetics analysis softwareBioinformatics20015,102
95A general method for numerically simulating the stochastic time evolution of coupled chemical reactionsJournal of Computational Physics19765,049
96Atomic Decomposition by Basis PursuitSIAM Journal of Scientific Computing19984,968
97Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equationsJournal of Computational Physics20194,963
98Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella samplingJournal of Computational Physics19774,897
99The rapid generation of mutation data matrices from protein sequencesBioinformatics19924,891
100Profile hidden Markov modelsBioinformatics19984,873