# | Title | Journal | Year | Citations |
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|
1 | Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads | PLoS Computational Biology | 2017 | 5,684 |
2 | BEAST 2: A Software Platform for Bayesian Evolutionary Analysis | PLoS Computational Biology | 2014 | 5,546 |
3 | Accelerated Profile HMM Searches | PLoS Computational Biology | 2011 | 5,431 |
4 | Software for Computing and Annotating Genomic Ranges | PLoS Computational Biology | 2013 | 3,514 |
5 | BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis | PLoS Computational Biology | 2019 | 2,798 |
6 | The Human Connectome: A Structural Description of the Human Brain | PLoS Computational Biology | 2005 | 2,725 |
7 | MAGMA: Generalized Gene-Set Analysis of GWAS Data | PLoS Computational Biology | 2015 | 2,562 |
8 | mixOmics: An R package for ‘omics feature selection and multiple data integration | PLoS Computational Biology | 2017 | 2,493 |
9 | Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible | PLoS Computational Biology | 2014 | 2,462 |
10 | Efficiency and Cost of Economical Brain Functional Networks | PLoS Computational Biology | 2007 | 2,173 |
11 | Inferring Correlation Networks from Genomic Survey Data | PLoS Computational Biology | 2012 | 2,014 |
12 | OpenMM 7: Rapid development of high performance algorithms for molecular dynamics | PLoS Computational Biology | 2017 | 1,798 |
13 | Bayesian Phylogeography Finds Its Roots | PLoS Computational Biology | 2009 | 1,578 |
14 | MUMmer4: A fast and versatile genome alignment system | PLoS Computational Biology | 2018 | 1,575 |
15 | MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data | PLoS Computational Biology | 2016 | 1,564 |
16 | Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples | PLoS Computational Biology | 2009 | 1,528 |
17 | Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ | PLoS Computational Biology | 2010 | 1,492 |
18 | CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing | PLoS Computational Biology | 2016 | 1,382 |
19 | Functional Brain Networks Develop from a “Local to Distributed” Organization | PLoS Computational Biology | 2009 | 1,314 |
20 | Microbial Co-occurrence Relationships in the Human Microbiome | PLoS Computational Biology | 2012 | 1,313 |
21 | Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges | PLoS Computational Biology | 2012 | 1,305 |
22 | Sparse and Compositionally Robust Inference of Microbial Ecological Networks | PLoS Computational Biology | 2015 | 1,177 |
23 | Universally Sloppy Parameter Sensitivities in Systems Biology Models | PLoS Computational Biology | 2007 | 1,051 |
24 | CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures | PLoS Computational Biology | 2012 | 1,046 |
25 | Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease | PLoS Computational Biology | 2008 | 1,012 |
26 | Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation | PLoS Computational Biology | 2011 | 1,002 |
27 | Chapter 11: Genome-Wide Association Studies | PLoS Computational Biology | 2012 | 975 |
28 | Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation | PLoS Computational Biology | 2014 | 968 |
29 | Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome | PLoS Computational Biology | 2012 | 965 |
30 | Is My Network Module Preserved and Reproducible? | PLoS Computational Biology | 2011 | 920 |
31 | Multivariable association discovery in population-scale meta-omics studies | PLoS Computational Biology | 2021 | 917 |
32 | ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes | PLoS Computational Biology | 2015 | 878 |
33 | The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics | PLoS Computational Biology | 2007 | 866 |
34 | A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes | PLoS Computational Biology | 2005 | 856 |
35 | OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement | PLoS Computational Biology | 2018 | 826 |
36 | iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections | PLoS Computational Biology | 2014 | 823 |
37 | An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data | PLoS Computational Biology | 2009 | 784 |
38 | Associating Genes and Protein Complexes with Disease via Network Propagation | PLoS Computational Biology | 2010 | 778 |
39 | A Toolbox for Representational Similarity Analysis | PLoS Computational Biology | 2014 | 767 |
40 | A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach | PLoS Computational Biology | 2008 | 757 |
41 | Transcriptomics technologies | PLoS Computational Biology | 2017 | 752 |
42 | Predicting Network Activity from High Throughput Metabolomics | PLoS Computational Biology | 2013 | 747 |
43 | Geometric Interpretation of Gene Coexpression Network Analysis | PLoS Computational Biology | 2008 | 738 |
44 | Structural Properties of the Caenorhabditis elegans Neuronal Network | PLoS Computational Biology | 2011 | 729 |
45 | Projecting social contact matrices in 152 countries using contact surveys and demographic data | PLoS Computational Biology | 2017 | 709 |
46 | Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition | PLoS Computational Biology | 2014 | 707 |
47 | Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference | PLoS Computational Biology | 2012 | 696 |
48 | Properties of MHC Class I Presented Peptides That Enhance Immunogenicity | PLoS Computational Biology | 2013 | 681 |
49 | Hierarchical Models in the Brain | PLoS Computational Biology | 2008 | 677 |
50 | Discovering Motifs in Ranked Lists of DNA Sequences | PLoS Computational Biology | 2007 | 647 |