| BEAST 2: A Software Platform for Bayesian Evolutionary Analysis | 2014/04/10 | English | 4,432 |
| Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads | 2017/06/08 | English | 4,169 |
| Accelerated Profile HMM Searches | 2011/10/20 | English | 3,643 |
| Software for Computing and Annotating Genomic Ranges | 2013/08/08 | English | 2,242 |
| BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis | 2019/04/08 | English | 1,999 |
| Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible | 2014/04/03 | English | 1,838 |
| The Human Connectome: A Structural Description of the Human Brain | 2005/01/01 | English | 1,813 |
| mixOmics: An R package for ‘omics feature selection and multiple data integration | 2017/11/03 | English | 1,719 |
| Efficiency and Cost of Economical Brain Functional Networks | 2007/02/02 | English | 1,669 |
| MAGMA: Generalized Gene-Set Analysis of GWAS Data | 2015/04/17 | English | 1,557 |
| Inferring Correlation Networks from Genomic Survey Data | 2012/09/20 | English | 1,424 |
| OpenMM 7: Rapid development of high performance algorithms for molecular dynamics | 2017/07/26 | English | 1,256 |
| Bayesian Phylogeography Finds Its Roots | 2009/09/25 | English | 1,206 |
| Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples | 2009/04/10 | English | 1,189 |
| Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ | 2010/12/02 | English | 1,109 |
| MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data | 2016/06/21 | English | 1,050 |
| CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing | 2016/04/21 | English | 1,050 |
| Microbial Co-occurrence Relationships in the Human Microbiome | 2012/07/12 | English | 1,021 |
| MUMmer4: A fast and versatile genome alignment system | 2018/01/26 | English | 1,010 |
| Functional Brain Networks Develop from a “Local to Distributed” Organization | 2009/05/01 | English | 990 |
| Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges | 2012/02/23 | English | 939 |
| CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures | 2012/10/18 | English | 841 |
| Sparse and Compositionally Robust Inference of Microbial Ecological Networks | 2015/05/07 | English | 816 |
| Universally Sloppy Parameter Sensitivities in Systems Biology Models | 2007/10/05 | English | 746 |
| Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease | 2008/06/27 | English | 725 |
| Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome | 2012/06/13 | English | 689 |
| Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation | 2011/05/26 | English | 673 |
| A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes | 2005/11/11 | English | 652 |
| Polarizable Water Model for the Coarse-Grained MARTINI Force Field | 2010/06/10 | English | 645 |
| Chapter 11: Genome-Wide Association Studies | 2012/12/27 | English | 633 |