| # | Title | Journal | Year | Citations |
|---|
| 1 | The RAST Server: Rapid Annotations using Subsystems Technology | BMC Genomics | 2008 | 9,977 |
| 2 | The Anatomy of the Grid: Enabling Scalable Virtual Organizations | International Journal of High Performance Computing Applications | 2001 | 4,854 |
| 3 | The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes | BMC Bioinformatics | 2008 | 3,200 |
| 4 | RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes | Scientific Reports | 2015 | 2,080 |
| 5 | The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus | Nature | 1997 | 1,460 |
| 6 | Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center | Nucleic Acids Research | 2017 | 1,445 |
| 7 | The use of gene clusters to infer functional coupling | Proceedings of the National Academy of Sciences of the United States of America | 1999 | 1,185 |
| 8 | The complete genome of the hyperthermophilic bacterium Aquifex aeolicus | Nature | 1998 | 1,120 |
| 9 | Efficient Management of Parallelism in Object-Oriented Numerical Software Libraries | | 1997 | 1,072 |
| 10 | The minimum information about a genome sequence (MIGS) specification | Nature Biotechnology | 2008 | 1,069 |
| 11 | Uniqueness of positive solutions of Δu−u+up=0 in Rn | Archive for Rational Mechanics and Analysis | 1989 | 1,004 |
| 12 | High-throughput generation, optimization and analysis of genome-scale metabolic models | Nature Biotechnology | 2010 | 974 |
| 13 | KBase: The United States Department of Energy Systems Biology Knowledgebase | Nature Biotechnology | 2018 | 955 |
| 14 | Transient Simulation of Last Deglaciation with a New Mechanism for Bølling-Allerød Warming | Science | 2009 | 843 |
| 15 | Functional metagenomic profiling of nine biomes | Nature | 2008 | 842 |
| 16 | The data grid: Towards an architecture for the distributed management and analysis of large scientific datasets | Journal of Network and Computer Applications | 2000 | 802 |
| 17 | Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 669 |
| 18 | The anatomy of the grid: enabling scalable virtual organizations | | 0 | 617 |
| 19 | Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications | Nature Biotechnology | 2011 | 608 |
| 20 | Condor-G: A Computation Management Agent for Multi-Institutional Grids | Cluster Computing | 2002 | 557 |
| 21 | Mixed-integer nonlinear optimization | Acta Numerica | 2013 | 535 |
| 22 | Application of Interior-Point Methods to Model Predictive Control | Journal of Optimization Theory and Applications | 1998 | 425 |
| 23 | Nuclear energy density optimization | Physical Review C | 2010 | 385 |
| 24 | The khmer software package: enabling efficient nucleotide sequence analysis | F1000Research | 2015 | 362 |
| 25 | A community authorization service for group collaboration | | 0 | 360 |
| 26 | Active Thermochemical Tables: thermochemistry for the 21st century | Journal of Physics: Conference Series | 2005 | 360 |
| 27 | Adaptive computing on the grid using AppLeS | IEEE Transactions on Parallel and Distributed Systems | 2003 | 348 |
| 28 | QoS guided Min-Min heuristic for grid task scheduling | Journal of Computer Science and Technology | 2003 | 341 |
| 29 | Chimera: a virtual data system for representing, querying, and automating data derivation | | 0 | 340 |
| 30 | Data sieving and collective I/O in ROMIO | | 1999 | 337 |
| 31 | Condor-G: a computation management agent for multi-institutional grids | | 0 | 323 |
| 32 | Nuclear energy density optimization: Large deformations | Physical Review C | 2012 | 316 |
| 33 | Tetrahedral mesh improvement using swapping and smoothing | International Journal for Numerical Methods in Engineering | 1997 | 304 |
| 34 | Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes | Cold Spring Harbor Protocols | 2010 | 291 |
| 35 | The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools | BMC Bioinformatics | 2012 | 291 |
| 36 | The Globus project: a status report | | 0 | 279 |
| 37 | Security for Grid services | | 0 | 277 |
| 38 | A Definition of the Domains Archaea, Bacteria and Eucarya in Terms of Small Subunit Ribosomal RNA Characteristics | Systematic and Applied Microbiology | 1991 | 274 |
| 39 | Optimized Chiral Nucleon-Nucleon Interaction at Next-to-Next-to-Leading Order | Physical Review Letters | 2013 | 267 |
| 40 | ADIFOR–Generating Derivative Codes from Fortran Programs | Scientific Programming | 1992 | 266 |
| 41 | On implementing MPI-IO portably and with high performance | | 1999 | 266 |
| 42 | Searching for patterns in genomic data | Trends in Genetics | 1997 | 258 |
| 43 | Swift: Fast, Reliable, Loosely Coupled Parallel Computation | | 2007 | 243 |
| 44 | Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans | Applied and Environmental Microbiology | 2008 | 228 |
| 45 | A Java commodity grid kit | Concurrency Computation Practice and Experience | 2001 | 221 |
| 46 | Generalized communicators in the Message Passing Interface | | 0 | 209 |
| 47 | A Computational Framework for Uncertainty Quantification and Stochastic Optimization in Unit Commitment With Wind Power Generation | IEEE Transactions on Power Systems | 2011 | 206 |
| 48 | The Physiology of the Grid | | 0 | 205 |
| 49 | Eliminating parasitic currents in the lattice Boltzmann equation method for nonideal gases | Physical Review E | 2006 | 202 |
| 50 | A quality of service architecture that combines resource reservation and application adaptation | | 0 | 200 |
