| # | Title | Journal | Year | Citations |
|---|
| 1 | QIIME allows analysis of high-throughput community sequencing data | Nature Methods | 2010 | 31,818 |
| 2 | Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes | Science | 2011 | 5,253 |
| 3 | Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale | Applied and Environmental Microbiology | 2009 | 3,268 |
| 4 | Evolution of Mammals and Their Gut Microbes | Science | 2008 | 3,171 |
| 5 | Bacterial Community Variation in Human Body Habitats Across Space and Time | Science | 2009 | 2,713 |
| 6 | The Treatment-Naive Microbiome in New-Onset Crohn’s Disease | Cell Host and Microbe | 2014 | 2,582 |
| 7 | Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities | Applied and Environmental Microbiology | 2007 | 2,418 |
| 8 | On the proper treatment of connectionism | Behavioral and Brain Sciences | 1988 | 1,959 |
| 9 | Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans | Science | 2011 | 1,712 |
| 10 | Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy | Cell | 2012 | 1,603 |
| 11 | High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity | Gastroenterology | 2009 | 1,344 |
| 12 | Worlds within worlds: evolution of the vertebrate gut microbiota | Nature Reviews Microbiology | 2008 | 1,342 |
| 13 | Bayesian community-wide culture-independent microbial source tracking | Nature Methods | 2011 | 1,284 |
| 14 | Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex | Nature Methods | 2008 | 1,190 |
| 15 | Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data | ISME Journal | 2010 | 1,025 |
| 16 | Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor | Science | 2013 | 1,012 |
| 17 | A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses | ISME Journal | 2009 | 984 |
| 18 | The influence of sex, handedness, and washing on the diversity of hand surface bacteria | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 980 |
| 19 | Moving pictures of the human microbiome | Genome Biology | 2011 | 934 |
| 20 | Network Anomaly Detection: Methods, Systems and Tools | IEEE Communications Surveys and Tutorials | 2014 | 885 |
| 21 | Information content of binding sites on nucleotide sequences | Journal of Molecular Biology | 1986 | 872 |
| 22 | Microbial community profiling for human microbiome projects: Tools, techniques, and challenges | Genome Research | 2009 | 805 |
| 23 | Toward Open Set Recognition | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2013 | 759 |
| 24 | Tensor product variable binding and the representation of symbolic structures in connectionist systems | Artificial Intelligence | 1990 | 758 |
| 25 | An architecture-based approach to self-adaptive software | IEEE Intelligent Systems | 1999 | 722 |
| 26 | Enterotypes in the landscape of gut microbial community composition | Nature Microbiology | 2018 | 717 |
| 27 | Scale-free networks are rare | Nature Communications | 2019 | 632 |
| 28 | Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications | Nature Biotechnology | 2011 | 608 |
| 29 | Advancing Our Understanding of the Human Microbiome Using QIIME | Methods in Enzymology | 2013 | 553 |
| 30 | Knitro: An Integrated Package for Nonlinear Optimization | Nonconvex Optimization and Its Applications | 2006 | 521 |
| 31 | Cognitive walkthroughs: a method for theory-based evaluation of user interfaces | International Journal of Man-Machine Studies | 1992 | 513 |
| 32 | Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities | Current Protocols in Bioinformatics | 2011 | 507 |
| 33 | Evolution of Symbiotic Bacteria in the Distal Human Intestine | PLoS Biology | 2007 | 490 |
| 34 | Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities | Current Protocols in Microbiology | 2012 | 486 |
| 35 | Fast-Find: a novel computational approach to analyzing combinatorial motifs | BMC Bioinformatics | 2006 | 467 |
| 36 | Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice | Cell Host and Microbe | 2012 | 459 |
| 37 | Qiita: rapid, web-enabled microbiome meta-analysis | Nature Methods | 2018 | 459 |
| 38 | The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins | Science Translational Medicine | 2011 | 456 |
| 39 | A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets | PLoS Computational Biology | 2013 | 446 |
| 40 | Bacterial community structures are unique and resilient in full-scale bioenergy systems | Proceedings of the National Academy of Sciences of the United States of America | 2011 | 412 |
| 41 | Supervised classification of human microbiota | FEMS Microbiology Reviews | 2011 | 377 |
| 42 | Probability Models for Open Set Recognition | IEEE Transactions on Pattern Analysis and Machine Intelligence | 2014 | 365 |
| 43 | Temporal variability is a personalized feature of the human microbiome | Genome Biology | 2014 | 355 |
| 44 | Operational transformation in real-time group editors | Genome Biology | 1998 | 346 |
| 45 | Approximate solution of the trust region problem by minimization over two-dimensional subspaces | Mathematical Programming | 1988 | 311 |
| 46 | Using Relevance to Reduce Network Size Automatically | Connection Science | 1989 | 286 |
| 47 | An Efficient Implementation of Edmonds' Algorithm for Maximum Matching on Graphs | Journal of the ACM | 1976 | 283 |
| 48 | Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei | Applied and Environmental Microbiology | 2009 | 273 |
| 49 | Positional strategies for mean payoff games | International Journal of Game Theory | 1979 | 266 |
| 50 | Learning Complex, Extended Sequences Using the Principle of History Compression | Neural Computation | 1992 | 261 |
