| # | Title | Journal | Year | Citations |
|---|
| 1 | Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly | Nature Microbiology | 2018 | 1,268 |
| 2 | Expanded encyclopaedias of DNA elements in the human and mouse genomes | Nature | 2020 | 1,252 |
| 3 | The Human Phenotype Ontology in 2017 | Nucleic Acids Research | 2017 | 699 |
| 4 | A unified catalog of 204,938 reference genomes from the human gut microbiome | Nature Biotechnology | 2021 | 628 |
| 5 | Enhancer redundancy provides phenotypic robustness in mammalian development | Nature | 2018 | 514 |
| 6 | An integrated expression atlas of miRNAs and their promoters in human and mouse | Nature Biotechnology | 2017 | 456 |
| 7 | Mutant phenotypes for thousands of bacterial genes of unknown function | Nature | 2018 | 433 |
| 8 | Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation | Nature Neuroscience | 2018 | 290 |
| 9 | High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types | Cell Reports | 2019 | 279 |
| 10 | An atlas of dynamic chromatin landscapes in mouse fetal development | Nature | 2020 | 257 |
| 11 | Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome | Nature Microbiology | 2021 | 248 |
| 12 | The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity | Frontiers in Microbiology | 2016 | 219 |
| 13 | Whole genome analysis of a schistosomiasis-transmitting freshwater snail | Nature Communications | 2017 | 216 |
| 14 | The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions | MBio | 2016 | 215 |
| 15 | A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) | Scientific Reports | 2018 | 215 |
| 16 | Interactions between plants and soil shaping the root microbiome under abiotic stress | Biochemical Journal | 2019 | 198 |
| 17 | Learning representations of microbe–metabolite interactions | Nature Methods | 2019 | 184 |
| 18 | Exometabolite niche partitioning among sympatric soil bacteria | Nature Communications | 2015 | 178 |
| 19 | The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation | Journal of Biomedical Semantics | 2016 | 173 |
| 20 | Genome-wide identification of bacterial plant colonization genes | PLoS Biology | 2017 | 173 |
| 21 | Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms | Nature Microbiology | 2019 | 170 |
| 22 | Ultraconserved Enhancers Are Required for Normal Development | Cell | 2018 | 169 |
| 23 | Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy | Nature Communications | 2016 | 152 |
| 24 | Gene content evolution in the arthropods | Genome Biology | 2020 | 150 |
| 25 | Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism | Proceedings of the National Academy of Sciences of the United States of America | 2020 | 149 |
| 26 | Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome | Nature Microbiology | 2017 | 138 |
| 27 | The changing mouse embryo transcriptome at whole tissue and single-cell resolution | Nature | 2020 | 131 |
| 28 | Linking soil biology and chemistry in biological soil crust using isolate exometabolomics | Nature Communications | 2018 | 129 |
| 29 | Species- and site-specific genome editing in complex bacterial communities | Nature Microbiology | 2022 | 127 |
| 30 | Phage therapy: From biological mechanisms to future directions | Cell | 2023 | 125 |
| 31 | SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database | Nucleic Acids Research | 2019 | 122 |
| 32 | Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome | Genome Biology | 2019 | 114 |
| 33 | A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome | MSystems | 2019 | 112 |
| 34 | Cooking shapes the structure and function of the gut microbiome | Nature Microbiology | 2019 | 112 |
| 35 | Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning | ACS Synthetic Biology | 2019 | 107 |
| 36 | Quantifying the local adaptive landscape of a nascent bacterial community | Nature Communications | 2023 | 103 |
| 37 | Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder | Cell Stem Cell | 2020 | 101 |
| 38 | Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants | Cell | 2020 | 100 |
| 39 | Genomic analyses implicate noncoding de novo variants in congenital heart disease | Nature Genetics | 2020 | 97 |
| 40 | Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics | Nature Communications | 2021 | 93 |
| 41 | High-throughput mapping of the phage resistance landscape in E. coli | PLoS Biology | 2020 | 91 |
| 42 | EcoFABs: advancing microbiome science through standardized fabricated ecosystems | Nature Methods | 2019 | 90 |
| 43 | A metabolic pathway for catabolizing levulinic acid in bacteria | Nature Microbiology | 2017 | 86 |
| 44 | CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria | Nature Microbiology | 2019 | 85 |
| 45 | Spatiotemporal DNA methylome dynamics of the developing mouse fetus | Nature | 2020 | 84 |
| 46 | Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments | Cell Reports | 2021 | 82 |
| 47 | The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology | Environmental Science & Technology | 2018 | 79 |
| 48 | Drought and plant litter chemistry alter microbial gene expression and metabolite production | ISME Journal | 2020 | 79 |
| 49 | Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers | Cell Stem Cell | 2019 | 72 |
| 50 | A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS) | Nature Protocols | 2021 | 70 |
