Standout Papers

UCHIME improves sensitivity and speed of chimera detection 2005 2026 2012 2019 12.0k
  1. UCHIME improves sensitivity and speed of chimera detection (2011)
    R. C. Edgar, Brian J. Haas et al. Bioinformatics
  2. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences (2013)
    Morgan G. I. Langille, Jesse Zaneveld et al. Nature Biotechnology
  3. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2010)
    J. Gregory Caporaso, Christian L. Lauber et al. Proceedings of the National Academy of Sciences
  4. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms (2012)
    J. Gregory Caporaso, Christian L. Lauber et al. The ISME Journal
  5. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities (2005)
    Catherine Lozupone, Rob Knight Applied and Environmental Microbiology
  6. A core gut microbiome in obese and lean twins (2008)
    Peter J. Turnbaugh, Micah Hamady et al. Nature
  7. Obesity alters gut microbial ecology (2005)
    Ruth E. Ley, Fredrik Bäckhed et al. Proceedings of the National Academy of Sciences
  8. Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes (2011)
    Gary D. Wu, Jun Chen et al. Science
  9. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea (2011)
    Daniel McDonald, Morgan N. Price et al. The ISME Journal
  10. The Human Microbiome Project (2007)
    Peter J. Turnbaugh, Ruth E. Ley et al. Nature
  11. Diversity, stability and resilience of the human gut microbiota (2012)
    Catherine Lozupone, Jesse Stombaugh et al. Nature
  12. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin (2018)
    Nicholas A. Bokulich, Benjamin D. Kaehler et al. Microbiome
  13. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing (2012)
    Nicholas A. Bokulich, Sathish Subramanian et al. Nature Methods
  14. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns (2010)
    Maria Gloria Domínguez-Bello, Elizabeth K. Costello et al. Proceedings of the National Academy of Sciences
  15. Soil bacterial and fungal communities across a pH gradient in an arable soil (2010)
    Johannes Rousk, Erland Bååth et al. The ISME Journal
  16. Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale (2009)
    Christian L. Lauber, Micah Hamady et al. Applied and Environmental Microbiology
  17. PyNAST: a flexible tool for aligning sequences to a template alignment (2009)
    J. Gregory Caporaso, Kyle Bittinger et al. Bioinformatics
  18. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons (2011)
    Brian J. Haas, Dirk Gevers et al. Genome Research
  19. Evolution of Mammals and Their Gut Microbes (2008)
    Ruth E. Ley, Micah Hamady et al. Science
  20. The Impact of the Gut Microbiota on Human Health: An Integrative View (2012)
    José C. Clemente, Luke K. Ursell et al. Cell
  21. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease (2016)
    Timothy R. Sampson, Justine W. Debelius et al. Cell
  22. Bacterial Community Variation in Human Body Habitats Across Space and Time (2009)
    Elizabeth K. Costello, Christian L. Lauber et al. Science
  23. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice (2009)
    Peter J. Turnbaugh, Vanessa K. Ridaura et al. Science Translational Medicine
  24. Human Genetics Shape the Gut Microbiome (2014)
    Julia K. Goodrich, Jillian L. Waters et al. Cell
  25. UniFrac: an effective distance metric for microbial community comparison (2010)
    Catherine Lozupone, Manuel E. Lladser et al. The ISME Journal
  26. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities (2007)
    Catherine Lozupone, Micah Hamady et al. Applied and Environmental Microbiology
  27. Succession of microbial consortia in the developing infant gut microbiome (2010)
    Jeremy E. Koenig, Aymé Spor et al. Proceedings of the National Academy of Sciences
  28. Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5 (2010)
    Matam Vijay–Kumar, J D Aitken et al. Science
  29. Current understanding of the human microbiome (2018)
    Jack A. Gilbert, Martin J. Blaser et al. Nature Medicine
  30. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys (2015)
    William A. Walters, Embriette R. Hyde et al. mSystems
  31. Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy (2012)
    Omry Koren, Julia K. Goodrich et al. Cell
  32. The Long-Term Stability of the Human Gut Microbiota (2013)
    Jeremiah J. Faith, Janaki L. Guruge et al. Science
  33. Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans (2011)
    Brian D. Muegge, Justin Kuczynski et al. Science
  34. Analysis of composition of microbiomes: a novel method for studying microbial composition (2015)
    Siddhartha Mandal, Will Van Treuren et al. Microbial Ecology in Health and Disease
  35. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients (2011)
    Noah Fierer, Christian L. Lauber et al. The ISME Journal
  36. Normalization and microbial differential abundance strategies depend upon data characteristics (2017)
    Sophie Weiss, Zhenjiang Zech Xu et al. Microbiome
  37. Global patterns in bacterial diversity (2007)
    Catherine Lozupone, Rob Knight Proceedings of the National Academy of Sciences
  38. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns (2017)
    Amnon Amir, Daniel McDonald et al. mSystems
  39. UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context (2006)
    Catherine Lozupone, Micah Hamady et al. BMC Bioinformatics
  40. Bayesian community-wide culture-independent microbial source tracking (2011)
    Dan Knights, Justin Kuczynski et al. Nature Methods
  41. High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity (2009)
    Marie A. Hildebrandt, Christian Hoffmann et al. Gastroenterology
  42. Worlds within worlds: evolution of the vertebrate gut microbiota (2008)
    Ruth E. Ley, Catherine Lozupone et al. Nature Reviews Microbiology
  43. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex (2008)
    Micah Hamady, Jeffrey J. Walker et al. Nature Methods
  44. Examining the global distribution of dominant archaeal populations in soil (2010)
    Scott T. Bates, Donna Berg-Lyons et al. The ISME Journal
  45. The gut–liver axis and the intersection with the microbiome (2018)
    Anupriya Tripathi, Justine W. Debelius et al. Nature Reviews Gastroenterology & Hepatology
  46. Species-level functional profiling of metagenomes and metatranscriptomes (2018)
    Eric A. Franzosa, Lauren J. McIver et al. Nature Methods
  47. Bacterial phylogeny structures soil resistomes across habitats (2014)
    Kevin J. Forsberg, Sanket Patel et al. Nature
  48. EMPeror: a tool for visualizing high-throughput microbial community data (2013)
    Yoshiki Vázquez‐Baeza, Meg Pirrung et al. GigaScience
  49. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses (2009)
    Ryan T. Jones, Michael S. Robeson et al. The ISME Journal
  50. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data (2009)
    Micah Hamady, Catherine Lozupone et al. The ISME Journal
  51. Human oral, gut, and plaque microbiota in patients with atherosclerosis (2010)
    Omry Koren, Aymé Spor et al. Proceedings of the National Academy of Sciences
  52. The influence of sex, handedness, and washing on the diversity of hand surface bacteria (2008)
    Noah Fierer, Micah Hamady et al. Proceedings of the National Academy of Sciences
  53. Moving pictures of the human microbiome (2011)
    J. Gregory Caporaso, Christian L. Lauber et al. Genome biology
  54. Dynamics of the human gut microbiome in inflammatory bowel disease (2017)
    Jonas Halfvarson, Colin Brislawn et al. Nature Microbiology
  55. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor (2013)
    Michelle I. Smith, Tanya Yatsunenko et al. Science
  56. Defining the human microbiome (2012)
    Luke K. Ursell, Jessica L. Metcalf et al. Nutrition Reviews
  57. Defining seasonal marine microbial community dynamics (2011)
    Jack A. Gilbert, Joshua A. Steele et al. The ISME Journal
  58. The microbiome and human cancer (2021)
    Gregory D. Sepich‐Poore, Laurence Zitvogel et al. Science
  59. Strains, functions and dynamics in the expanded Human Microbiome Project (2017)
    Jason Lloyd‐Price, Anup Mahurkar et al. Nature
  60. GABA-modulating bacteria of the human gut microbiota (2018)
    Philip Strandwitz, Ki Hyun Kim et al. Nature Microbiology
  61. Cohabiting family members share microbiota with one another and with their dogs (2013)
    Se Jin Song, Christian L. Lauber et al. eLife
  62. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges (2009)
    Micah Hamady, Rob Knight Genome Research
  63. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis (2012)
    Karen E. Sullam, Steven D. Essinger et al. Molecular Ecology
  64. Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models (2017)
    Egle Cekanaviciute, Bryan B. Yoo et al. Proceedings of the National Academy of Sciences
  65. Genetic Determinants of the Gut Microbiome in UK Twins (2016)
    Julia K. Goodrich, Emily Davenport et al. Cell Host & Microbe
  66. Gut Microbes and the Brain: Paradigm Shift in Neuroscience (2014)
    Emeran A. Mayer, Rob Knight et al. Journal of Neuroscience
  67. Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish (2012)
    Ivana Semova, Juliana Debrito Carten et al. Cell Host & Microbe
  68. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome (2017)
    Erin M. Hill‐Burns, Justine W. Debelius et al. Movement Disorders
  69. Meta‐analyses of human gut microbes associated with obesity and IBD (2014)
    William A. Walters, Zhenjiang Zech Xu et al. FEBS Letters
  70. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer (2016)
    Maria Gloria Domínguez-Bello, Nan Shen et al. Nature Medicine
  71. Longitudinal analysis of microbial interaction between humans and the indoor environment (2014)
    Simon Lax, Daniel P. Smith et al. Science
  72. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations (2018)
    Raphael Eisenhofer, Jeremiah J. Minich et al. Trends in Microbiology
  73. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome (2012)
    Daniel McDonald, José C. Clemente et al. GigaScience
  74. Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities (2011)
    Justin Kuczynski, Jesse Stombaugh et al. Current Protocols in Bioinformatics
  75. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania (2017)
    Samuel A. Smits, Jeff Leach et al. Science
  76. The under-recognized dominance of Verrucomicrobia in soil bacterial communities (2011)
    Scott T. Bates, Kathryn G. Eilers et al. Soil Biology and Biochemistry
  77. Short pyrosequencing reads suffice for accurate microbial community analysis (2007)
    Zhirong Liu, Catherine Lozupone et al. Nucleic Acids Research
  78. The Earth Microbiome project: successes and aspirations (2014)
    Jack A. Gilbert, Janet Jansson et al. BMC Biology
  79. Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat (2009)
    Andrew L. Goodman, Nathan P. McNulty et al. Cell Host & Microbe
  80. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision (2016)
    Sophie Weiss, Will Van Treuren et al. The ISME Journal
  81. Experimental and analytical tools for studying the human microbiome (2011)
    Justin Kuczynski, Christian L. Lauber et al. Nature Reviews Genetics
  82. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes (2010)
    Haiyan Chu, Noah Fierer et al. Environmental Microbiology
  83. Microbiota and Host Nutrition across Plant and Animal Kingdoms (2015)
    Stéphane Hacquard, Rubén Garrido‐Oter et al. Cell Host & Microbe
  84. Conducting a Microbiome Study (2014)
    Julia K. Goodrich, Sara C. Di Rienzi et al. Cell
  85. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves (2010)
    Robert M. Bowers, Rob Knight et al. Environmental Microbiology
  86. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems (2010)
    Kelly S. Ramirez, Christian L. Lauber et al. Ecology
  87. Specialized Metabolites from the Microbiome in Health and Disease (2014)
    Gil Sharon, Neha Garg et al. Cell Metabolism
  88. Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States (2013)
    Noah Fierer, Joshua Ladau et al. Science
  89. Subsistence strategies in traditional societies distinguish gut microbiomes (2015)
    Alexandra J. Obregón-Tito, Raúl Y. Tito et al. Nature Communications

Immediate Impact

2 by Nobel laureates 86 from Science/Nature 251 standout
Sub-graph 1 of 11

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34 intermediate papers

Works of Rob Knight being referenced

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
2012 Standout
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
2010 Standout
and 40 more

Author Peers

Author Last Decade Papers Cites
Rob Knight 130173 48459 32000 865 220.4k
Mark A. Bradford 109099 20661 15196 224 236.6k
Steven L. Salzberg 106489 20210 4645 233 174.6k
Jeffrey I. Gordon 101040 9089 32007 486 143.5k
Peer Bork 93864 15446 5381 510 140.1k
Willem M. de Vos 66433 7344 14515 872 95.5k
Philip Hugenholtz 39033 30365 2581 415 75.0k
Ruth E. Ley 50139 5841 19387 148 72.1k
Sudhir Kumar 87726 41260 1122 276 211.5k
Ulrich K. Laemmli 153352 12889 14935 84 259.7k
Tom Maniatis 120104 14554 5530 278 188.4k

All Works

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2026