Rob Knight

About

Rob Knight is the founding Director of the Center for Microbiome Innovation and a Professor of Pediatrics, Bioengineering, Computer Science & Engineering, and Data Science at the University of California San Diego. He holds the Wolfe Family Endowed Chair in Microbiome Research at Rady Children's Hospital and is a Visiting Fellow at the Hong Kong Jockey Club Institute of Advanced Science at the Hong Kong University of Science and Technology. Knight was elected to the National Academy of Engineering in 2024 and is a Fellow of the American Association for the Advancement of Science, the American Academy of Microbiology, and the American Institute for Medical and Biological Engineering. He has received prestigious awards including the 2019 NIH Director’s Pioneer Award and the 2017 Massry Prize. Knight is the author of the book "Follow Your Gut: The Enormous Impact of Tiny Microbes" and coauthor of "Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System," and has coauthored over 1000 scientific articles. His 2014 TED talk has been viewed over 2 million times. Knight's laboratory has developed many of the software tools and laboratory techniques that have enabled high-throughput microbiome science, including QIIME and UniFrac. His work has been cited over half a million times. He is a co-founder of the Earth Microbiome Project, the American Gut Project, and the companies Biota, Inc., and Micronoma, Inc. Additionally, he serves as Vice President of the…

Research topics

• Biology
• Bioinformatics
• Computer Science
• Computational biology
• Genetics
• Medicine
• Artificial Intelligence
• Biochemistry
• Internal medicine
• Endocrinology

Selected publications

• Large-scale association analyses identify host factors influencing human gut microbiome composition

  Nature Genetics · 2021 · 1803 citations

  DOI

• The microbiome and human cancer

  Science · 2021 · 1230 citations

  Senior authorCorresponding

  Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies have provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors in cancer immunotherapy, and engineerable to treat metastases. Despite these findings, the number of microbes known to directly cause carcinogenesis remains small. Critically evaluating and building frameworks for such evidence in light of modern cancer biology is an import…

  DOI

• RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancerdiagnostic approach

  Nature · 2020 · 1033 citations

  Senior authorCorresponding
  DOI

• Structure-based protein function prediction using graph convolutional networks

  Nature Communications · 2021 · 874 citations

  The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting protein functions by leveraging sequence features extracted from a protein language model and protein structures. It outperforms current leading methods and sequence-based Convolutional Neural Networks and scales to the size of current sequence reposito…

  DOI

• Global chemical effects of the microbiome include new bile-acid conjugations

  Nature · 2020 · 581 citations

  DOI

Recent grants

• NIH Grant R01HG004872

  NIH · $1.8M · 2013

• NIH Grant P01DK078669

  NIH · $31.3M · 2021

• Alzheimer's Gut Microbiome Project

  NIH · $28.4M · 2019–2026

Frequent coauthors

• Pieter C. Dorrestein

  University of California, San Diego

  352 shared

• Daniel McDonald

  University of California, San Diego

  342 shared

• J. Gregory Caporaso

  Translational Genomics Research Institute

  276 shared

• Jack A. Gilbert

  University of California, San Diego

  219 shared

• Yoshiki Vázquez‐Baeza

  Jacobs (United States)

  210 shared

• Noah Fierer

  200 shared

• Pedro Belda‐Ferre

  University of California, San Diego

  161 shared

• Se Jin Song

  University of California, San Diego

  159 shared

Labs

• Knight LabPI

Awards & honors

• 2019 NIH Director’s Pioneer Award
• 2017 Massry Prize
• 2015 Vilceck Prize in Creative Promise for the Life Sciences
• Fellow of the American Association for the Advancement of Sc…
• Fellow of the American Academy of Microbiology

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