Dan Knights

About

My data science lab has been involved in various aspects of microbiome research. We have developed methods for analyzing microbiome data, and we have applied those methods in clinical studies to better diagnose and predict disease. We have also been involved in several data science projects related to sustainability.

Research topics

• Bioinformatics
• Biology
• Computational biology
• Medicine
• Computer Science
• Internal medicine
• Pathology
• Psychology
• Data science
• Immunology

Selected publications

• Reporting guidelines for human microbiome research: the STORMS checklist

  Nature Medicine · 2021 · 452 citations

  The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-ind…

  DOI

• Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

  Cell · 2020 · 440 citations

  DOI

• Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration

  Nature Microbiology · 2022 · 171 citations

  While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and hos…

  DOI

• Shallow shotgun sequencing reduces technical variation in microbiome analysis

  Scientific Reports · 2023-05-11 · 55 citations

  articleOpen accessSenior author

  The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive al…

  PublisherOA PDFDOI

• Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

  Cell · 2025-01-23 · 50 citations

  articleOpen access

  Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhan…

  PublisherDOI

Recent grants

• Early life antibiotics, gut microbiome development, and risk of childhood obesity

  NIH · $3.7M · 2016–2022

Frequent coauthors

• Rob Knight

  University of California, San Diego

  103 shared

• Tonya Ward

  89 shared

• Gabriel A. Al‐Ghalith

  72 shared

• Robin R. Shields‐Cutler

  Macalester College

  68 shared

• Jonathan B. Clayton

  University of Nebraska at Omaha

  47 shared

• Curtis Huttenhower

  Harvard University

  47 shared

• Ramnik J. Xavier

  Broad Institute

  45 shared

• Luke Thompson

  Mississippi State University

  43 shared

Labs

• Knights LabPI

  Data mining and machine learning to understand the natural world and human microbiome

Awards & honors

• 2023: Charles E. Bowers Faculty Teaching Award
• 2015: McKnight Land-Grant Professorship

Similar researchers at University of Minnesota

• Yousef Saadh-81
• Joseph Konstanh-74
• Chad L. Myersh-72