James M. Tiedje

Research interests

Publications

• Emerging contaminants: A One Health perspective

  The Innovation · 2024 · https://doi.org/10.1016/j.xinn.2024.100612

• Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

  Environmental Science & Technology · 2022 · https://doi.org/10.1021/acs.est.2c02976

• Artificial intelligence: A powerful paradigm for scientific research

  The Innovation · 2021 · https://doi.org/10.1016/j.xinn.2021.100179

• An omics-based framework for assessing the health risk of antimicrobial resistance genes

  Nature Communications · 2021 · https://doi.org/10.1038/s41467-021-25096-3

• Technologies and perspectives for achieving carbon neutrality

  The Innovation · 2021 · https://doi.org/10.1016/j.xinn.2021.100180

• Climate warming enhances microbial network complexity and stability

  Nature Climate Change · 2021 · 10.1038/s41558-021-00989-9

• A general framework for quantitatively assessing ecological stochasticity

  Proceedings of the National Academy of Sciences · 2019 · 10.1073/pnas.1904623116

• ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

  Bioinformatics · 2018 · 10.1093/bioinformatics/bty053

• Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

  The ISME Journal · 2015 · 10.1038/ismej.2015.59

• Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

  The ISME Journal · 2014 · 10.1038/ismej.2014.226

• Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

  mBio · 2014 · 10.1128/mbio.00889-14

• Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

  Proceedings of the National Academy of Sciences · 2014 · 10.1073/pnas.1324044111

• Diverse and abundant antibiotic resistance genes in Chinese swine farms

  Proceedings of the National Academy of Sciences · 2013 · 10.1073/pnas.1222743110

• Ribosomal Database Project: data and tools for high throughput rRNA analysis

  Nucleic Acids Research · 2013 · 10.1093/nar/gkt1244

• In-feed antibiotic effects on the swine intestinal microbiome

  Proceedings of the National Academy of Sciences · 2012 · 10.1073/pnas.1120238109

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

  Nature Biotechnology · 2011 · 10.1038/nbt.1823

• The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

  Nucleic Acids Research · 2008 · 10.1093/nar/gkn879

• Towards environmental systems biology of Shewanella

  Nature Reviews Microbiology · 2008 · 10.1038/nrmicro1947

• Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

  Applied and Environmental Microbiology · 2007 · 10.1128/aem.00062-07

• DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

  INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · 2007 · 10.1099/ijs.0.64483-0

• The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

  Nucleic Acids Research · 2006 · 10.1093/nar/gkl889

• Towards a Genome-Based Taxonomy for Prokaryotes

  Journal of Bacteriology · 2005 · 10.1128/jb.187.18.6258-6264.2005

• Genomic insights that advance the species definition for prokaryotes

  Proceedings of the National Academy of Sciences · 2005 · 10.1073/pnas.0409727102

• Interactions between Aboveground and Belowground Biodiversity in Terrestrial Ecosystems: Patterns, Mechanisms, and Feedbacks

  BioScience · 2000 · 10.1641/0006-3568(2000)050[1049:ibaabb]2.0.co;2

• Ecology of Denitrification and Dissimilatory Nitrate Reduction to Ammonium

  Medical Entomology and Zoology · 1988

• Phases of denitrification following oxygen depletion in soil

  Soil Biology and Biochemistry · 1979 · 10.1016/0038-0717(79)90071-3

Current projects

No projects listed.