Hugenholtz, Philip

CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 12,496

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 10,891

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 3,603

Defining the core Arabidopsis thaliana root microbiome

Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T. G. D., et al. (2012) · Nature

Plant-Microbe Interactions and ImmunityMicrobial Community Ecology and Physiology

Cited by 2,879

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 2,624

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature

Metal Extraction and BioleachingGenomics and Phylogenetic Studies

Cited by 2,417

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 2,402

Insights into the phylogeny and coding potential of microbial dark matter

Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 2,394

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 1,882

Emerging Pathogenic Links Between Microbiota and the Gut-Lung Axis

Budden, K. F., Gellatly, S. L., Wood, D. L. A., Cooper, M. A., Morrison, M., Hugenholtz, P., & Hansbro, P. M. (2017) · Nature Reviews Microbiology

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,606

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 1,367

American Gut: an Open Platform for Citizen-Science Microbiome Research

McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · mSystems

Gut microbiota and healthResearch Data Management Practices

Cited by 878

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 580

Genome Project Standards in a New Era of Sequencing

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., et al. (2009) · Science

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 400

A rooted phylogeny resolves early bacterial evolution

Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 285

Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa

Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P., et al. (2007) · Journal of Clinical Microbiology

Nosocomial Infections in ICUBacterial biofilms and quorum sensing

Cited by 180

A long-awaited taxogenomic investigation of the family Halomonadaceae

de la Haba, R. R., Arahal, D. R., Sánchez-Porro, C., Chuvochina, M., Wittouck, S., Hugenholtz, P., & Ventosa, A. (2023) · Frontiers in Microbiology

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 53

Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions

Leong, L. E. X., Denman, S. E., Hugenholtz, P., & McSweeney, C. S. (2016) · Microbial Ecology

Ruminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas Production

Cited by 33