Dorrestein, Pieter C.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology

Scientific Computing and Data ManagementGut microbiota and health

Cited by 23,742

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., et al. (2016) · Nature Biotechnology

Metabolomics and Mass Spectrometry StudiesMass Spectrometry Techniques and Applications

Cited by 4,629

Best practices for analysing microbiomes

Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 2,030

Integrative analysis of multimodal mass spectrometry data in MZmine 3

Schmid, R., Heuckeroth, S., Korf, A., Smirnov, A., Myers, O., Dyrlund, T. S., Bushuiev, R., Murray, K. J., Hoffmann, N., Lu, M., et al. (2023) · Nature Biotechnology

Metabolomics and Mass Spectrometry StudiesMass Spectrometry Techniques and Applications

Cited by 1,241

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis

Nakatsuji, T., Chen, T. H., Narala, S., Chun, K. A., Two, A. M., Yun, T., Shafiq, F., Kotol, P. F., Bouslimani, A., Melnik, A. V., et al. (2017) · Science Translational Medicine

Dermatology and Skin DiseasesAntimicrobial Resistance in Staphylococcus

Cited by 1,095

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

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra

Dührkop, K., Nothias, L.-F., Fleischauer, M., Reher, R., Ludwig, M., Hoffmann, M. A., Petras, D., Gerwick, W. H., Rousu, J., Dorrestein, P. C., et al. (2021) · Nature Biotechnology

Metabolomics and Mass Spectrometry StudiesMass Spectrometry Techniques and Applications

Cited by 860

ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs

Yang, L., Lin, C., Liu, W., Zhang, J., Ohgi, K. A., Grinstein, J. D., Dorrestein, P. C., & Rosenfeld, M. G. (2011) · Cell

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 612

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

Shalapour, S., Lin, X.-J., Bastian, I. N., Brain, J., Burt, A. D., Aksenov, A. A., Vrbanac, A. F., Li, W., Perkins, A., Matsutani, T., et al. (2017) · Nature

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

Cited by 589

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

Quinn, R. A., Melnik, A. V., Vrbanac, A., Fu, T., Patras, K. A., Christy, M. P., Bodai, Z., Belda-Ferre, P., Tripathi, A., Chung, L. K., et al. (2020) · Nature

Gut microbiota and healthMetabolomics and Mass Spectrometry Studies

Cited by 579

NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

Kim, H. W., Wang, M., Leber, C. A., Nothias, L.-F., Reher, R., Kang, K. B., van der Hooft, J. J. J., Dorrestein, P. C., Gerwick, W. H., & Cottrell, G. W. (2021) · Journal of Natural Products

Computational Drug Discovery MethodsMicrobial Natural Products and Biosynthesis

Cited by 551

Specialized metabolites from the microbiome in health and disease

Sharon, G., Garg, N., Debelius, J., Knight, R., Dorrestein, P. C., & Mazmanian, S. K. (2014) · Cell Metabolism

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 544

PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression.

Liu, W., Tanasa, B., Tyurina, O. V., Zhou, T. Y., Gassmann, R., Liu, W. T., Ohgi, K. A., Benner, C., Garcia-Bassets, I., Aggarwal, A. K., et al. (2010) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 441

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation

Nothias, L.-F., Nothias-Esposito, M., da Silva, R., Wang, M., Protsyuk, I., Zhang, Z., Sarvepalli, A., Leyssen, P., Touboul, D., Costa, J., et al. (2018) · Journal of Natural Products

Mass Spectrometry Techniques and ApplicationsComputational Drug Discovery Methods

Cited by 433

High-confidence structural annotation of metabolites absent from spectral libraries

Hoffmann, M. A., Nothias, L.-F., Ludwig, M., Fleischauer, M., Gentry, E. C., Witting, M., Dorrestein, P. C., Dührkop, K., & Böcker, S. (2022) · Nature Biotechnology

Metabolomics and Mass Spectrometry StudiesComputational Drug Discovery Methods

Cited by 388

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Mills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., et al. (2022) · Nature Microbiology

Gut microbiota and healthInflammatory Bowel Disease

Cited by 385

Imaging mass spectrometry in microbiology

Watrous, J. D., & Dorrestein, P. C. (2011) · Nature Reviews Microbiology

Mass Spectrometry Techniques and ApplicationsBacterial Identification and Susceptibility Testing

Cited by 338

Finding the Missing Links among Metabolites, Microbes, and the Host

Dorrestein, P. C., Mazmanian, S. K., & Knight, R. (2014) · Immunity

Gut microbiota and healthMetabolomics and Mass Spectrometry Studies

Cited by 317

Mass spectrometry searches using MASST

Wang, M., Jarmusch, A. K., Vargas, F., Aksenov, A. A., Gauglitz, J. M., Weldon, K., Petras, D., da Silva, R., Quinn, R., Melnik, A. V., et al. (2020) · Nature Biotechnology

Metabolomics and Mass Spectrometry StudiesMass Spectrometry Techniques and Applications

Cited by 281

Balance Trees Reveal Microbial Niche Differentiation

Morton, J. T., Sanders, J., Quinn, R. A., McDonald, D., Gonzalez, A., Vázquez-Baeza, Y., Navas-Molina, J. A., Song, S. J., Metcalf, J. L., Hyde, E. R., et al. (2017) · mSystems

Microbial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Cited by 254

Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase

Patterson, A., Rimal, B., Collins, S., Granda, M., Koo, I., Solanka, S., Hoque, N., Gentry, E., Yan, T., Bisanz, J., et al. (2022) · Nature

Gut microbiota and healthDrug Transport and Resistance Mechanisms

Cited by 252

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

Moree, W. J., Phelan, V. V., Wu, C.-H., Bandeira, N., Cornett, D. S., Duggan, B. M., & Dorrestein, P. C. (2012) · Proceedings of the National Academy of Sciences

Mass Spectrometry Techniques and ApplicationsBacterial biofilms and quorum sensing

Cited by 239

The impact of skin care products on skin chemistry and microbiome dynamics

Bouslimani, A., da Silva, R., Kosciolek, T., Janssen, S., Callewaert, C., Amir, A., Dorrestein, K., Melnik, A. V., Zaramela, L. S., Kim, J.-N., et al. (2019) · BMC Biology

Dermatology and Skin DiseasesContact Dermatitis and Allergies

Cited by 234

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome

Taylor, B. C., Lejzerowicz, F., Poirel, M., Shaffer, J. P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., et al. (2020) · mSystems

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 203